Daily Papers

In this paper, we consider enhancing medical visual-language pre-training (VLP) with domain-specific knowledge, by exploiting the paired image-text reports from the radiological daily practice. In particular, we make the following contributions: First, unlike existing works that directly process the raw reports, we adopt a novel triplet extraction module to extract the medical-related information, avoiding unnecessary complexity from language grammar and enhancing the supervision signals; Second, we propose a novel triplet encoding module with entity translation by querying a knowledge base, to exploit the rich domain knowledge in medical field, and implicitly build relationships between medical entities in the language embedding space; Third, we propose to use a Transformer-based fusion model for spatially aligning the entity description with visual signals at the image patch level, enabling the ability for medical diagnosis; Fourth, we conduct thorough experiments to validate the effectiveness of our architecture, and benchmark on numerous public benchmarks, e.g., ChestX-ray14, RSNA Pneumonia, SIIM-ACR Pneumothorax, COVIDx CXR-2, COVID Rural, and EdemaSeverity. In both zero-shot and fine-tuning settings, our model has demonstrated strong performance compared with the former methods on disease classification and grounding.

Aspect Sentiment Triplet Extraction (ASTE) is the task of extracting the triplets of target entities, their associated sentiment, and opinion spans explaining the reason for the sentiment. Existing research efforts mostly solve this problem using pipeline approaches, which break the triplet extraction process into several stages. Our observation is that the three elements within a triplet are highly related to each other, and this motivates us to build a joint model to extract such triplets using a sequence tagging approach. However, how to effectively design a tagging approach to extract the triplets that can capture the rich interactions among the elements is a challenging research question. In this work, we propose the first end-to-end model with a novel position-aware tagging scheme that is capable of jointly extracting the triplets. Our experimental results on several existing datasets show that jointly capturing elements in the triplet using our approach leads to improved performance over the existing approaches. We also conducted extensive experiments to investigate the model effectiveness and robustness.

In this paper, we describe our shared task submissions for Subtask 2 in CASE-2022, Event Causality Identification with Casual News Corpus. The challenge focused on the automatic detection of all cause-effect-signal spans present in the sentence from news-media. We detect cause-effect-signal spans in a sentence using T5 -- a pre-trained autoregressive language model. We iteratively identify all cause-effect-signal span triplets, always conditioning the prediction of the next triplet on the previously predicted ones. To predict the triplet itself, we consider different causal relationships such as causerightarroweffectrightarrowsignal. Each triplet component is generated via a language model conditioned on the sentence, the previous parts of the current triplet, and previously predicted triplets. Despite training on an extremely small dataset of 160 samples, our approach achieved competitive performance, being placed second in the competition. Furthermore, we show that assuming either causerightarroweffect or effectrightarrowcause order achieves similar results.

Composed Image Retrieval (CIR) aims to retrieve a target image based on a reference image and conditioning text, enabling controllable searches. Due to the expensive dataset construction cost for CIR triplets, a zero-shot (ZS) CIR setting has been actively studied to eliminate the need for human-collected triplet datasets. The mainstream of ZS-CIR employs an efficient projection module that projects a CLIP image embedding to the CLIP text token embedding space, while fixing the CLIP encoders. Using the projected image embedding, these methods generate image-text composed features by using the pre-trained text encoder. However, their CLIP image and text encoders suffer from the task discrepancy between the pre-training task (text leftrightarrow image) and the target CIR task (image + text leftrightarrow image). Conceptually, we need expensive triplet samples to reduce the discrepancy, but we use cheap text triplets instead and update the text encoder. To that end, we introduce the Reducing Task Discrepancy of text encoders for Composed Image Retrieval (RTD), a plug-and-play training scheme for the text encoder that enhances its capability using a novel target-anchored text contrastive learning. We also propose two additional techniques to improve the proposed learning scheme: a hard negatives-based refined batch sampling strategy and a sophisticated concatenation scheme. Integrating RTD into the state-of-the-art projection-based ZS-CIR methods significantly improves performance across various datasets and backbones, demonstrating its efficiency and generalizability.

Weakly-Supervised Scene Graph Generation (WSSGG) research has recently emerged as an alternative to the fully-supervised approach that heavily relies on costly annotations. In this regard, studies on WSSGG have utilized image captions to obtain unlocalized triplets while primarily focusing on grounding the unlocalized triplets over image regions. However, they have overlooked the two issues involved in the triplet formation process from the captions: 1) Semantic over-simplification issue arises when extracting triplets from captions, where fine-grained predicates in captions are undesirably converted into coarse-grained predicates, resulting in a long-tailed predicate distribution, and 2) Low-density scene graph issue arises when aligning the triplets in the caption with entity/predicate classes of interest, where many triplets are discarded and not used in training, leading to insufficient supervision. To tackle the two issues, we propose a new approach, i.e., Large Language Model for weakly-supervised SGG (LLM4SGG), where we mitigate the two issues by leveraging the LLM's in-depth understanding of language and reasoning ability during the extraction of triplets from captions and alignment of entity/predicate classes with target data. To further engage the LLM in these processes, we adopt the idea of Chain-of-Thought and the in-context few-shot learning strategy. To validate the effectiveness of LLM4SGG, we conduct extensive experiments on Visual Genome and GQA datasets, showing significant improvements in both Recall@K and mean Recall@K compared to the state-of-the-art WSSGG methods. A further appeal is that LLM4SGG is data-efficient, enabling effective model training with a small amount of training images.

Large-scale pre-trained models (PTMs) have been widely used in document-oriented NLP tasks, such as question answering. However, the encoding-task coupling requirement results in the repeated encoding of the same documents for different tasks and queries, which is highly computationally inefficient. To this end, we target to decouple document encoding from downstream tasks, and propose to represent each document as a plug-and-play document module, i.e., a document plugin, for PTMs (PlugD). By inserting document plugins into the backbone PTM for downstream tasks, we can encode a document one time to handle multiple tasks, which is more efficient than conventional encoding-task coupling methods that simultaneously encode documents and input queries using task-specific encoders. Extensive experiments on 8 datasets of 4 typical NLP tasks show that PlugD enables models to encode documents once and for all across different scenarios. Especially, PlugD can save 69% computational costs while achieving comparable performance to state-of-the-art encoding-task coupling methods. Additionally, we show that PlugD can serve as an effective post-processing way to inject knowledge into task-specific models, improving model performance without any additional model training.

In recent years, language models have become increasingly larger and more complex. However, the input representations for these models continue to rely on simple and greedy subword tokenization methods. In this paper, we propose a novel tokenization method that factorizes subwords onto discrete triplets using a VQ-VAE model. The effectiveness of the proposed tokenization method, referred to as the Factorizer, is evaluated on language modeling and morpho-syntactic tasks for 7 diverse languages. Results indicate that this method is more appropriate and robust for morphological tasks than the commonly used byte-pair encoding (BPE) tokenization algorithm.

Large Language Models (LLMs) have reshaped the landscape of artificial intelligence by demonstrating exceptional performance across various tasks. However, substantial computational requirements make their deployment challenging on devices with limited resources. Recently, compression methods using low-rank matrix techniques have shown promise, yet these often lead to degraded accuracy or introduce significant overhead in parameters and inference latency. This paper introduces Modular Decomposition (MoDeGPT), a novel structured compression framework that does not need recovery fine-tuning while resolving the above drawbacks. MoDeGPT partitions the Transformer block into modules comprised of matrix pairs and reduces the hidden dimensions via reconstructing the module-level outputs. MoDeGPT is developed based on a theoretical framework that utilizes three well-established matrix decomposition algorithms -- Nystr\"om approximation, CR decomposition, and SVD -- and applies them to our redefined transformer modules. Our comprehensive experiments show MoDeGPT, without backward propagation, matches or surpasses previous structured compression methods that rely on gradient information, and saves 98% of compute costs on compressing a 13B model. On Llama-2/3 and OPT models, MoDeGPT maintains 90-95% zero-shot performance with 25-30% compression rates. Moreover, the compression can be done on a single GPU within a few hours and increases the inference throughput by up to 46%.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Recent advancements in multimodal pre-training methods have shown promising efficacy in 3D representation learning by aligning features across 3D modality, their 2D counterpart modality, and corresponding language modality. However, the methods used by existing multimodal pre-training frameworks to gather multimodal data for 3D applications lack scalability and comprehensiveness, potentially constraining the full potential of multimodal learning. The main bottleneck lies in the language modality's scalability and comprehensiveness. To address this bottleneck, we introduce ULIP-2, a multimodal pre-training framework that leverages state-of-the-art multimodal large language models (LLMs) pre-trained on extensive knowledge to automatically generate holistic language counterparts for 3D objects. We conduct experiments on two large-scale datasets, Objaverse and ShapeNet55, and release our generated three-modality triplet datasets (3D Point Cloud - Image - Language), named "ULIP-Objaverse Triplets" and "ULIP-ShapeNet Triplets". ULIP-2 requires only 3D data itself and eliminates the need for any manual annotation effort, demonstrating its scalability; and ULIP-2 achieves remarkable improvements on downstream zero-shot classification on ModelNet40 (74% Top1 Accuracy). Moreover, ULIP-2 sets a new record on the real-world ScanObjectNN benchmark (91.5% Overall Accuracy) while utilizing only 1.4 million parameters(~10x fewer than current SOTA), signifying a breakthrough in scalable multimodal 3D representation learning without human annotations. The code and datasets are available at https://github.com/salesforce/ULIP.

In Composed Image Retrieval (CIR), a user combines a query image with text to describe their intended target. Existing methods rely on supervised learning of CIR models using labeled triplets consisting of the query image, text specification, and the target image. Labeling such triplets is expensive and hinders broad applicability of CIR. In this work, we propose to study an important task, Zero-Shot Composed Image Retrieval (ZS-CIR), whose goal is to build a CIR model without requiring labeled triplets for training. To this end, we propose a novel method, called Pic2Word, that requires only weakly labeled image-caption pairs and unlabeled image datasets to train. Unlike existing supervised CIR models, our model trained on weakly labeled or unlabeled datasets shows strong generalization across diverse ZS-CIR tasks, e.g., attribute editing, object composition, and domain conversion. Our approach outperforms several supervised CIR methods on the common CIR benchmark, CIRR and Fashion-IQ. Code will be made publicly available at https://github.com/google-research/composed_image_retrieval.

Multi-modal models show appealing performance in visual recognition tasks recently, as free-form text-guided training evokes the ability to understand fine-grained visual content. However, current models are either inefficient or cannot be trivially upgraded to scene text recognition (STR) due to the composition difference between natural and text images. We propose a novel instruction-guided scene text recognition (IGTR) paradigm that formulates STR as an instruction learning problem and understands text images by predicting character attributes, e.g., character frequency, position, etc. IGTR first devises left langle condition,question,answerright rangle instruction triplets, providing rich and diverse descriptions of character attributes. To effectively learn these attributes through question-answering, IGTR develops lightweight instruction encoder, cross-modal feature fusion module and multi-task answer head, which guides nuanced text image understanding. Furthermore, IGTR realizes different recognition pipelines simply by using different instructions, enabling a character-understanding-based text reasoning paradigm that considerably differs from current methods. Experiments on English and Chinese benchmarks show that IGTR outperforms existing models by significant margins, while maintaining a small model size and efficient inference speed. Moreover, by adjusting the sampling of instructions, IGTR offers an elegant way to tackle the recognition of both rarely appearing and morphologically similar characters, which were previous challenges. Code at https://github.com/Topdu/OpenOCR{this http URL}.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

As the model size of pre-trained language models (PLMs) grows rapidly, full fine-tuning becomes prohibitively expensive for model training and storage. In vision-and-language (VL), parameter-efficient tuning (PET) techniques are proposed to integrate modular modifications (e.g., Adapter and LoRA) into encoder-decoder PLMs. By tuning a small set of trainable parameters, these techniques perform on par with full fine-tuning. However, excessive modular modifications and neglecting the functionality gap between the encoders and decoders can lead to performance degradation, while existing PET techniques (e.g., VL-Adapter) overlook these critical issues. In this paper, we propose a Vision-and-Language Parameter-Efficient Tuning (VL-PET) framework to impose effective control over modular modifications via a novel granularity-controlled mechanism. Considering different granularity-controlled matrices generated by this mechanism, a variety of model-agnostic VL-PET modules can be instantiated from our framework for better efficiency and effectiveness trade-offs. We further propose lightweight PET module designs to enhance VL alignment and modeling for the encoders and maintain text generation for the decoders. Extensive experiments conducted on four image-text tasks and four video-text tasks demonstrate the efficiency, effectiveness and transferability of our VL-PET framework. In particular, our VL-PET-large with lightweight PET module designs significantly outperforms VL-Adapter by 2.92% (3.41%) and LoRA by 3.37% (7.03%) with BART-base (T5-base) on image-text tasks. Furthermore, we validate the enhanced effect of employing our VL-PET designs on existing PET techniques, enabling them to achieve significant performance improvements. Our code is available at https://github.com/HenryHZY/VL-PET.

Composed Image Retrieval (CoIR) has recently gained popularity as a task that considers both text and image queries together, to search for relevant images in a database. Most CoIR approaches require manually annotated datasets, comprising image-text-image triplets, where the text describes a modification from the query image to the target image. However, manual curation of CoIR triplets is expensive and prevents scalability. In this work, we instead propose a scalable automatic dataset creation methodology that generates triplets given video-caption pairs, while also expanding the scope of the task to include composed video retrieval (CoVR). To this end, we mine paired videos with a similar caption from a large database, and leverage a large language model to generate the corresponding modification text. Applying this methodology to the extensive WebVid2M collection, we automatically construct our WebVid-CoVR dataset, resulting in 1.6 million triplets. Moreover, we introduce a new benchmark for CoVR with a manually annotated evaluation set, along with baseline results. Our experiments further demonstrate that training a CoVR model on our dataset effectively transfers to CoIR, leading to improved state-of-the-art performance in the zero-shot setup on both the CIRR and FashionIQ benchmarks. Our code, datasets, and models are publicly available at https://imagine.enpc.fr/~ventural/covr.

This article introduces byteSteady -- a fast model for classification using byte-level n-gram embeddings. byteSteady assumes that each input comes as a sequence of bytes. A representation vector is produced using the averaged embedding vectors of byte-level n-grams, with a pre-defined set of n. The hashing trick is used to reduce the number of embedding vectors. This input representation vector is then fed into a linear classifier. A straightforward application of byteSteady is text classification. We also apply byteSteady to one type of non-language data -- DNA sequences for gene classification. For both problems we achieved competitive classification results against strong baselines, suggesting that byteSteady can be applied to both language and non-language data. Furthermore, we find that simple compression using Huffman coding does not significantly impact the results, which offers an accuracy-speed trade-off previously unexplored in machine learning.

Pre-trained language models have been successful in natural language generation (NLG) tasks. While various decoding methods have been employed, they often produce suboptimal results. We first present an empirical analysis of three NLG tasks: summarization, machine translation, and constrained text generation. We found that selecting the best output from the results of multiple decoding methods can significantly improve performance. To further improve reranking for NLG tasks, we proposed a novel method, PairReranker, which uses a single encoder and a pairwise loss function to jointly encode a source input and a pair of candidates and compare them. Experiments on three NLG tasks demonstrated the effectiveness and flexibility of PairReranker, showing strong results, compared with previous baselines. In addition, our PairReranker can generalize to significantly improve GPT-3 (text-davinci-003) results (e.g., 24.55\% on CommonGen and 11.35\% on WMT18 zh-en), even though our rerankers are not trained with any GPT-3 candidates.

The task of triplet extraction aims to extract pairs of entities and their corresponding relations from unstructured text. Most existing methods train an extraction model on training data involving specific target relations, and are incapable of extracting new relations that were not observed at training time. Generalizing the model to unseen relations typically requires fine-tuning on synthetic training data which is often noisy and unreliable. We show that by reducing triplet extraction to a template infilling task over a pre-trained language model (LM), we can equip the extraction model with zero-shot learning capabilities and eliminate the need for additional training data. We propose a novel framework, ZETT (ZEro-shot Triplet extraction by Template infilling), that aligns the task objective to the pre-training objective of generative transformers to generalize to unseen relations. Experiments on FewRel and Wiki-ZSL datasets demonstrate that ZETT shows consistent and stable performance, outperforming previous state-of-the-art methods, even when using automatically generated templates. https://github.com/megagonlabs/zett/

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

We tackle NED by comparing entities in short sentences with graphs. Creating a context vector from graphs through deep learning is a challenging problem that has never been applied to NED. Our main contribution is to present an experimental study of recent neural techniques, as well as a discussion about which graph features are most important for the disambiguation task. In addition, a new dataset () is created to allow a clean and scalable evaluation of NED with entries, and to be used as a reference in future research. In the end our results show that a Bi-LSTM encoding of the graph triplets performs best, improving upon the baseline models and scoring an F1 value of 91.6% on the test set

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Byte-pair encoding (BPE) is a ubiquitous algorithm in the subword tokenization process of language models as it provides multiple benefits. However, this process is solely based on pre-training data statistics, making it hard for the tokenizer to handle infrequent spellings. On the other hand, though robust to misspellings, pure character-level models often lead to unreasonably long sequences and make it harder for the model to learn meaningful words. To alleviate these challenges, we propose a character-based subword module (char2subword) that learns the subword embedding table in pre-trained models like BERT. Our char2subword module builds representations from characters out of the subword vocabulary, and it can be used as a drop-in replacement of the subword embedding table. The module is robust to character-level alterations such as misspellings, word inflection, casing, and punctuation. We integrate it further with BERT through pre-training while keeping BERT transformer parameters fixed--and thus, providing a practical method. Finally, we show that incorporating our module to mBERT significantly improves the performance on the social media linguistic code-switching evaluation (LinCE) benchmark.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Given an image and a target modification (e.g an image of the Eiffel tower and the text "without people and at night-time"), Compositional Image Retrieval (CIR) aims to retrieve the relevant target image in a database. While supervised approaches rely on annotating triplets that is costly (i.e. query image, textual modification, and target image), recent research sidesteps this need by using large-scale vision-language models (VLMs), performing Zero-Shot CIR (ZS-CIR). However, state-of-the-art approaches in ZS-CIR still require training task-specific, customized models over large amounts of image-text pairs. In this work, we propose to tackle CIR in a training-free manner via our Compositional Image Retrieval through Vision-by-Language (CIReVL), a simple, yet human-understandable and scalable pipeline that effectively recombines large-scale VLMs with large language models (LLMs). By captioning the reference image using a pre-trained generative VLM and asking a LLM to recompose the caption based on the textual target modification for subsequent retrieval via e.g. CLIP, we achieve modular language reasoning. In four ZS-CIR benchmarks, we find competitive, in-part state-of-the-art performance - improving over supervised methods. Moreover, the modularity of CIReVL offers simple scalability without re-training, allowing us to both investigate scaling laws and bottlenecks for ZS-CIR while easily scaling up to in parts more than double of previously reported results. Finally, we show that CIReVL makes CIR human-understandable by composing image and text in a modular fashion in the language domain, thereby making it intervenable, allowing to post-hoc re-align failure cases. Code will be released upon acceptance.

The ability to describe images with natural language sentences is the hallmark for image and language understanding. Such a system has wide ranging applications such as annotating images and using natural sentences to search for images.In this project we focus on the task of bidirectional image retrieval: such asystem is capable of retrieving an image based on a sentence (image search) andretrieve sentence based on an image query (image annotation). We present asystem based on a global ranking objective function which uses a combinationof convolutional neural networks (CNN) and multi layer perceptrons (MLP).It takes a pair of image and sentence and processes them in different channels,finally embedding it into a common multimodal vector space. These embeddingsencode abstract semantic information about the two inputs and can be comparedusing traditional information retrieval approaches. For each such pair, the modelreturns a score which is interpretted as a similarity metric. If this score is high,the image and sentence are likely to convey similar meaning, and if the score is low then they are likely not to. The visual input is modeled via deep convolutional neural network. On theother hand we explore three models for the textual module. The first one isbag of words with an MLP. The second one uses n-grams (bigram, trigrams,and a combination of trigram & skip-grams) with an MLP. The third is morespecialized deep network specific for modeling variable length sequences (SSE).We report comparable performance to recent work in the field, even though ouroverall model is simpler. We also show that the training time choice of how wecan generate our negative samples has a significant impact on performance, and can be used to specialize the bi-directional system in one particular task.

We provide a construction for categorical representation learning and introduce the foundations of "categorifier". The central theme in representation learning is the idea of everything to vector. Every object in a dataset S can be represented as a vector in R^n by an encoding map E: Obj(S)toR^n. More importantly, every morphism can be represented as a matrix E: Hom(S)toR^{n}_{n}. The encoding map E is generally modeled by a deep neural network. The goal of representation learning is to design appropriate tasks on the dataset to train the encoding map (assuming that an encoding is optimal if it universally optimizes the performance on various tasks). However, the latter is still a set-theoretic approach. The goal of the current article is to promote the representation learning to a new level via a category-theoretic approach. As a proof of concept, we provide an example of a text translator equipped with our technology, showing that our categorical learning model outperforms the current deep learning models by 17 times. The content of the current article is part of the recent US patent proposal (patent application number: 63110906).

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

Convolution is a broadly useful operation with applications including signal processing, machine learning, probability, optics, polynomial multiplication, and efficient parsing. Usually, however, this operation is understood and implemented in more specialized forms, hiding commonalities and limiting usefulness. This paper formulates convolution in the common algebraic framework of semirings and semimodules and populates that framework with various representation types. One of those types is the grand abstract template and itself generalizes to the free semimodule monad. Other representations serve varied uses and performance trade-offs, with implementations calculated from simple and regular specifications. Of particular interest is Brzozowski's method for regular expression matching. Uncovering the method's essence frees it from syntactic manipulations, while generalizing from boolean to weighted membership (such as multisets and probability distributions) and from sets to n-ary relations. The classic trie data structure then provides an elegant and efficient alternative to syntax. Pleasantly, polynomial arithmetic requires no additional implementation effort, works correctly with a variety of representations, and handles multivariate polynomials and power series with ease. Image convolution also falls out as a special case.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

In this work, we investigate a typical scenario in code generation where a developer edits existing code in real time and requests a code assistant, e.g., a large language model, to re-predict the next token or next line on the fly. Naively, the LLM needs to re-encode the entire KV cache to provide an accurate prediction. However, this process is computationally expensive, especially when the sequence length is long. Simply encoding the edited subsequence and integrating it to the original KV cache meets the temporal confusion problem, leading to significantly worse performance. We address this efficiency and accuracy trade-off by introducing \textbf{Positional \textbf{Integrity Encoding} (PIE). Building upon the rotary positional encoding, PIE first removes the rotary matrices in the Key cache that introduce temporal confusion and then reapplies the correct rotary matrices. This process ensures that positional relationships between tokens are correct and requires only a single round of matrix multiplication. We validate the effectiveness of PIE through extensive experiments on the RepoBench-C-8k dataset, utilizing DeepSeek-Coder models with 1.3B, 6.7B, and 33B parameters. Our evaluation includes three real-world coding tasks: code insertion, code deletion, and multi-place code editing. Results demonstrate that PIE reduces computational overhead by over 85% compared to the standard full recomputation approach across all model sizes and tasks while well approximating the model performance.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

Style representations aim to embed texts with similar writing styles closely and texts with different styles far apart, regardless of content. However, the contrastive triplets often used for training these representations may vary in both style and content, leading to potential content leakage in the representations. We introduce StyleDistance, a novel approach to training stronger content-independent style embeddings. We use a large language model to create a synthetic dataset of near-exact paraphrases with controlled style variations, and produce positive and negative examples across 40 distinct style features for precise contrastive learning. We assess the quality of our synthetic data and embeddings through human and automatic evaluations. StyleDistance enhances the content-independence of style embeddings, which generalize to real-world benchmarks and outperform leading style representations in downstream applications. Our model can be found at https://huggingface.co/StyleDistance/styledistance .

We present LLM-Blender, an ensembling framework designed to attain consistently superior performance by leveraging the diverse strengths of multiple open-source large language models (LLMs). Our framework consists of two modules: PairRanker and GenFuser, addressing the observation that optimal LLMs for different examples can significantly vary. PairRanker employs a specialized pairwise comparison method to distinguish subtle differences between candidate outputs. It jointly encodes the input text and a pair of candidates, using cross-attention encoders to determine the superior one. Our results demonstrate that PairRanker exhibits the highest correlation with ChatGPT-based ranking. Then, GenFuser aims to merge the top-ranked candidates, generating an improved output by capitalizing on their strengths and mitigating their weaknesses. To facilitate large-scale evaluation, we introduce a benchmark dataset, MixInstruct, which is a mixture of multiple instruction datasets featuring oracle pairwise comparisons. Our LLM-Blender significantly outperform individual LLMs and baseline methods across various metrics, establishing a substantial performance gap.

Post-training quantization is the leading method for addressing memory-related bottlenecks in LLM inference, but unfortunately, it suffers from significant performance degradation below 4-bit precision. An alternative approach involves training compressed models directly at a low bitwidth (e.g., binary or ternary models). However, the performance, training dynamics, and scaling trends of such models are not yet well understood. To address this issue, we train and openly release the Spectra LLM suite consisting of 54 language models ranging from 99M to 3.9B parameters, trained on 300B tokens. Spectra includes FloatLMs, post-training quantized QuantLMs (3, 4, 6, and 8 bits), and ternary LLMs (TriLMs) - our improved architecture for ternary language modeling, which significantly outperforms previously proposed ternary models of a given size (in bits), matching half-precision models at scale. For example, TriLM 3.9B is (bit-wise) smaller than the half-precision FloatLM 830M, but matches half-precision FloatLM 3.9B in commonsense reasoning and knowledge benchmarks. However, TriLM 3.9B is also as toxic and stereotyping as FloatLM 3.9B, a model six times larger in size. Additionally, TriLM 3.9B lags behind FloatLM in perplexity on validation splits and web-based corpora but performs better on less noisy datasets like Lambada and PennTreeBank. To enhance understanding of low-bitwidth models, we are releasing 500+ intermediate checkpoints of the Spectra suite at https://github.com/NolanoOrg/SpectraSuite{https://github.com/NolanoOrg/SpectraSuite}.

In this paper, we aim to do code completion based on implementing a Neural Network from Li et. al.. Our contribution is that we use an encoding that is in-between character and word encoding called Byte Pair Encoding (BPE). We use this on the source code files treating them as natural text without first going through the abstract syntax tree (AST). We have implemented two models: an attention-enhanced LSTM and a pointer network, where the pointer network was originally introduced to solve out of vocabulary problems. We are interested to see if BPE can replace the need for the pointer network for code completion.

We propose a novel approach to optimizing a byte-level representation for end-to-end automatic speech recognition (ASR). Byte-level representation is often used by large scale multilingual ASR systems when the character set of the supported languages is large. The compactness and universality of byte-level representation allow the ASR models to use smaller output vocabularies and therefore, provide more flexibility. UTF-8 is a commonly used byte-level representation for multilingual ASR, but it is not designed to optimize machine learning tasks directly. By using auto-encoder and vector quantization, we show that we can optimize a byte-level representation for ASR and achieve better accuracy. Our proposed framework can incorporate information from different modalities, and provides an error correction mechanism. In an English/Mandarin dictation task, we show that a bilingual ASR model built with this approach can outperform UTF-8 representation by 5% relative in error rate.

High-quality training triplets (instruction, original image, edited image) are essential for instruction-based image editing. Predominant training datasets (e.g., InsPix2Pix) are created using text-to-image generative models (e.g., Stable Diffusion, DALL-E) which are not trained for image editing. Accordingly, these datasets suffer from inaccurate instruction following, poor detail preserving, and generation artifacts. In this paper, we propose to address the training data quality issue with multi-perspective reward data instead of refining the ground-truth image quality. 1) we first design a quantitative metric system based on best-in-class LVLM (Large Vision Language Model), i.e., GPT-4o in our case, to evaluate the generation quality from 3 perspectives, namely, instruction following, detail preserving, and generation quality. For each perspective, we collected quantitative score in 0sim 5 and text descriptive feedback on the specific failure points in ground-truth edited images, resulting in a high-quality editing reward dataset, i.e., RewardEdit20K. 2) We further proposed a novel training framework to seamlessly integrate the metric output, regarded as multi-reward, into editing models to learn from the imperfect training triplets. During training, the reward scores and text descriptions are encoded as embeddings and fed into both the latent space and the U-Net of the editing models as auxiliary conditions. During inference, we set these additional conditions to the highest score with no text description for failure points, to aim at the best generation outcome. Experiments indicate that our multi-reward conditioned model outperforms its no-reward counterpart on two popular editing pipelines, i.e., InsPix2Pix and SmartEdit. The code and dataset will be released.

Large language models (LLMs) exhibit exceptional performance across a wide range of tasks; however, their token-by-token autoregressive generation process significantly hinders inference speed. Speculative decoding presents a promising draft-then-verify framework that reduces generation latency while maintaining output distribution fidelity. Nevertheless, the draft model introduces additional computational overhead, becoming a performance bottleneck and increasing the time to first token (TTFT). Previous approaches to mitigate draft model overhead have primarily relied on heuristics and generally failed to match the quality of the draft language models. To address these challenges, we propose DuoDecoding, a novel approach that strategically deploys the draft and target models on the CPU and GPU respectively, enabling parallel decoding while preserving draft quality. Our method incorporates a hardware-aware optimal draft budget to minimize idle times and employs dynamic multi-sequence drafting to enhance draft quality. Extensive experiments across seven tasks show that DuoDecoding achieves up to 2.61x speedup in generation latency, while reducing TTFT to 83% of that in conventional speculative decoding. The Code is available at https://github.com/KaiLv69/DuoDecoding.

Recently, there has been a surge in the popularity of pre trained large language models (LLMs) (such as GPT-4), sweeping across the entire Natural Language Processing (NLP) and Computer Vision (CV) communities. These LLMs have demonstrated advanced multi-modal understanding capabilities and showcased strong performance across various benchmarks. The LLM has started to embody traits of artificial general intelligence, which holds vital guidance for enhancing brain-like characteristics within visual encoding models. Hence, This paper proposes a new multi-modal training paradigm, aligning with LLM, for encoding fMRI activity in visual cortex. Based on this paradigm, we trained an encoding model in fMRI data named the LLM-Visual Encoding Model (LLM-VEM). Specifically, we utilize LLM (miniGPT4) to generate descriptive text for all stimulus images, forming a high-quality textual description set. Moreover, we use the pre-trained text encoder (CLIP) to process these detailed descriptions, obtaining the text embedding features. Next, we use the contrast loss function to minimize the distance between the image embedding features and the text embedding features to complete the alignment operation of the stimulus image and text information. With the assistance of the pre-trained LLM, this alignment process facilitates better learning of the visual encoding model, resulting in higher precision. The final experimental results indicate that our training paradigm has significantly aided in enhancing the performance of the visual encoding model.

Text-to-image person re-identification (TIReID) is a compelling topic in the cross-modal community, which aims to retrieve the target person based on a textual query. Although numerous TIReID methods have been proposed and achieved promising performance, they implicitly assume the training image-text pairs are correctly aligned, which is not always the case in real-world scenarios. In practice, the image-text pairs inevitably exist under-correlated or even false-correlated, a.k.a noisy correspondence (NC), due to the low quality of the images and annotation errors. To address this problem, we propose a novel Robust Dual Embedding method (RDE) that can learn robust visual-semantic associations even with NC. Specifically, RDE consists of two main components: 1) A Confident Consensus Division (CCD) module that leverages the dual-grained decisions of dual embedding modules to obtain a consensus set of clean training data, which enables the model to learn correct and reliable visual-semantic associations. 2) A Triplet-Alignment Loss (TAL) relaxes the conventional triplet-ranking loss with hardest negatives, which tends to rapidly overfit NC, to a log-exponential upper bound over all negatives, thus preventing the model from overemphasizing false image-text pairs. We conduct extensive experiments on three public benchmarks, namely CUHK-PEDES, ICFG-PEDES, and RSTPReID, to evaluate the performance and robustness of our RDE. Our method achieves state-of-the-art results both with and without synthetic noisy correspondences on all three datasets.

This article proposes to auto-encode text at byte-level using convolutional networks with a recursive architecture. The motivation is to explore whether it is possible to have scalable and homogeneous text generation at byte-level in a non-sequential fashion through the simple task of auto-encoding. We show that non-sequential text generation from a fixed-length representation is not only possible, but also achieved much better auto-encoding results than recurrent networks. The proposed model is a multi-stage deep convolutional encoder-decoder framework using residual connections, containing up to 160 parameterized layers. Each encoder or decoder contains a shared group of modules that consists of either pooling or upsampling layers, making the network recursive in terms of abstraction levels in representation. Results for 6 large-scale paragraph datasets are reported, in 3 languages including Arabic, Chinese and English. Analyses are conducted to study several properties of the proposed model.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

With large language models (LLMs) widely deployed in long content generation recently, there has emerged an increasing demand for efficient long-sequence inference support. However, key-value (KV) cache, which is stored to avoid re-computation, has emerged as a critical bottleneck by growing linearly in size with the sequence length. Due to the auto-regressive nature of LLMs, the entire KV cache will be loaded for every generated token, resulting in low utilization of computational cores and high latency. While various compression methods for KV cache have been proposed to alleviate this issue, they suffer from degradation in generation quality. We introduce TriForce, a hierarchical speculative decoding system that is scalable to long sequence generation. This approach leverages the original model weights and dynamic sparse KV cache via retrieval as a draft model, which serves as an intermediate layer in the hierarchy and is further speculated by a smaller model to reduce its drafting latency. TriForce not only facilitates impressive speedups for Llama2-7B-128K, achieving up to 2.31times on an A100 GPU but also showcases scalability in handling even longer contexts. For the offloading setting on two RTX 4090 GPUs, TriForce achieves 0.108s/tokenx2014only half as slow as the auto-regressive baseline on an A100, which attains 7.78times on our optimized offloading system. Additionally, TriForce performs 4.86times than DeepSpeed-Zero-Inference on a single RTX 4090 GPU. TriForce's robustness is highlighted by its consistently outstanding performance across various temperatures. The code is available at https://github.com/Infini-AI-Lab/TriForce.

We introduce KodCode, a synthetic dataset that addresses the persistent challenge of acquiring high-quality, verifiable training data across diverse difficulties and domains for training Large Language Models for coding. Existing code-focused resources typically fail to ensure either the breadth of coverage (e.g., spanning simple coding tasks to advanced algorithmic problems) or verifiable correctness (e.g., unit tests). In contrast, KodCode comprises question-solution-test triplets that are systematically validated via a self-verification procedure. Our pipeline begins by synthesizing a broad range of coding questions, then generates solutions and test cases with additional attempts allocated to challenging problems. Finally, post-training data synthesis is done by rewriting questions into diverse formats and generating responses under a test-based reject sampling procedure from a reasoning model (DeepSeek R1). This pipeline yields a large-scale, robust and diverse coding dataset. KodCode is suitable for supervised fine-tuning and the paired unit tests also provide great potential for RL tuning. Fine-tuning experiments on coding benchmarks (HumanEval(+), MBPP(+), BigCodeBench, and LiveCodeBench) demonstrate that KodCode-tuned models achieve state-of-the-art performance, surpassing models like Qwen2.5-Coder-32B-Instruct and DeepSeek-R1-Distill-Llama-70B.

Transformers' ability to generalize to longer sequences than they have been trained on, known as length extrapolation, degrades as sequence length increases. Most of Relative Positional Encoding (RPE) methods address this problem by either adding constant linear biases or learning general biases, lacking the ability to specialize for different sequences. In this work, inspired by ALiBi, we propose Context-aware Biases for Length Extrapolation (Cable), that learns token-specific biases for each head in decoder-based transformers. Cable learns adaptive, context-aware biases, overcoming the limitations of fixed patterns by adding dynamic biases specific to each token in the sequence. Results show that when tested on a sequence length of 1024, a GPT-3 Medium (334M parameters) with our positional encoding, trained on a sequence length of 512, achieves better perplexity (-0.65) than a similar network with sinusoidal positional encoding trained on a sequence length of 1024. This is achieved with 48% lower memory usage, and only 3.5% higher training time. Furthermore, our method notably improves the extrapolation ability of existing RPE methods on the Edu-FineWeb10B and WikiText-103 datasets. Code is available at: https://github.com/axiomlab/Cable

Creating neural text encoders for written Swiss German is challenging due to a dearth of training data combined with dialectal variation. In this paper, we build on several existing multilingual encoders and adapt them to Swiss German using continued pre-training. Evaluation on three diverse downstream tasks shows that simply adding a Swiss German adapter to a modular encoder achieves 97.5% of fully monolithic adaptation performance. We further find that for the task of retrieving Swiss German sentences given Standard German queries, adapting a character-level model is more effective than the other adaptation strategies. We release our code and the models trained for our experiments at https://github.com/ZurichNLP/swiss-german-text-encoders

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Deploying language models often requires handling model size vs. performance trade-offs to satisfy downstream latency constraints while preserving the model's usefulness. Model distillation is commonly employed to reduce model size while maintaining acceptable performance. However, distillation can be inefficient since it involves multiple training steps. In this work, we introduce MODULARSTARENCODER, a modular multi-exit encoder with 1B parameters, useful for multiple tasks within the scope of code retrieval. MODULARSTARENCODER is trained with a novel self-distillation mechanism that significantly improves lower-layer representations-allowing different portions of the model to be used while still maintaining a good trade-off in terms of performance. Our architecture focuses on enhancing text-to-code and code-to-code search by systematically capturing syntactic and semantic structures across multiple levels of representation. Specific encoder layers are targeted as exit heads, allowing higher layers to guide earlier layers during training. This self-distillation effect improves intermediate representations, increasing retrieval recall at no extra training cost. In addition to the multi-exit scheme, our approach integrates a repository-level contextual loss that maximally utilizes the training context window, further enhancing the learned representations. We also release a new dataset constructed via code translation, seamlessly expanding traditional text-to-code benchmarks with code-to-code pairs across diverse programming languages. Experimental results highlight the benefits of self-distillation through multi-exit supervision.

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Recent works learn 3D representation explicitly under text-3D guidance. However, limited text-3D data restricts the vocabulary scale and text control of generations. Generators may easily fall into a stereotype concept for certain text prompts, thus losing open-vocabulary generation ability. To tackle this issue, we introduce a conditional 3D generative model, namely TextField3D. Specifically, rather than using the text prompts as input directly, we suggest to inject dynamic noise into the latent space of given text prompts, i.e., Noisy Text Fields (NTFs). In this way, limited 3D data can be mapped to the appropriate range of textual latent space that is expanded by NTFs. To this end, an NTFGen module is proposed to model general text latent code in noisy fields. Meanwhile, an NTFBind module is proposed to align view-invariant image latent code to noisy fields, further supporting image-conditional 3D generation. To guide the conditional generation in both geometry and texture, multi-modal discrimination is constructed with a text-3D discriminator and a text-2.5D discriminator. Compared to previous methods, TextField3D includes three merits: 1) large vocabulary, 2) text consistency, and 3) low latency. Extensive experiments demonstrate that our method achieves a potential open-vocabulary 3D generation capability.

In this work we present a new State-of-The-Art on the text-to-video retrieval task on MSR-VTT, LSMDC, MSVD, YouCook2 and TGIF obtained by a single model. Three different data sources are combined: weakly-supervised videos, crowd-labeled text-image pairs and text-video pairs. A careful analysis of available pre-trained networks helps to choose the best prior-knowledge ones. We introduce three-stage training procedure that provides high transfer knowledge efficiency and allows to use noisy datasets during training without prior knowledge degradation. Additionally, double positional encoding is used for better fusion of different modalities and a simple method for non-square inputs processing is suggested.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Large-scale text encoders in text-to-image (T2I) diffusion models have demonstrated exceptional performance in generating high-quality images from textual prompts. Unlike denoising modules that rely on multiple iterative steps, text encoders require only a single forward pass to produce text embeddings. However, despite their minimal contribution to total inference time and floating-point operations (FLOPs), text encoders demand significantly higher memory usage, up to eight times more than denoising modules. To address this inefficiency, we propose Skip and Re-use layers (Skrr), a simple yet effective pruning strategy specifically designed for text encoders in T2I diffusion models. Skrr exploits the inherent redundancy in transformer blocks by selectively skipping or reusing certain layers in a manner tailored for T2I tasks, thereby reducing memory consumption without compromising performance. Extensive experiments demonstrate that Skrr maintains image quality comparable to the original model even under high sparsity levels, outperforming existing blockwise pruning methods. Furthermore, Skrr achieves state-of-the-art memory efficiency while preserving performance across multiple evaluation metrics, including the FID, CLIP, DreamSim, and GenEval scores.

Large Language Models (LLMs) have demonstrated remarkable success in various natural language processing and software engineering tasks, such as code generation. The LLMs are mainly utilized in the prompt-based zero/few-shot paradigm to guide the model in accomplishing the task. GPT-based models are one of the popular ones studied for tasks such as code comment generation or test generation. These tasks are `generative' tasks. However, there is limited research on the usage of LLMs for `non-generative' tasks such as classification using the prompt-based paradigm. In this preliminary exploratory study, we investigated the applicability of LLMs for Code Clone Detection (CCD), a non-generative task. By building a mono-lingual and cross-lingual CCD dataset derived from CodeNet, we first investigated two different prompts using ChatGPT to detect Type-4 code clones in Java-Java and Java-Ruby pairs in a zero-shot setting. We then conducted an analysis to understand the strengths and weaknesses of ChatGPT in CCD. ChatGPT surpasses the baselines in cross-language CCD attaining an F1-score of 0.877 and achieves comparable performance to fully fine-tuned models for mono-lingual CCD, with an F1-score of 0.878. Also, the prompt and the difficulty level of the problems has an impact on the performance of ChatGPT. Finally we provide insights and future directions based on our initial analysis

Multimodel Large Language Models(MLLMs) have achieved promising OCR-free Document Understanding performance by increasing the supported resolution of document images. However, this comes at the cost of generating thousands of visual tokens for a single document image, leading to excessive GPU memory and slower inference times, particularly in multi-page document comprehension. In this work, to address these challenges, we propose a High-resolution DocCompressor module to compress each high-resolution document image into 324 tokens, guided by low-resolution global visual features. With this compression module, to strengthen multi-page document comprehension ability and balance both token efficiency and question-answering performance, we develop the DocOwl2 under a three-stage training framework: Single-image Pretraining, Multi-image Continue-pretraining, and Multi-task Finetuning. DocOwl2 sets a new state-of-the-art across multi-page document understanding benchmarks and reduces first token latency by more than 50%, demonstrating advanced capabilities in multi-page questioning answering, explanation with evidence pages, and cross-page structure understanding. Additionally, compared to single-image MLLMs trained on similar data, our DocOwl2 achieves comparable single-page understanding performance with less than 20% of the visual tokens. Our codes, models, and data are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl2.

In this paper we present our submission for the EACL 2021 SRW; a methodology that aims at bridging the gap between high and low-resource languages in the context of Open Information Extraction, showcasing it on the Greek language. The goals of this paper are twofold: First, we build Neural Machine Translation (NMT) models for English-to-Greek and Greek-to-English based on the Transformer architecture. Second, we leverage these NMT models to produce English translations of Greek text as input for our NLP pipeline, to which we apply a series of pre-processing and triple extraction tasks. Finally, we back-translate the extracted triples to Greek. We conduct an evaluation of both our NMT and OIE methods on benchmark datasets and demonstrate that our approach outperforms the current state-of-the-art for the Greek natural language.

Diffusion-based text-to-image models have demonstrated impressive achievements in diversity and aesthetics but struggle to generate images with legible visual texts. Existing backbone models have limitations such as misspelling, failing to generate texts, and lack of support for Chinese text, but their development shows promising potential. In this paper, we propose a series of methods, aiming to empower backbone models to generate visual texts in English and Chinese. We first conduct a preliminary study revealing that Byte Pair Encoding (BPE) tokenization and the insufficient learning of cross-attention modules restrict the performance of the backbone models. Based on these observations, we make the following improvements: (1) We design a mixed granularity input strategy to provide more suitable text representations; (2) We propose to augment the conventional training objective with three glyph-aware training losses, which enhance the learning of cross-attention modules and encourage the model to focus on visual texts. Through experiments, we demonstrate that our methods can effectively empower backbone models to generate semantic relevant, aesthetically appealing, and accurate visual text images, while maintaining their fundamental image generation quality.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Code generation aims to understand the problem description and generate corresponding code snippets, where existing works generally decompose such complex tasks into intermediate steps by prompting strategies, such as Chain-of-Thought and its variants. While these studies have achieved some success, their effectiveness is highly dependent on the capabilities of advanced Large Language Models (LLMs) such as GPT-4, particularly in terms of API calls, which significantly limits their practical applicability. Consequently, how to enhance the code generation capabilities of small and medium-scale code LLMs without significantly increasing training costs is an appealing challenge. In this paper, we suggest that code comments are the natural logic pivot between natural language and code language and propose using comments to boost the code generation ability of code LLMs. Concretely, we propose MANGO (comMents As Natural loGic pivOts), including a comment contrastive training strategy and a corresponding logical comment decoding strategy. Experiments are performed on HumanEval and MBPP, utilizing StarCoder and WizardCoder as backbone models, and encompassing model parameter sizes between 3B and 7B. The results indicate that MANGO significantly improves the code pass rate based on the strong baselines. Meanwhile, the robustness of the logical comment decoding strategy is notably higher than the Chain-of-thoughts prompting. The code is publicly available at https://github.com/pppa2019/Mango.

Next-token prediction models have predominantly relied on decoder-only Transformers with causal attention, driven by the common belief that causal attention is essential to prevent "cheating" by masking future tokens. We challenge this widely accepted notion and argue that this design choice is about efficiency rather than necessity. While decoder-only Transformers are still a good choice for practical reasons, they are not the only viable option. In this work, we introduce Encoder-only Next Token Prediction (ENTP). We explore the differences between ENTP and decoder-only Transformers in expressive power and complexity, highlighting potential advantages of ENTP. We introduce the Triplet-Counting task and show, both theoretically and experimentally, that while ENTP can perform this task easily, a decoder-only Transformer cannot. Finally, we empirically demonstrate ENTP's superior performance across various realistic tasks, such as length generalization and in-context learning.

The success of the GPT series proves that GPT can extract general information from sequences, thereby benefiting all downstream tasks. This motivates us to use pre-trained models to explore the hidden information in DNA sequences. However, data and task requirements in DNA sequence analysis are complexity and diversity as DNA relevant data includes different types of information, such as sequences, expression levels, etc, while there is currently no model specifically designed for these characteristics. Hereby, we present DNAGPT, a generalized foundation model pre-trained on over 10 billion base pairs from 9 species which can be fine-tuned for any DNA sequence analysis task. Our model can simultaneously process or output DNA sequences and numbers. In addition, our unique token design allows users to design prompts according to their own task requirements, making it applicable to any type of task. We have evaluated our model on classification, regression, and generation tasks. We demonstrate that DNAGPT benefits from pre-training, and therefore can bring performance gains to any downstream task. Our model is not only a new attempt in the field of genomes analysis, but also provides a new direction for the application of foundation models in biology.

General-purpose Large Language Models (LLMs) like GPT-4 have achieved remarkable advancements in machine translation (MT) by leveraging extensive web content. On the other hand, translation-specific LLMs are built by pre-training on domain-specific monolingual corpora and fine-tuning with human-annotated translation data. Despite the superior performance, these methods either demand an unprecedented scale of computing and data or substantial human editing and annotation efforts. In this paper, we develop MT-Ladder, a novel model-agnostic and cost-effective tool to refine the performance of general LLMs for MT. MT-Ladder is trained on pseudo-refinement triplets which can be easily obtained from existing LLMs without additional human cost. During training, we propose a hierarchical fine-tuning strategy with an easy-to-hard schema, improving MT-Ladder's refining performance progressively. The trained MT-Ladder can be seamlessly integrated with any general-purpose LLMs to boost their translation performance. By utilizing Gemma-2B/7B as the backbone, MT-Ladder-2B can elevate raw translations to the level of top-tier open-source models (e.g., refining BigTranslate-13B with +6.91 BLEU and +3.52 COMET for XX-En), and MT-Ladder-7B can further enhance model performance to be on par with the state-of-the-art GPT-4. Extensive ablation and analysis corroborate the effectiveness of MT-Ladder in diverse settings. Our code is available at https://github.com/fzp0424/Ladder

Compositional image retrieval (CIR) is a multimodal learning task where a model combines a query image with a user-provided text modification to retrieve a target image. CIR finds applications in a variety of domains including product retrieval (e-commerce) and web search. Existing methods primarily focus on fully-supervised learning, wherein models are trained on datasets of labeled triplets such as FashionIQ and CIRR. This poses two significant challenges: (i) curating such triplet datasets is labor intensive; and (ii) models lack generalization to unseen objects and domains. In this work, we propose SCOT (Self-supervised COmpositional Training), a novel zero-shot compositional pretraining strategy that combines existing large image-text pair datasets with the generative capabilities of large language models to contrastively train an embedding composition network. Specifically, we show that the text embedding from a large-scale contrastively-pretrained vision-language model can be utilized as proxy target supervision during compositional pretraining, replacing the target image embedding. In zero-shot settings, this strategy surpasses SOTA zero-shot compositional retrieval methods as well as many fully-supervised methods on standard benchmarks such as FashionIQ and CIRR.

We introduce OmniFlow, a novel generative model designed for any-to-any generation tasks such as text-to-image, text-to-audio, and audio-to-image synthesis. OmniFlow advances the rectified flow (RF) framework used in text-to-image models to handle the joint distribution of multiple modalities. It outperforms previous any-to-any models on a wide range of tasks, such as text-to-image and text-to-audio synthesis. Our work offers three key contributions: First, we extend RF to a multi-modal setting and introduce a novel guidance mechanism, enabling users to flexibly control the alignment between different modalities in the generated outputs. Second, we propose a novel architecture that extends the text-to-image MMDiT architecture of Stable Diffusion 3 and enables audio and text generation. The extended modules can be efficiently pretrained individually and merged with the vanilla text-to-image MMDiT for fine-tuning. Lastly, we conduct a comprehensive study on the design choices of rectified flow transformers for large-scale audio and text generation, providing valuable insights into optimizing performance across diverse modalities. The Code will be available at https://github.com/jacklishufan/OmniFlows.

Humans write code in a fundamentally interactive manner and rely on constant execution feedback to correct errors, resolve ambiguities, and decompose tasks. While LLMs have recently exhibited promising coding capabilities, current coding benchmarks mostly consider a static instruction-to-code sequence transduction process, which has the potential for error propagation and a disconnect between the generated code and its final execution environment. To address this gap, we introduce InterCode, a lightweight, flexible, and easy-to-use framework of interactive coding as a standard reinforcement learning (RL) environment, with code as actions and execution feedback as observations. Our framework is language and platform agnostic, uses self-contained Docker environments to provide safe and reproducible execution, and is compatible out-of-the-box with traditional seq2seq coding methods, while enabling the development of new methods for interactive code generation. We use InterCode to create two interactive code environments with Bash and SQL as action spaces, leveraging data from the static Spider and NL2Bash datasets. We demonstrate InterCode's viability as a testbed by evaluating multiple state-of-the-art LLMs configured with different prompting strategies such as ReAct and Plan & Solve. Our results showcase the benefits of interactive code generation and demonstrate that InterCode can serve as a challenging benchmark for advancing code understanding and generation capabilities. InterCode is designed to be easily extensible and can even be used to incorporate new tasks such as Capture the Flag, a popular coding puzzle that is inherently multi-step and involves multiple programming languages. Project site with code and data: https://intercode-benchmark.github.io

A major consideration in multilingual language modeling is how to best represent languages with diverse vocabularies and scripts. Although contemporary text encoding methods cover most of the world's writing systems, they exhibit bias towards the high-resource languages of the Global West. As a result, texts of underrepresented languages tend to be segmented into long sequences of linguistically meaningless units. To address the disparities, we introduce a new paradigm that encodes the same information with segments of consistent size across diverse languages. Our encoding convention (MYTE) is based on morphemes, as their inventories are more balanced across languages than characters, which are used in previous methods. We show that MYTE produces shorter encodings for all 99 analyzed languages, with the most notable improvements for non-European languages and non-Latin scripts. This, in turn, improves multilingual LM performance and diminishes the perplexity gap throughout diverse languages.

Mathematical formulas are a fundamental and widely used component in various scientific fields, serving as a universal language for expressing complex concepts and relationships. While state-of-the-art transformer models excel in processing and understanding natural language, they encounter challenges with mathematical notation, which involves a complex structure and diverse representations. This study focuses on the development of specialized training datasets to enhance the encoding of mathematical content. We introduce Math Mutator (MAMUT), a framework capable of generating equivalent and falsified versions of a given mathematical formula in LaTeX notation, effectively capturing the mathematical variety in notation of the same concept. Based on MAMUT, we have generated four large mathematical datasets containing diverse notation, which can be used to train language models with enhanced mathematical embeddings.

Most multi-modal tasks can be formulated into problems of either generation or embedding. Existing models usually tackle these two types of problems by decoupling language modules into a text decoder for generation, and a text encoder for embedding. To explore the minimalism of multi-modal paradigms, we attempt to achieve only one model per modality in this work. We propose a Multi-Modal Generative Embedding Model (MM-GEM), whereby the generative and embedding objectives are encapsulated in one Large Language Model. We also propose a PoolAggregator to boost efficiency and enable the ability of fine-grained embedding and generation. A surprising finding is that these two objectives do not significantly conflict with each other. For example, MM-GEM instantiated from ViT-Large and TinyLlama shows competitive performance on benchmarks for multimodal embedding models such as cross-modal retrieval and zero-shot classification, while has good ability of image captioning. Additionally, MM-GEM can seamlessly execute region-level image caption generation and retrieval tasks. Besides, the advanced text model in MM-GEM brings over 5% improvement in Recall@1 for long text and image retrieval.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

Search-based dialog models typically re-encode the dialog history at every turn, incurring high cost. Curved Contrastive Learning, a representation learning method that encodes relative distances between utterances into the embedding space via a bi-encoder, has recently shown promising results for dialog modeling at far superior efficiency. While high efficiency is achieved through independently encoding utterances, this ignores the importance of contextualization. To overcome this issue, this study introduces triple-encoders, which efficiently compute distributed utterance mixtures from these independently encoded utterances through a novel hebbian inspired co-occurrence learning objective without using any weights. Empirically, we find that triple-encoders lead to a substantial improvement over bi-encoders, and even to better zero-shot generalization than single-vector representation models without requiring re-encoding. Our code/model is publicly available.

Knowledge-Intensive Visual Question Answering (KI-VQA) refers to answering a question about an image whose answer does not lie in the image. This paper presents a new pipeline for KI-VQA tasks, consisting of a retriever and a reader. First, we introduce DEDR, a symmetric dual encoding dense retrieval framework in which documents and queries are encoded into a shared embedding space using uni-modal (textual) and multi-modal encoders. We introduce an iterative knowledge distillation approach that bridges the gap between the representation spaces in these two encoders. Extensive evaluation on two well-established KI-VQA datasets, i.e., OK-VQA and FVQA, suggests that DEDR outperforms state-of-the-art baselines by 11.6% and 30.9% on OK-VQA and FVQA, respectively. Utilizing the passages retrieved by DEDR, we further introduce MM-FiD, an encoder-decoder multi-modal fusion-in-decoder model, for generating a textual answer for KI-VQA tasks. MM-FiD encodes the question, the image, and each retrieved passage separately and uses all passages jointly in its decoder. Compared to competitive baselines in the literature, this approach leads to 5.5% and 8.5% improvements in terms of question answering accuracy on OK-VQA and FVQA, respectively.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

Scene Text Recognition (STR) methods have demonstrated robust performance in word-level text recognition. However, in real applications the text image is sometimes long due to detected with multiple horizontal words. It triggers the requirement to build long text recognition models from readily available short (i.e., word-level) text datasets, which has been less studied previously. In this paper, we term this task Out of Length (OOL) text recognition. We establish the first Long Text Benchmark (LTB) to facilitate the assessment of different methods in long text recognition. Meanwhile, we propose a novel method called OOL Text Recognition with sub-String Matching (SMTR). SMTR comprises two cross-attention-based modules: one encodes a sub-string containing multiple characters into next and previous queries, and the other employs the queries to attend to the image features, matching the sub-string and simultaneously recognizing its next and previous character. SMTR can recognize text of arbitrary length by iterating the process above. To avoid being trapped in recognizing highly similar sub-strings, we introduce a regularization training to compel SMTR to effectively discover subtle differences between similar sub-strings for precise matching. In addition, we propose an inference augmentation strategy to alleviate confusion caused by identical sub-strings in the same text and improve the overall recognition efficiency. Extensive experimental results reveal that SMTR, even when trained exclusively on short text, outperforms existing methods in public short text benchmarks and exhibits a clear advantage on LTB. Code: https://github.com/Topdu/OpenOCR.

Understanding how semantic meaning is encoded in the representation spaces of large language models is a fundamental problem in interpretability. In this paper, we study the two foundational questions in this area. First, how are categorical concepts, such as {'mammal', 'bird', 'reptile', 'fish'}, represented? Second, how are hierarchical relations between concepts encoded? For example, how is the fact that 'dog' is a kind of 'mammal' encoded? We show how to extend the linear representation hypothesis to answer these questions. We find a remarkably simple structure: simple categorical concepts are represented as simplices, hierarchically related concepts are orthogonal in a sense we make precise, and (in consequence) complex concepts are represented as polytopes constructed from direct sums of simplices, reflecting the hierarchical structure. We validate these theoretical results on the Gemma large language model, estimating representations for 957 hierarchically related concepts using data from WordNet.

The emergence of accurate open large language models (LLMs) has led to a race towards quantization techniques for such models enabling execution on end-user devices. In this paper, we revisit the problem of "extreme" LLM compression--defined as targeting extremely low bit counts, such as 2 to 3 bits per parameter, from the point of view of classic methods in Multi-Codebook Quantization (MCQ). Our work builds on top of Additive Quantization, a classic algorithm from the MCQ family, and adapts it to the quantization of language models. The resulting algorithm advances the state-of-the-art in LLM compression, outperforming all recently-proposed techniques in terms of accuracy at a given compression budget. For instance, when compressing Llama 2 models to 2 bits per parameter, our algorithm quantizes the 7B model to 6.93 perplexity (a 1.29 improvement relative to the best prior work, and 1.81 points from FP16), the 13B model to 5.70 perplexity (a .36 improvement) and the 70B model to 3.94 perplexity (a .22 improvement) on WikiText2. We release our implementation of Additive Quantization for Language Models AQLM as a baseline to facilitate future research in LLM quantization.

Recent multilingual pretrained language models (mPLMs) often avoid using language embeddings -- learnable vectors assigned to different languages. These embeddings are discarded for two main reasons: (1) mPLMs are expected to have a single, unified parameter set across all languages, and (2) they need to function seamlessly as universal text encoders without requiring language IDs as input. However, this removal increases the burden on token embeddings to encode all language-specific information, which may hinder the model's ability to produce more language-neutral representations. To address this challenge, we propose Language-Script Aware Multilingual Pretraining (LangSAMP), a method that incorporates both language and script embeddings to enhance representation learning while maintaining a simple architecture. Specifically, we integrate these embeddings into the output of the transformer blocks before passing the final representations to the language modeling head for prediction. We apply LangSAMP to the continual pretraining of XLM-R on a highly multilingual corpus covering more than 500 languages. The resulting model consistently outperforms the baseline. Extensive analysis further shows that language/script embeddings encode language/script-specific information, which improves the selection of source languages for crosslingual transfer. We make our code and models publicly available at https://github.com/cisnlp/LangSAMP.

In this work, we explore a cost-effective framework for multilingual image generation. We find that, unlike models tuned on high-quality images with multilingual annotations, leveraging text encoders pre-trained on widely available, noisy Internet image-text pairs significantly enhances data efficiency in text-to-image (T2I) generation across multiple languages. Based on this insight, we introduce MuLan, Multi-Language adapter, a lightweight language adapter with fewer than 20M parameters, trained alongside a frozen text encoder and image diffusion model. Compared to previous multilingual T2I models, this framework offers: (1) Cost efficiency. Using readily accessible English data and off-the-shelf multilingual text encoders minimizes the training cost; (2) High performance. Achieving comparable generation capabilities in over 110 languages with CLIP similarity scores nearly matching those in English (38.61 for English vs. 37.61 for other languages); and (3) Broad applicability. Seamlessly integrating with compatible community tools like LoRA, LCM, ControlNet, and IP-Adapter, expanding its potential use cases.

Speculative decoding (SD), where an extra draft model is employed to provide multiple draft tokens first and then the original target model verifies these tokens in parallel, has shown great power for LLM inference acceleration. However, existing SD methods suffer from the mutual waiting problem, i.e., the target model gets stuck when the draft model is guessing tokens, and vice versa. This problem is directly incurred by the asynchronous execution of the draft model and the target model, and is exacerbated due to the fixed draft length in speculative decoding. To address these challenges, we propose a conceptually simple, flexible, and general framework to boost speculative decoding, namely Parallel spEculative decoding with Adaptive dRaft Length (PEARL). Specifically, PEARL proposes pre-verify to verify the first draft token in advance during the drafting phase, and post-verify to generate more draft tokens during the verification phase. PEARL parallels the drafting phase and the verification phase via applying the two strategies, and achieves adaptive draft length for different scenarios, which effectively alleviates the mutual waiting problem. Moreover, we theoretically demonstrate that the mean accepted tokens of PEARL is more than existing draft-then-verify works. Experiments on various text generation benchmarks demonstrate the effectiveness of our \name, leading to a superior speedup performance up to 3.79times and 1.52times, compared to auto-regressive decoding and vanilla speculative decoding, respectively.

The multi-codebook speech codec enables the application of large language models (LLM) in TTS but bottlenecks efficiency and robustness due to multi-sequence prediction. To avoid this obstacle, we propose Single-Codec, a single-codebook single-sequence codec, which employs a disentangled VQ-VAE to decouple speech into a time-invariant embedding and a phonetically-rich discrete sequence. Furthermore, the encoder is enhanced with 1) contextual modeling with a BLSTM module to exploit the temporal information, 2) a hybrid sampling module to alleviate distortion from upsampling and downsampling, and 3) a resampling module to encourage discrete units to carry more phonetic information. Compared with multi-codebook codecs, e.g., EnCodec and TiCodec, Single-Codec demonstrates higher reconstruction quality with a lower bandwidth of only 304bps. The effectiveness of Single-Code is further validated by LLM-TTS experiments, showing improved naturalness and intelligibility.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

While multilingual language models like XLM-R have advanced multilingualism in NLP, they still perform poorly in extremely low-resource languages. This situation is exacerbated by the fact that modern LLMs such as LLaMA and Qwen support far fewer languages than XLM-R, making text generation models non-existent for many languages in the world. To tackle this challenge, we propose a novel framework for adapting multilingual encoders to text generation in extremely low-resource languages. By reusing the weights between the encoder and the decoder, our framework allows the model to leverage the learned semantic space of the encoder, enabling efficient learning and effective generalization in low-resource languages. Applying this framework to four Chinese minority languages, we present XLM-SWCM, and demonstrate its superior performance on various downstream tasks even when compared with much larger models.

Text-rich images, where text serves as the central visual element guiding the overall understanding, are prevalent in real-world applications, such as presentation slides, scanned documents, and webpage snapshots. Tasks involving multiple text-rich images are especially challenging, as they require not only understanding the content of individual images but reasoning about inter-relationships and logical flows across multiple visual inputs. Despite the importance of these scenarios, current multimodal large language models (MLLMs) struggle to handle such tasks due to two key challenges: (1) the scarcity of high-quality instruction tuning datasets for text-rich multi-image scenarios, and (2) the difficulty in balancing image resolution with visual feature sequence length. To address these challenges, we propose \OurMethod, a MLLM designed specifically for handling vision-language tasks involving multiple text-rich images. First, we curated about one million high-quality multimodal instruction-tuning data, tailored to text-rich, multi-image scenarios. Second, we developed an adaptive high-resolution multi-image encoding module to dynamically optimize the allocation of visual sequence length based on the original aspect ratios and resolutions of the input images. Experiments across a wide range of benchmarks demonstrate our model's superior capabilities in text-rich, multi-image evaluations and competitive performance in general domain evaluations.

Hyper-relational knowledge graphs (HKGs) extend standard knowledge graphs by associating attribute-value qualifiers to triples, which effectively represent additional fine-grained information about its associated triple. Hyper-relational knowledge graph completion (HKGC) aims at inferring unknown triples while considering its qualifiers. Most existing approaches to HKGC exploit a global-level graph structure to encode hyper-relational knowledge into the graph convolution message passing process. However, the addition of multi-hop information might bring noise into the triple prediction process. To address this problem, we propose HyperFormer, a model that considers local-level sequential information, which encodes the content of the entities, relations and qualifiers of a triple. More precisely, HyperFormer is composed of three different modules: an entity neighbor aggregator module allowing to integrate the information of the neighbors of an entity to capture different perspectives of it; a relation qualifier aggregator module to integrate hyper-relational knowledge into the corresponding relation to refine the representation of relational content; a convolution-based bidirectional interaction module based on a convolutional operation, capturing pairwise bidirectional interactions of entity-relation, entity-qualifier, and relation-qualifier. realize the depth perception of the content related to the current statement. Furthermore, we introduce a Mixture-of-Experts strategy into the feed-forward layers of HyperFormer to strengthen its representation capabilities while reducing the amount of model parameters and computation. Extensive experiments on three well-known datasets with four different conditions demonstrate HyperFormer's effectiveness. Datasets and code are available at https://github.com/zhiweihu1103/HKGC-HyperFormer.

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction~(MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions~(PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales~(i.e., chain numbers). Specifically, we propose \textsc{PromptMSP}, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models. The code, data and checkpoints are released at https://github.com/zqgao22/PromptMSP.

Many new proposals for scene text recognition (STR) models have been introduced in recent years. While each claim to have pushed the boundary of the technology, a holistic and fair comparison has been largely missing in the field due to the inconsistent choices of training and evaluation datasets. This paper addresses this difficulty with three major contributions. First, we examine the inconsistencies of training and evaluation datasets, and the performance gap results from inconsistencies. Second, we introduce a unified four-stage STR framework that most existing STR models fit into. Using this framework allows for the extensive evaluation of previously proposed STR modules and the discovery of previously unexplored module combinations. Third, we analyze the module-wise contributions to performance in terms of accuracy, speed, and memory demand, under one consistent set of training and evaluation datasets. Such analyses clean up the hindrance on the current comparisons to understand the performance gain of the existing modules.

Cross-lingual transfer learning is an important property of multilingual large language models (LLMs). But how do LLMs represent relationships between languages? Every language model has an input layer that maps tokens to vectors. This ubiquitous layer of language models is often overlooked. We find that similarities between these input embeddings are highly interpretable and that the geometry of these embeddings differs between model families. In one case (XLM-RoBERTa), embeddings encode language: tokens in different writing systems can be linearly separated with an average of 99.2% accuracy. Another family (mT5) represents cross-lingual semantic similarity: the 50 nearest neighbors for any token represent an average of 7.61 writing systems, and are frequently translations. This result is surprising given that there is no explicit parallel cross-lingual training corpora and no explicit incentive for translations in pre-training objectives. Our research opens the door for investigations in 1) The effect of pre-training and model architectures on representations of languages and 2) The applications of cross-lingual representations embedded in language models.

Language models of code (LMs) work well when the surrounding code in the vicinity of generation provides sufficient context. This is not true when it becomes necessary to use types or functionality defined in another module or library, especially those not seen during training. LMs suffer from limited awareness of such global context and end up hallucinating, e.g., using types defined in other files incorrectly. Recent work tries to overcome this issue by retrieving global information to augment the local context. However, this bloats the prompt or requires architecture modifications and additional training. Integrated development environments (IDEs) assist developers by bringing the global context at their fingertips using static analysis. We extend this assistance, enjoyed by developers, to the LMs. We propose a notion of monitors that use static analysis in the background to guide the decoding. Unlike a priori retrieval, static analysis is invoked iteratively during the entire decoding process, providing the most relevant suggestions on demand. We demonstrate the usefulness of our proposal by monitoring for type-consistent use of identifiers whenever an LM generates code for object dereference. To evaluate our approach, we curate PragmaticCode, a dataset of open-source projects with their development environments. On models of varying parameter scale, we show that monitor-guided decoding consistently improves the ability of an LM to not only generate identifiers that match the ground truth but also improves compilation rates and agreement with ground truth. We find that LMs with fewer parameters, when guided with our monitor, can outperform larger LMs. With monitor-guided decoding, SantaCoder-1.1B achieves better compilation rate and next-identifier match than the much larger text-davinci-003 model. The datasets and code will be released at https://aka.ms/monitors4codegen .

The widespread adoption of scalable mobile sensing has led to large amounts of time series data for real-world applications. A fundamental application is multivariate time series forecasting (MTSF), which aims to predict future time series values based on historical observations. Existing MTSF methods suffer from limited parameterization and small-scale training data. Recently, Large language models (LLMs) have been introduced in time series, which achieve promising forecasting performance but incur heavy computational costs. To solve these challenges, we propose TimeCMA, an LLM-empowered framework for time series forecasting with cross-modality alignment. We design a dual-modality encoding module with two branches, where the time series encoding branch extracts relatively low-quality yet pure embeddings of time series through an inverted Transformer. In addition, the LLM-empowered encoding branch wraps the same time series as prompts to obtain high-quality yet entangled prompt embeddings via a Pre-trained LLM. Then, we design a cross-modality alignment module to retrieve high-quality and pure time series embeddings from the prompt embeddings. Moreover, we develop a time series forecasting module to decode the aligned embeddings while capturing dependencies among multiple variables for forecasting. Notably, we tailor the prompt to encode sufficient temporal information into a last token and design the last token embedding storage to reduce computational costs. Extensive experiments on real data offer insight into the accuracy and efficiency of the proposed framework.

An image editing model should be able to perform diverse edits, ranging from object replacement, changing attributes or style, to performing actions or movement, which require many forms of reasoning. Current general instruction-guided editing models have significant shortcomings with action and reasoning-centric edits. Object, attribute or stylistic changes can be learned from visually static datasets. On the other hand, high-quality data for action and reasoning-centric edits is scarce and has to come from entirely different sources that cover e.g. physical dynamics, temporality and spatial reasoning. To this end, we meticulously curate the AURORA Dataset (Action-Reasoning-Object-Attribute), a collection of high-quality training data, human-annotated and curated from videos and simulation engines. We focus on a key aspect of quality training data: triplets (source image, prompt, target image) contain a single meaningful visual change described by the prompt, i.e., truly minimal changes between source and target images. To demonstrate the value of our dataset, we evaluate an AURORA-finetuned model on a new expert-curated benchmark (AURORA-Bench) covering 8 diverse editing tasks. Our model significantly outperforms previous editing models as judged by human raters. For automatic evaluations, we find important flaws in previous metrics and caution their use for semantically hard editing tasks. Instead, we propose a new automatic metric that focuses on discriminative understanding. We hope that our efforts : (1) curating a quality training dataset and an evaluation benchmark, (2) developing critical evaluations, and (3) releasing a state-of-the-art model, will fuel further progress on general image editing.

As an efficient alternative to conventional full finetuning, parameter-efficient finetuning (PEFT) is becoming the prevailing method to adapt pretrained language models. In PEFT, a lightweight module is learned on each dataset while the underlying pretrained language model remains unchanged, resulting in multiple compact modules representing diverse skills when applied to various domains and tasks. In this paper, we propose to compose these parameter-efficient modules through linear arithmetic operations in the weight space, thereby integrating different module capabilities. Specifically, we first define addition and negation operators for the module, and then further compose these two basic operators to perform flexible arithmetic. Our approach requires no additional training and enables highly flexible module composition. We apply different arithmetic operations to compose the parameter-efficient modules for (1) distribution generalization, (2) multi-tasking, (3) unlearning, and (4) domain transfer. Additionally, we extend our approach to detoxify Alpaca-LoRA, the latest instruction-tuned large language model based on LLaMA. Empirical results demonstrate that our approach produces new and effective parameter-efficient modules that significantly outperform existing ones across all settings.

Medical vision-and-language pre-training (Med-VLP) has shown promising improvements on many downstream medical tasks owing to its applicability to extracting generic representations from medical images and texts. Practically, there exist two typical types, i.e., the fusion-encoder type and the dual-encoder type, depending on whether a heavy fusion module is used. The former is superior at multi-modal tasks owing to the sufficient interaction between modalities; the latter is good at uni-modal and cross-modal tasks due to the single-modality encoding ability. To take advantage of these two types, we propose an effective yet straightforward scheme named PTUnifier to unify the two types. We first unify the input format by introducing visual and textual prompts, which serve as a feature bank that stores the most representative images/texts. By doing so, a single model could serve as a foundation model that processes various tasks adopting different input formats (i.e., image-only, text-only, and image-text-pair). Furthermore, we construct a prompt pool (instead of static ones) to improve diversity and scalability. Experimental results show that our approach achieves state-of-the-art results on a broad range of tasks, spanning uni-modal tasks (i.e., image/text classification and text summarization), cross-modal tasks (i.e., image-to-text generation and image-text/text-image retrieval), and multi-modal tasks (i.e., visual question answering), demonstrating the effectiveness of our approach. Note that the adoption of prompts is orthogonal to most existing Med-VLP approaches and could be a beneficial and complementary extension to these approaches.

Using Large Language Models (LLMs) has gained popularity among software developers for generating source code. However, the use of LLM-generated code can introduce risks of adding suboptimal, defective, and vulnerable code. This makes it necessary to devise methods for the accurate detection of LLM-generated code. Toward this goal, we perform a case study of Claude 3 Haiku (or Claude 3 for brevity) on CodeSearchNet dataset. We divide our analyses into two parts: function-level and class-level. We extract 22 software metric features, such as Code Lines and Cyclomatic Complexity, for each level of granularity. We then analyze code snippets generated by Claude 3 and their human-authored counterparts using the extracted features to understand how unique the code generated by Claude 3 is. In the following step, we use the unique characteristics of Claude 3-generated code to build Machine Learning (ML) models and identify which features of the code snippets make them more detectable by ML models. Our results indicate that Claude 3 tends to generate longer functions, but shorter classes than humans, and this characteristic can be used to detect Claude 3-generated code with ML models with 82% and 66% accuracies for function-level and class-level snippets, respectively.

The widespread adoption of large language models such as ChatGPT and Bard has led to unprecedented demand for these technologies. The burgeoning cost of inference for ever-increasing model sizes coupled with hardware shortages has limited affordable access and poses a pressing need for efficiency approaches geared towards high throughput and performance. Multi-input multi-output (MIMO) algorithms such as data multiplexing, offer a promising solution with a many-fold increase in throughput by performing inference for multiple inputs at the cost of a single input. Yet these approaches are not currently performant enough to be deployed in modern systems. We change that by developing MUX-PLMs, a class of high throughput pre-trained language models (PLMs) trained with data multiplexing, that can be fine-tuned for any downstream task to yield high-throughput high-performance. Our novel multiplexing and demultiplexing modules proficiently entangle and disentangle inputs, and enable high-performance high throughput that are competitive with vanilla PLMs while achieving 2x/5x inference speedup with only a 1-4% drop on a broad suite of tasks.

This work introduces a general code generation framework that incorporates infilling operations into auto-regressive decoding. Our approach capitalizes on the observation that recent code language models with infilling capabilities can perform self-infilling: whereas infilling operations aim to fill in the middle based on a predefined prefix and suffix, self-infilling sequentially generates both such surrounding context and the infilled content. We utilize this feature to develop an infilling-augmented decoding process that facilitates non-monotonic generation. This approach allows for postponing the generation of uncertain code snippets until a definitive suffix is established, leading to improved control over the generation sequence. In addition, it facilitates a looping mechanism, which can iteratively update and synchronize each piece of generation in a cyclic manner. Extensive experiments are conducted to demonstrate that our proposed decoding process is effective in enhancing regularity and quality across several code generation benchmarks.

Simultaneous machine translation (SiMT) is usually done via sequence-level knowledge distillation (Seq-KD) from a full-sentence neural machine translation (NMT) model. However, there is still a significant performance gap between NMT and SiMT. In this work, we propose to leverage monolingual data to improve SiMT, which trains a SiMT student on the combination of bilingual data and external monolingual data distilled by Seq-KD. Preliminary experiments on En-Zh and En-Ja news domain corpora demonstrate that monolingual data can significantly improve translation quality (e.g., +3.15 BLEU on En-Zh). Inspired by the behavior of human simultaneous interpreters, we propose a novel monolingual sampling strategy for SiMT, considering both chunk length and monotonicity. Experimental results show that our sampling strategy consistently outperforms the random sampling strategy (and other conventional typical NMT monolingual sampling strategies) by avoiding the key problem of SiMT -- hallucination, and has better scalability. We achieve +0.72 BLEU improvements on average against random sampling on En-Zh and En-Ja. Data and codes can be found at https://github.com/hexuandeng/Mono4SiMT.

Large language model (LLM) decoding involves generating a sequence of tokens based on a given context, where each token is predicted one at a time using the model's learned probabilities. The typical autoregressive decoding method requires a separate forward pass through the model for each token generated, which is computationally inefficient and poses challenges for deploying LLMs in latency-sensitive scenarios. The main limitations of current decoding methods stem from their inefficiencies and resource demands. Existing approaches either necessitate fine-tuning smaller models, which is resource-intensive, or rely on fixed retrieval schemes to construct drafts for the next tokens, which lack adaptability and fail to generalize across different models and contexts. To address these issues, we introduce a novel methodology called ADED, which accelerates LLM decoding without requiring fine-tuning. Our approach involves an adaptive draft-verification process that evolves over time to improve efficiency. We utilize a tri-gram matrix-based LLM representation to dynamically approximate the output distribution of the LLM, allowing the model to adjust to changing token probabilities during the decoding process. Additionally, we implement a draft construction mechanism that effectively balances exploration and exploitation, ensuring that the drafts generated are both diverse and close to the true output distribution of the LLM. The importance of this design lies in its ability to optimize the draft distribution adaptively, leading to faster and more accurate decoding. Through extensive experiments on various benchmark datasets and LLM architectures, we demonstrate that ADED significantly accelerates the decoding process while maintaining high accuracy, making it suitable for deployment in a wide range of practical applications.

We extend Textual Inversion to learn pseudo-words that represent a concept at different resolutions. This allows us to generate images that use the concept with different levels of detail and also to manipulate different resolutions using language. Once learned, the user can generate images at different levels of agreement to the original concept; "A photo of S^*(0)" produces the exact object while the prompt "A photo of S^*(0.8)" only matches the rough outlines and colors. Our framework allows us to generate images that use different resolutions of an image (e.g. details, textures, styles) as separate pseudo-words that can be composed in various ways. We open-soure our code in the following URL: https://github.com/giannisdaras/multires_textual_inversion

Decoding methods for large language models often trade-off between diversity of outputs and parallelism of computation. Methods such as beam search and Gumbel top-k sampling can guarantee a different output for each element of the beam, but are not easy to parallelize. Alternatively, methods such as temperature sampling and its modifications (top-k sampling, nucleus sampling, typical decoding, and others), are embarrassingly parallel, but have no guarantees about duplicate samples. We present a framework for sampling according to an arithmetic code book implicitly defined by a large language model, compatible with common sampling variations, with provable beam diversity under certain conditions, as well as being embarrassingly parallel and providing unbiased and consistent expectations from the original model. We demonstrate the effectiveness of our approach on WMT machine translation, more than halving the standard deviation when estimating expected BLEU score reward, and closing the BLEU score gap between independent sampling and beam search by up to 63%.

The last year has seen astonishing progress in text-prompted image generation premised on the idea of a cross-modal representation space in which the text and image domains are represented jointly. In ASR, this idea has found application as joint speech-text encoders that can scale to the capacities of very large parameter models by being trained on both unpaired speech and text. While these methods show promise, they have required special treatment of the sequence-length mismatch inherent in speech and text, either by up-sampling heuristics or an explicit alignment model. In this work, we offer evidence that joint speech-text encoders naturally achieve consistent representations across modalities by disregarding sequence length, and argue that consistency losses could forgive length differences and simply assume the best alignment. We show that such a loss improves downstream WER in both a large-parameter monolingual and multilingual system.

Recent developments show that Large Language Models (LLMs) produce state-of-the-art performance on natural language (NL) to code generation for resource-rich general-purpose languages like C++, Java, and Python. However, their practical usage for structured domain-specific languages (DSLs) such as YAML, JSON is limited due to domain-specific schema, grammar, and customizations generally unseen by LLMs during pre-training. Efforts have been made to mitigate this challenge via in-context learning through relevant examples or by fine-tuning. However, it suffers from problems, such as limited DSL samples and prompt sensitivity but enterprises maintain good documentation of the DSLs. Therefore, we propose DocCGen, a framework that can leverage such rich knowledge by breaking the NL-to-Code generation task for structured code languages into a two-step process. First, it detects the correct libraries using the library documentation that best matches the NL query. Then, it utilizes schema rules extracted from the documentation of these libraries to constrain the decoding. We evaluate our framework for two complex structured languages, Ansible YAML and Bash command, consisting of two settings: Out-of-domain (OOD) and In-domain (ID). Our extensive experiments show that DocCGen consistently improves different-sized language models across all six evaluation metrics, reducing syntactic and semantic errors in structured code. We plan to open-source the datasets and code to motivate research in constrained code generation.

Neural sequence-to-sequence models provide a competitive approach to the task of mapping a question in natural language to an SQL query, also referred to as text-to-SQL generation. The Byte-Pair Encoding algorithm (BPE) has previously been used to improve machine translation (MT) between natural languages. In this work, we adapt BPE for text-to-SQL generation. As the datasets for this task are rather small compared to MT, we present a novel stopping criterion that prevents overfitting the BPE encoding to the training set. Additionally, we present AST BPE, which is a version of BPE that uses the Abstract Syntax Tree (AST) of the SQL statement to guide BPE merges and therefore produce BPE encodings that generalize better. We improved the accuracy of a strong attentive seq2seq baseline on five out of six English text-to-SQL tasks while reducing training time by more than 50% on four of them due to the shortened targets. Finally, on two of these tasks we exceeded previously reported accuracies.

The application of large-language models (LLMs) to digital hardware code generation is an emerging field. Most LLMs are primarily trained on natural language and software code. Hardware code, such as Verilog, represents only a small portion of the training data and few hardware benchmarks exist. To address this gap, the open-source VerilogEval benchmark was released in 2023, providing a consistent evaluation framework for LLMs on code completion tasks. It was tested on state-of-the-art models at the time including GPT-4. However, VerilogEval and other Verilog generation benchmarks lack failure analysis and, in present form, are not conducive to exploring prompting techniques. Also, since VerilogEval's release, both commercial and open-source models have seen continued development. In this work, we evaluate new commercial and open-source models of varying sizes against an improved VerilogEval benchmark suite. We enhance VerilogEval's infrastructure and dataset by automatically classifying failures, introduce new prompts for supporting in-context learning (ICL) examples, and extend the supported tasks to specification-to-RTL translation. We find a measurable improvement in commercial state-of-the-art models, with GPT-4 Turbo achieving a 59% pass rate on spec-to-RTL tasks. We also study the performance of open-source and domain-specific models that have emerged, and demonstrate that models can benefit substantially from ICL. We find that recently-released Llama 3.1 405B achieves a pass rate of 58%, effectively matching that of GPT-4 Turbo, and that the much smaller domain-specific RTL-Coder 6.7B models achieve an impressive 37% pass rate. However, prompt engineering is key to achieving good pass rates, and varies widely with model and task. A benchmark infrastructure that allows for prompt engineering and failure analysis is key to continued model development and deployment.

This paper demonstrates that multilingual pretraining and multilingual fine-tuning are both critical for facilitating cross-lingual transfer in zero-shot translation, where the neural machine translation (NMT) model is tested on source languages unseen during supervised training. Following this idea, we present SixT+, a strong many-to-English NMT model that supports 100 source languages but is trained with a parallel dataset in only six source languages. SixT+ initializes the decoder embedding and the full encoder with XLM-R large and then trains the encoder and decoder layers with a simple two-stage training strategy. SixT+ achieves impressive performance on many-to-English translation. It significantly outperforms CRISS and m2m-100, two strong multilingual NMT systems, with an average gain of 7.2 and 5.0 BLEU respectively. Additionally, SixT+ offers a set of model parameters that can be further fine-tuned to other unsupervised tasks. We demonstrate that adding SixT+ initialization outperforms state-of-the-art explicitly designed unsupervised NMT models on Si<->En and Ne<->En by over 1.2 average BLEU. When applied to zero-shot cross-lingual abstractive summarization, it produces an average performance gain of 12.3 ROUGE-L over mBART-ft. We conduct detailed analyses to understand the key ingredients of SixT+, including multilinguality of the auxiliary parallel data, positional disentangled encoder, and the cross-lingual transferability of its encoder.

Audio codec models are widely used in audio communication as a crucial technique for compressing audio into discrete representations. Nowadays, audio codec models are increasingly utilized in generation fields as intermediate representations. For instance, AudioLM is an audio generation model that uses the discrete representation of SoundStream as a training target, while VALL-E employs the Encodec model as an intermediate feature to aid TTS tasks. Despite their usefulness, two challenges persist: (1) training these audio codec models can be difficult due to the lack of publicly available training processes and the need for large-scale data and GPUs; (2) achieving good reconstruction performance requires many codebooks, which increases the burden on generation models. In this study, we propose a group-residual vector quantization (GRVQ) technique and use it to develop a novel High Fidelity Audio Codec model, HiFi-Codec, which only requires 4 codebooks. We train all the models using publicly available TTS data such as LibriTTS, VCTK, AISHELL, and more, with a total duration of over 1000 hours, using 8 GPUs. Our experimental results show that HiFi-Codec outperforms Encodec in terms of reconstruction performance despite requiring only 4 codebooks. To facilitate research in audio codec and generation, we introduce AcademiCodec, the first open-source audio codec toolkit that offers training codes and pre-trained models for Encodec, SoundStream, and HiFi-Codec. Code and pre-trained model can be found on: https://github.com/yangdongchao/AcademiCodec{https://github.com/yangdongchao/AcademiCodec}

High-quality instruction data is critical for aligning large language models (LLMs). Although some models, such as Llama-3-Instruct, have open weights, their alignment data remain private, which hinders the democratization of AI. High human labor costs and a limited, predefined scope for prompting prevent existing open-source data creation methods from scaling effectively, potentially limiting the diversity and quality of public alignment datasets. Is it possible to synthesize high-quality instruction data at scale by extracting it directly from an aligned LLM? We present a self-synthesis method for generating large-scale alignment data named Magpie. Our key observation is that aligned LLMs like Llama-3-Instruct can generate a user query when we input only the left-side templates up to the position reserved for user messages, thanks to their auto-regressive nature. We use this method to prompt Llama-3-Instruct and generate 4 million instructions along with their corresponding responses. We perform a comprehensive analysis of the extracted data and select 300K high-quality instances. To compare Magpie data with other public instruction datasets, we fine-tune Llama-3-8B-Base with each dataset and evaluate the performance of the fine-tuned models. Our results indicate that in some tasks, models fine-tuned with Magpie perform comparably to the official Llama-3-8B-Instruct, despite the latter being enhanced with 10 million data points through supervised fine-tuning (SFT) and subsequent feedback learning. We also show that using Magpie solely for SFT can surpass the performance of previous public datasets utilized for both SFT and preference optimization, such as direct preference optimization with UltraFeedback. This advantage is evident on alignment benchmarks such as AlpacaEval, ArenaHard, and WildBench.

Multi-instrument music transcription aims to convert polyphonic music recordings into musical scores assigned to each instrument. This task is challenging for modeling as it requires simultaneously identifying multiple instruments and transcribing their pitch and precise timing, and the lack of fully annotated data adds to the training difficulties. This paper introduces YourMT3+, a suite of models for enhanced multi-instrument music transcription based on the recent language token decoding approach of MT3. We enhance its encoder by adopting a hierarchical attention transformer in the time-frequency domain and integrating a mixture of experts. To address data limitations, we introduce a new multi-channel decoding method for training with incomplete annotations and propose intra- and cross-stem augmentation for dataset mixing. Our experiments demonstrate direct vocal transcription capabilities, eliminating the need for voice separation pre-processors. Benchmarks across ten public datasets show our models' competitiveness with, or superiority to, existing transcription models. Further testing on pop music recordings highlights the limitations of current models. Fully reproducible code and datasets are available with demos at https://github.com/mimbres/YourMT3.

We introduce a new benchmark, ChartMimic, aimed at assessing the visually-grounded code generation capabilities of large multimodal models (LMMs). ChartMimic utilizes information-intensive visual charts and textual instructions as inputs, requiring LMMs to generate the corresponding code for chart rendering. ChartMimic includes 1,000 human-curated (figure, instruction, code) triplets, which represent the authentic chart use cases found in scientific papers across various domains(e.g., Physics, Computer Science, Economics, etc). These charts span 18 regular types and 4 advanced types, diversifying into 191 subcategories. Furthermore, we propose multi-level evaluation metrics to provide an automatic and thorough assessment of the output code and the rendered charts. Unlike existing code generation benchmarks, ChartMimic places emphasis on evaluating LMMs' capacity to harmonize a blend of cognitive capabilities, encompassing visual understanding, code generation, and cross-modal reasoning. The evaluation of 3 proprietary models and 11 open-weight models highlights the substantial challenges posed by ChartMimic. Even the advanced GPT-4V, Claude-3-opus only achieve an average score of 73.2 and 53.7, respectively, indicating significant room for improvement. We anticipate that ChartMimic will inspire the development of LMMs, advancing the pursuit of artificial general intelligence.

A wide array of sequence models are built on a framework modeled after Transformers, comprising alternating sequence mixer and channel mixer layers. This paper studies a unifying matrix mixer view of sequence mixers that can be conceptualized as a linear map on the input sequence. This framework encompasses a broad range of well-known sequence models, including the self-attention of Transformers as well as recent strong alternatives such as structured state space models (SSMs), and allows understanding downstream characteristics such as efficiency and expressivity through properties of their structured matrix class. We identify a key axis of matrix parameterizations termed sequence alignment, which increases the flexibility and performance of matrix mixers, providing insights into the strong performance of Transformers and recent SSMs such as Mamba. Furthermore, the matrix mixer framework offers a systematic approach to developing sequence mixers with desired properties, allowing us to develop several new sub-quadratic sequence models. In particular, we propose a natural bidirectional extension of the Mamba model (Hydra), parameterized as a quasiseparable matrix mixer, which demonstrates superior performance over other sequence models including Transformers on non-causal tasks. As a drop-in replacement for attention layers, Hydra outperforms BERT by 0.8 points on the GLUE benchmark and ViT by 2% Top-1 accuracy on ImageNet.

Spreadsheets, with their extensive two-dimensional grids, various layouts, and diverse formatting options, present notable challenges for large language models (LLMs). In response, we introduce SpreadsheetLLM, pioneering an efficient encoding method designed to unleash and optimize LLMs' powerful understanding and reasoning capability on spreadsheets. Initially, we propose a vanilla serialization approach that incorporates cell addresses, values, and formats. However, this approach was limited by LLMs' token constraints, making it impractical for most applications. To tackle this challenge, we develop SheetCompressor, an innovative encoding framework that compresses spreadsheets effectively for LLMs. It comprises three modules: structural-anchor-based compression, inverse index translation, and data-format-aware aggregation. It significantly improves performance in spreadsheet table detection task, outperforming the vanilla approach by 25.6% in GPT4's in-context learning setting. Moreover, fine-tuned LLM with SheetCompressor has an average compression ratio of 25 times, but achieves a state-of-the-art 78.9% F1 score, surpassing the best existing models by 12.3%. Finally, we propose Chain of Spreadsheet for downstream tasks of spreadsheet understanding and validate in a new and demanding spreadsheet QA task. We methodically leverage the inherent layout and structure of spreadsheets, demonstrating that SpreadsheetLLM is highly effective across a variety of spreadsheet tasks.

This paper investigates the potential for large language models (LLMs) to develop private tonal languages for machine-to-machine (M2M) communication. Inspired by cryptophasia in human twins (affecting up to 50% of twin births) and natural tonal languages like Mandarin and Vietnamese, we implement a precise character-to-frequency mapping system that encodes the full ASCII character set (32-126) using musical semitones. Each character is assigned a unique frequency, creating a logarithmic progression beginning with space (220 Hz) and ending with tilde (50,175.42 Hz). This spans approximately 7.9 octaves, with higher characters deliberately mapped to ultrasonic frequencies beyond human perception (>20 kHz). Our implemented software prototype demonstrates this encoding through visualization, auditory playback, and ABC musical notation, allowing for analysis of information density and transmission speed. Testing reveals that tonal encoding can achieve information rates exceeding human speech while operating partially outside human perceptual boundaries. This work responds directly to concerns about AI systems catastrophically developing private languages within the next five years, providing a concrete prototype software example of how such communication might function and the technical foundation required for its emergence, detection, and governance.

Tokenizers are crucial for encoding information in Large Language Models, but their development has recently stagnated, and they contain inherent weaknesses. Major limitations include computational overhead, ineffective vocabulary use, and unnecessarily large embedding and head layers. Additionally, their performance is biased towards a reference corpus, leading to reduced effectiveness for underrepresented languages. To remedy these issues, we propose T-FREE, which directly embeds words through sparse activation patterns over character triplets, and does not require a reference corpus. T-FREE inherently exploits morphological similarities and allows for strong compression of embedding layers. In our exhaustive experimental evaluation, we achieve competitive downstream performance with a parameter reduction of more than 85% on these layers. Further, T-FREE shows significant improvements in cross-lingual transfer learning.

Contrastive Language-Image Pretraining (CLIP) models maximize the mutual information between text and visual modalities to learn representations. This makes the nature of the training data a significant factor in the efficacy of CLIP for downstream tasks. However, the lack of compositional diversity in contemporary image-text datasets limits the compositional reasoning ability of CLIP. We show that generating ``hard'' negative captions via in-context learning and synthesizing corresponding negative images with text-to-image generators offers a solution. We introduce a novel contrastive pre-training strategy that leverages these hard negative captions and images in an alternating fashion to train CLIP. We demonstrate that our method, named TripletCLIP, when applied to existing datasets such as CC3M and CC12M, enhances the compositional capabilities of CLIP, resulting in an absolute improvement of over 9% on the SugarCrepe benchmark on an equal computational budget, as well as improvements in zero-shot image classification and image retrieval. Our code, models, and data are available at: https://tripletclip.github.io

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

It is well noted that coordinate based MLPs benefit -- in terms of preserving high-frequency information -- through the encoding of coordinate positions as an array of Fourier features. Hitherto, the rationale for the effectiveness of these positional encodings has been solely studied through a Fourier lens. In this paper, we strive to broaden this understanding by showing that alternative non-Fourier embedding functions can indeed be used for positional encoding. Moreover, we show that their performance is entirely determined by a trade-off between the stable rank of the embedded matrix and the distance preservation between embedded coordinates. We further establish that the now ubiquitous Fourier feature mapping of position is a special case that fulfills these conditions. Consequently, we present a more general theory to analyze positional encoding in terms of shifted basis functions. To this end, we develop the necessary theoretical formulae and empirically verify that our theoretical claims hold in practice. Codes available at https://github.com/osiriszjq/Rethinking-positional-encoding.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

The attention module, which is a crucial component in Transformer, cannot scale efficiently to long sequences due to its quadratic complexity. Many works focus on approximating the dot-then-exponentiate softmax function in the original attention, leading to sub-quadratic or even linear-complexity Transformer architectures. However, we show that these methods cannot be applied to more powerful attention modules that go beyond the dot-then-exponentiate style, e.g., Transformers with relative positional encoding (RPE). Since in many state-of-the-art models, relative positional encoding is used as default, designing efficient Transformers that can incorporate RPE is appealing. In this paper, we propose a novel way to accelerate attention calculation for Transformers with RPE on top of the kernelized attention. Based upon the observation that relative positional encoding forms a Toeplitz matrix, we mathematically show that kernelized attention with RPE can be calculated efficiently using Fast Fourier Transform (FFT). With FFT, our method achieves O(nlog n) time complexity. Interestingly, we further demonstrate that properly using relative positional encoding can mitigate the training instability problem of vanilla kernelized attention. On a wide range of tasks, we empirically show that our models can be trained from scratch without any optimization issues. The learned model performs better than many efficient Transformer variants and is faster than standard Transformer in the long-sequence regime.

Existing large language models (LLMs) for register transfer level code generation face challenges like compilation failures and suboptimal power, performance, and area (PPA) efficiency. This is due to the lack of PPA awareness in conventional transformer decoding algorithms. In response, we present an automated transformer decoding algorithm that integrates Monte Carlo tree-search for lookahead, guiding the transformer to produce compilable, functionally correct, and PPA-optimized code. Empirical evaluation with a fine-tuned language model on RTL codesets shows that our proposed technique consistently generates functionally correct code compared to prompting-only methods and effectively addresses the PPA-unawareness drawback of naive large language models. For the largest design generated by the state-of-the-art LLM (16-bit adder), our technique can achieve a 31.8% improvement in the area-delay product.

The recent GPT-4 has demonstrated extraordinary multi-modal abilities, such as directly generating websites from handwritten text and identifying humorous elements within images. These features are rarely observed in previous vision-language models. We believe the primary reason for GPT-4's advanced multi-modal generation capabilities lies in the utilization of a more advanced large language model (LLM). To examine this phenomenon, we present MiniGPT-4, which aligns a frozen visual encoder with a frozen LLM, Vicuna, using just one projection layer. Our findings reveal that MiniGPT-4 possesses many capabilities similar to those exhibited by GPT-4 like detailed image description generation and website creation from hand-written drafts. Furthermore, we also observe other emerging capabilities in MiniGPT-4, including writing stories and poems inspired by given images, providing solutions to problems shown in images, teaching users how to cook based on food photos, etc. In our experiment, we found that only performing the pretraining on raw image-text pairs could produce unnatural language outputs that lack coherency including repetition and fragmented sentences. To address this problem, we curate a high-quality, well-aligned dataset in the second stage to finetune our model using a conversational template. This step proved crucial for augmenting the model's generation reliability and overall usability. Notably, our model is highly computationally efficient, as we only train a projection layer utilizing approximately 5 million aligned image-text pairs. Our code, pre-trained model, and collected dataset are available at https://minigpt-4.github.io/.

We present CM3Leon (pronounced "Chameleon"), a retrieval-augmented, token-based, decoder-only multi-modal language model capable of generating and infilling both text and images. CM3Leon uses the CM3 multi-modal architecture but additionally shows the extreme benefits of scaling up and tuning on more diverse instruction-style data. It is the first multi-modal model trained with a recipe adapted from text-only language models, including a large-scale retrieval-augmented pre-training stage and a second multi-task supervised fine-tuning (SFT) stage. It is also a general-purpose model that can do both text-to-image and image-to-text generation, allowing us to introduce self-contained contrastive decoding methods that produce high-quality outputs. Extensive experiments demonstrate that this recipe is highly effective for multi-modal models. CM3Leon achieves state-of-the-art performance in text-to-image generation with 5x less training compute than comparable methods (zero-shot MS-COCO FID of 4.88). After SFT, CM3Leon can also demonstrate unprecedented levels of controllability in tasks ranging from language-guided image editing to image-controlled generation and segmentation.

Despite the remarkable success of LLMs in English, there is a significant gap in performance in non-English languages. In order to address this, we introduce a novel recipe for creating a multilingual synthetic instruction tuning dataset, sPhinX, which is created by selectively translating instruction response pairs from English into 50 languages. We test the effectiveness of sPhinX by using it to fine-tune two state-of-the-art models, Phi-3-small and Mistral-7B and then evaluating them across a comprehensive suite of multilingual benchmarks that test reasoning, question answering, and reading comprehension. Our results show that Phi-3-small and Mistral-7B fine-tuned with sPhinX perform better on an average by 4.2%pt and 5%pt respectively as compared to the baselines. We also devise a strategy to incorporate N-shot examples in each fine-tuning sample which further boosts the performance of these models by 3%pt and 10%pt respectively. Additionally, sPhinX also outperforms other multilingual instruction tuning datasets on the same benchmarks along with being sample efficient and diverse, thereby reducing dataset creation costs. Additionally, instruction tuning with sPhinX does not lead to regression on most standard LLM benchmarks.

Multilingual neural machine translation models generally distinguish translation directions by the language tag (LT) in front of the source or target sentences. However, current LT strategies cannot indicate the desired target language as expected on zero-shot translation, i.e., the off-target issue. Our analysis reveals that the indication of the target language is sensitive to the placement of the target LT. For example, when placing the target LT on the decoder side, the indication would rapidly degrade along with decoding steps, while placing the target LT on the encoder side would lead to copying or paraphrasing the source input. To address the above issues, we propose a simple yet effective strategy named Language Converter Strategy (LCS). By introducing the target language embedding into the top encoder layers, LCS mitigates confusion in the encoder and ensures stable language indication for the decoder. Experimental results on MultiUN, TED, and OPUS-100 datasets demonstrate that LCS could significantly mitigate the off-target issue, with language accuracy up to 95.28%, 96.21%, and 85.35% meanwhile outperforming the vanilla LT strategy by 3.07, 3,3, and 7.93 BLEU scores on zero-shot translation, respectively.

To better support retrieval applications such as web search and question answering, growing effort is made to develop retrieval-oriented language models. Most of the existing works focus on improving the semantic representation capability for the contextualized embedding of [CLS] token. However, recent study shows that the ordinary tokens besides [CLS] may provide extra information, which helps to produce a better representation effect. As such, it's necessary to extend the current methods where all contextualized embeddings can be jointly pre-trained for the retrieval tasks. With this motivation, we propose a new pre-training method: duplex masked auto-encoder, a.k.a. DupMAE, which targets on improving the semantic representation capacity for the contextualized embeddings of both [CLS] and ordinary tokens. It introduces two decoding tasks: one is to reconstruct the original input sentence based on the [CLS] embedding, the other one is to minimize the bag-of-words loss (BoW) about the input sentence based on the entire ordinary tokens' embeddings. The two decoding losses are added up to train a unified encoding model. The embeddings from [CLS] and ordinary tokens, after dimension reduction and aggregation, are concatenated as one unified semantic representation for the input. DupMAE is simple but empirically competitive: with a small decoding cost, it substantially contributes to the model's representation capability and transferability, where remarkable improvements are achieved on MS MARCO and BEIR benchmarks.

Humans tend to decompose a sentence into different parts like sth do sth at someplace and then fill each part with certain content. Inspired by this, we follow the principle of modular design to propose a novel image captioner: learning to Collocate Visual-Linguistic Neural Modules (CVLNM). Unlike the widely used neural module networks in VQA, where the language (\ie, question) is fully observable, the task of collocating visual-linguistic modules is more challenging. This is because the language is only partially observable, for which we need to dynamically collocate the modules during the process of image captioning. To sum up, we make the following technical contributions to design and train our CVLNM: 1) distinguishable module design -- four modules in the encoder including one linguistic module for function words and three visual modules for different content words (\ie, noun, adjective, and verb) and another linguistic one in the decoder for commonsense reasoning, 2) a self-attention based module controller for robustifying the visual reasoning, 3) a part-of-speech based syntax loss imposed on the module controller for further regularizing the training of our CVLNM. Extensive experiments on the MS-COCO dataset show that our CVLNM is more effective, \eg, achieving a new state-of-the-art 129.5 CIDEr-D, and more robust, \eg, being less likely to overfit to dataset bias and suffering less when fewer training samples are available. Codes are available at https://github.com/GCYZSL/CVLMN

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

As the parameter size of large language models (LLMs) continues to expand, the need for a large memory footprint and high communication bandwidth have become significant bottlenecks for the training and inference of LLMs. To mitigate these bottlenecks, various tensor compression techniques have been proposed to reduce the data size, thereby alleviating memory requirements and communication pressure. Our research found that video codecs, despite being originally designed for compressing videos, show excellent efficiency when compressing various types of tensors. We demonstrate that video codecs can be versatile and general-purpose tensor codecs while achieving the state-of-the-art compression efficiency in various tasks. We further make use of the hardware video encoding and decoding module available on GPUs to create a framework capable of both inference and training with video codecs repurposed as tensor codecs. This greatly reduces the requirement for memory capacity and communication bandwidth, enabling training and inference of large models on consumer-grade GPUs.

Reverse engineering binaries is required to understand and analyse programs for which the source code is unavailable. Decompilers can transform the largely unreadable binaries into a more readable source code-like representation. However, reverse engineering is time-consuming, much of which is taken up by labelling the functions with semantic information. While the automated summarisation of decompiled code can help Reverse Engineers understand and analyse binaries, current work mainly focuses on summarising source code, and no suitable dataset exists for this task. In this work, we extend large pre-trained language models of source code to summarise decompiled binary functions. Furthermore, we investigate the impact of input and data properties on the performance of such models. Our approach consists of two main components; the data and the model. We first build CAPYBARA, a dataset of 214K decompiled function-documentation pairs across various compiler optimisations. We extend CAPYBARA further by generating synthetic datasets and deduplicating the data. Next, we fine-tune the CodeT5 base model with CAPYBARA to create BinT5. BinT5 achieves the state-of-the-art BLEU-4 score of 60.83, 58.82, and 44.21 for summarising source, decompiled, and synthetically stripped decompiled code, respectively. This indicates that these models can be extended to decompiled binaries successfully. Finally, we found that the performance of BinT5 is not heavily dependent on the dataset size and compiler optimisation level. We recommend future research to further investigate transferring knowledge when working with less expressive input formats such as stripped binaries.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

We present GlotScript, an open resource and tool for low resource writing system identification. GlotScript-R is a resource that provides the attested writing systems for more than 7,000 languages. It is compiled by aggregating information from existing writing system resources. GlotScript-T is a writing system identification tool that covers all 161 Unicode 15.0 scripts. For an input text, it returns its script distribution where scripts are identified by ISO 15924 codes. We also present two use cases for GlotScript. First, we demonstrate that GlotScript supports cleaning multilingual corpora such as mC4 and OSCAR. Second, we analyze the tokenization of a number of language models such as GPT-4 using GlotScript and provide insights on the coverage of low resource scripts and languages by each language model. We hope that GlotScript will become a useful resource for work on low resource languages in the NLP community. GlotScript-R and GlotScript-T are available at https://github.com/cisnlp/GlotScript.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

Models that rely on subword tokenization have significant drawbacks, such as sensitivity to character-level noise like spelling errors and inconsistent compression rates across different languages and scripts. While character- or byte-level models like ByT5 attempt to address these concerns, they have not gained widespread adoption -- processing raw byte streams without tokenization results in significantly longer sequence lengths, making training and inference inefficient. This work introduces MrT5 (MergeT5), a more efficient variant of ByT5 that integrates a token deletion mechanism in its encoder to dynamically shorten the input sequence length. After processing through a fixed number of encoder layers, a learnt delete gate determines which tokens are to be removed and which are to be retained for subsequent layers. MrT5 effectively ``merges'' critical information from deleted tokens into a more compact sequence, leveraging contextual information from the remaining tokens. In continued pre-training experiments, we find that MrT5 can achieve significant gains in inference runtime with minimal effect on performance. When trained on English text, MrT5 demonstrates the capability to transfer its deletion feature zero-shot across several languages, with significant additional improvements following multilingual training. Furthermore, MrT5 shows comparable accuracy to ByT5 on downstream evaluations such as XNLI and character-level tasks while reducing sequence lengths by up to 80%. Our approach presents a solution to the practical limitations of existing byte-level models.

The rapid advance of Large Language Models (LLMs) has catalyzed the development of Vision-Language Models (VLMs). Monolithic VLMs, which avoid modality-specific encoders, offer a promising alternative to the compositional ones but face the challenge of inferior performance. Most existing monolithic VLMs require tuning pre-trained LLMs to acquire vision abilities, which may degrade their language capabilities. To address this dilemma, this paper presents a novel high-performance monolithic VLM named HoVLE. We note that LLMs have been shown capable of interpreting images, when image embeddings are aligned with text embeddings. The challenge for current monolithic VLMs actually lies in the lack of a holistic embedding module for both vision and language inputs. Therefore, HoVLE introduces a holistic embedding module that converts visual and textual inputs into a shared space, allowing LLMs to process images in the same way as texts. Furthermore, a multi-stage training strategy is carefully designed to empower the holistic embedding module. It is first trained to distill visual features from a pre-trained vision encoder and text embeddings from the LLM, enabling large-scale training with unpaired random images and text tokens. The whole model further undergoes next-token prediction on multi-modal data to align the embeddings. Finally, an instruction-tuning stage is incorporated. Our experiments show that HoVLE achieves performance close to leading compositional models on various benchmarks, outperforming previous monolithic models by a large margin. Model available at https://huggingface.co/OpenGVLab/HoVLE.

Multilingual translation supports multiple translation directions by projecting all languages in a shared space, but the translation quality is undermined by the difference between languages in the text-only modality, especially when the number of languages is large. To bridge this gap, we introduce visual context as the universal language-independent representation to facilitate multilingual translation. In this paper, we propose a framework to leverage the multimodal prompt to guide the Multimodal Multilingual neural Machine Translation (m3P), which aligns the representations of different languages with the same meaning and generates the conditional vision-language memory for translation. We construct a multilingual multimodal instruction dataset (InstrMulti102) to support 102 languages. Our method aims to minimize the representation distance of different languages by regarding the image as a central language. Experimental results show that m3P outperforms previous text-only baselines and multilingual multimodal methods by a large margin. Furthermore, the probing experiments validate the effectiveness of our method in enhancing translation under the low-resource and massively multilingual scenario.

Post-training quantization (PTQ) reduces the memory footprint of LLMs by quantizing their weights to low-precision. In this work, we introduce QuIP#, a weight-only PTQ method that achieves state-of-the-art results in extreme compression regimes (le 4 bits per weight) using three novel techniques. First, QuIP# improves the incoherence processing from QuIP by using the randomized Hadamard transform, which is faster and has better theoretical properties. Second, QuIP# uses vector quantization techniques to take advantage of the ball-shaped sub-Gaussian distribution that incoherent weights possess: specifically, we introduce a set of hardware-efficient codebooks based on the highly symmetric E_8 lattice, which achieves the optimal 8-dimension unit ball packing. Third, QuIP# uses fine-tuning to improve fidelity to the original model. Our experiments show that QuIP# outperforms existing PTQ methods, enables new behaviors in PTQ scaling, and supports fast inference.

Despite achieving remarkable performance on various vision-language tasks, Transformer-based Vision-Language Models (VLMs) suffer from redundancy in inputs and parameters, significantly hampering their efficiency in real-world applications. Moreover, the degree of redundancy in token representations and model parameters, such as attention heads, varies significantly for different inputs. In light of the challenges, we propose SmartTrim, an adaptive acceleration framework for VLMs, which adjusts the computational overhead per instance. Specifically, we integrate lightweight modules into the original backbone to identify and prune redundant token representations and attention heads within each layer. Furthermore, we devise a self-distillation strategy to enhance the consistency between the predictions of the pruned model and its fully-capacity counterpart. Experimental results across various vision-language tasks consistently demonstrate that SmartTrim accelerates the original model by 2-3 times with minimal performance degradation, highlighting the effectiveness and efficiency compared to previous approaches. Code will be available at https://github.com/kugwzk/SmartTrim.

The field of advanced text-to-image generation is witnessing the emergence of unified frameworks that integrate powerful text encoders, such as CLIP and T5, with Diffusion Transformer backbones. Although there have been efforts to control output images with additional conditions, like canny and depth map, a comprehensive framework for arbitrary text-image interleaved control is still lacking. This gap is especially evident when attempting to merge concepts or visual elements from multiple images in the generation process. To mitigate the gap, we conducted preliminary experiments showing that large multimodal models (LMMs) offer an effective shared representation space, where image and text can be well-aligned to serve as a condition for external diffusion models. Based on this discovery, we propose Dream Engine, an efficient and unified framework designed for arbitrary text-image interleaved control in image generation models. Building on powerful text-to-image models like SD3.5, we replace the original text-only encoders by incorporating versatile multimodal information encoders such as QwenVL. Our approach utilizes a two-stage training paradigm, consisting of joint text-image alignment and multimodal interleaved instruction tuning. Our experiments demonstrate that this training method is effective, achieving a 0.69 overall score on the GenEval benchmark, and matching the performance of state-of-the-art text-to-image models like SD3.5 and FLUX.

Tokenization is an understudied and often neglected component of modern LLMs. Most published works use a single tokenizer for all experiments, often borrowed from another model, without performing ablations or analysis to optimize tokenization. Moreover, the tokenizer is generally kept unchanged when fine-tuning a base model. In this paper, we show that the size, pre-tokenization regular expression, and training data of a tokenizer can significantly impact the model's generation speed, effective context size, memory usage, and downstream performance. We train specialized Byte-Pair Encoding code tokenizers, and conduct extensive ablations on the impact of tokenizer design on the performance of LLMs for code generation tasks such as HumanEval and MBPP, and provide recommendations for tokenizer hyper-parameters selection and switching the tokenizer in a pre-trained LLM. We perform our experiments on models trained from scratch and from pre-trained models, verifying their applicability to a wide range of use-cases. We find that when fine-tuning on more than 50 billion tokens, we can specialize the tokenizer of a pre-trained LLM to obtain large gains in generation speed and effective context size.

In the realm of Large Language Models (LLMs), the ability to process long contexts is increasingly crucial for tasks such as multi-round dialogues, code generation, and document summarization. This paper addresses the challenges of enhancing the long-context performance, reducing computational complexity, and leveraging pretrained models collectively termed the "impossible triangle." We introduce E2LLM (Encoder Elongated Large Language Models), a novel approach that effectively navigates this paradox. The method involves splitting long contexts into chunks, compressing each into embedding vectors via a pretrained text encoder, and utilizing an adapter to align these representations with a decoder-only LLM. Two training objectives, focusing on reconstruction of the encoder output and long-context instruction fine-tuning, are employed to facilitate the understanding of soft prompts by the LLM. Experimental results demonstrate that E2LLM achieves superior performance in long-context scenarios while balancing efficiency, performance, and compatibility with pretrained models. Our framework thus represents a significant advancement in the field, contributing to effective long-text modeling.

With the recent focus on Large Language Models (LLMs), both StarCoder (Li et al., 2023) and Code Llama (Rozi\`ere et al., 2023) have demonstrated remarkable performance in code generation. However, there is still a need for improvement in code translation functionality with efficient training techniques. In response to this, we introduce SteloCoder, a decoder-only StarCoder-based LLM designed specifically for multi-programming language-to-Python code translation. In particular, SteloCoder achieves C++, C#, JavaScript, Java, or PHP-to-Python code translation without specifying the input programming language. We modified StarCoder model architecture by incorporating a Mixture-of-Experts (MoE) technique featuring five experts and a gating network for multi-task handling. Experts are obtained by StarCoder fine-tuning. Specifically, we use a Low-Rank Adaptive Method (LoRA) technique, limiting each expert size as only 0.06% of number of StarCoder's parameters. At the same time, to enhance training efficiency in terms of time, we adopt curriculum learning strategy and use self-instruct data for efficient fine-tuning. As a result, each expert takes only 6 hours to train on one single 80Gb A100 HBM. With experiments on XLCoST datasets, SteloCoder achieves an average of 73.76 CodeBLEU score in multi-programming language-to-Python translation, surpassing the top performance from the leaderboard by at least 3.5. This accomplishment is attributed to only 45M extra parameters with StarCoder as the backbone and 32 hours of valid training on one 80GB A100 HBM. The source code is release here: https://github.com/sade-adrien/SteloCoder.

Byte-Pair Encoding (BPE) is a popular algorithm used for tokenizing data in NLP, despite being devised initially as a compression method. BPE appears to be a greedy algorithm at face value, but the underlying optimization problem that BPE seeks to solve has not yet been laid down. We formalize BPE as a combinatorial optimization problem. Via submodular functions, we prove that the iterative greedy version is a 1{{sigma(mu^star)}}(1-e^{-{sigma(mu^star)}})-approximation of an optimal merge sequence, where {sigma(mu^star)} is the total backward curvature with respect to the optimal merge sequence mu^star. Empirically the lower bound of the approximation is approx 0.37. We provide a faster implementation of BPE which improves the runtime complexity from Oleft(N Mright) to Oleft(N log Mright), where N is the sequence length and M is the merge count. Finally, we optimize the brute-force algorithm for optimal BPE using memoization.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

In this paper, we investigate how the output representation of an end-to-end neural network affects multilingual automatic speech recognition (ASR). We study different representations including character-level, byte-level, byte pair encoding (BPE), and byte-level byte pair encoding (BBPE) representations, and analyze their strengths and weaknesses. We focus on developing a single end-to-end model to support utterance-based bilingual ASR, where speakers do not alternate between two languages in a single utterance but may change languages across utterances. We conduct our experiments on English and Mandarin dictation tasks, and we find that BBPE with penalty schemes can improve utterance-based bilingual ASR performance by 2% to 5% relative even with smaller number of outputs and fewer parameters. We conclude with analysis that indicates directions for further improving multilingual ASR.

Composed Image Retrieval (CIR) involves retrieving a target image based on a composed query of an image paired with text that specifies modifications or changes to the visual reference. CIR is inherently an instruction-following task, as the model needs to interpret and apply modifications to the image. In practice, due to the scarcity of annotated data in downstream tasks, Zero-Shot CIR (ZS-CIR) is desirable. While existing ZS-CIR models based on CLIP have shown promising results, their capability in interpreting and following modification instructions remains limited. Some research attempts to address this by incorporating Large Language Models (LLMs). However, these approaches still face challenges in effectively integrating multimodal information and instruction understanding. To tackle above challenges, we propose a novel embedding method utilizing an instruction-tuned Multimodal LLM (MLLM) to generate composed representation, which significantly enhance the instruction following capability for a comprehensive integration between images and instructions. Nevertheless, directly applying MLLMs introduces a new challenge since MLLMs are primarily designed for text generation rather than embedding extraction as required in CIR. To address this, we introduce a two-stage training strategy to efficiently learn a joint multimodal embedding space and further refining the ability to follow modification instructions by tuning the model in a triplet dataset similar to the CIR format. Extensive experiments on four public datasets: FashionIQ, CIRR, GeneCIS, and CIRCO demonstrates the superior performance of our model, outperforming state-of-the-art baselines by a significant margin. Codes are available at the GitHub repository.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

This article offers an empirical study on the different ways of encoding Chinese, Japanese, Korean (CJK) and English languages for text classification. Different encoding levels are studied, including UTF-8 bytes, characters, words, romanized characters and romanized words. For all encoding levels, whenever applicable, we provide comparisons with linear models, fastText and convolutional networks. For convolutional networks, we compare between encoding mechanisms using character glyph images, one-hot (or one-of-n) encoding, and embedding. In total there are 473 models, using 14 large-scale text classification datasets in 4 languages including Chinese, English, Japanese and Korean. Some conclusions from these results include that byte-level one-hot encoding based on UTF-8 consistently produces competitive results for convolutional networks, that word-level n-grams linear models are competitive even without perfect word segmentation, and that fastText provides the best result using character-level n-gram encoding but can overfit when the features are overly rich.

Previous work mainly focuses on improving cross-lingual transfer for NLU tasks with a multilingual pretrained encoder (MPE), or improving the performance on supervised machine translation with BERT. However, it is under-explored that whether the MPE can help to facilitate the cross-lingual transferability of NMT model. In this paper, we focus on a zero-shot cross-lingual transfer task in NMT. In this task, the NMT model is trained with parallel dataset of only one language pair and an off-the-shelf MPE, then it is directly tested on zero-shot language pairs. We propose SixT, a simple yet effective model for this task. SixT leverages the MPE with a two-stage training schedule and gets further improvement with a position disentangled encoder and a capacity-enhanced decoder. Using this method, SixT significantly outperforms mBART, a pretrained multilingual encoder-decoder model explicitly designed for NMT, with an average improvement of 7.1 BLEU on zero-shot any-to-English test sets across 14 source languages. Furthermore, with much less training computation cost and training data, our model achieves better performance on 15 any-to-English test sets than CRISS and m2m-100, two strong multilingual NMT baselines.

Code generation models have increasingly become integral to aiding software development, offering assistance in tasks such as code completion, debugging, and code translation. Although current research has thoroughly examined the correctness of code produced by code generation models, a vital aspect, i.e., the efficiency of the generated code, has often been neglected. This paper presents EffiBench, a benchmark with 1,000 efficiency-critical coding problems for assessing the efficiency of code generated by code generation models. EffiBench contains a diverse set of LeetCode coding problems. Each problem is paired with an executable human-written canonical solution. With EffiBench, we empirically examine the capability of 21 Large Language Models (13 open-sourced and 8 closed-sourced) in generating efficient code. The results demonstrate that GPT-4-turbo generates the most efficient code, significantly outperforming Palm-2-chat-bison, Claude-instant-1, Gemini-pro, GPT-4, and GPT-3.5. Nevertheless, its code efficiency is still worse than the efficiency of human-written canonical solutions. In particular, the average and worst execution time of GPT-4-turbo generated code is 1.69 and 45.49 times that of the canonical solutions.

Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences between LLMs used for NLP, which effectively handle multiple tasks and are available in small sizes, and protein language models that are often specialized for specific tasks and only exist in larger sizes. In this work, we introduce two small protein language models, based on Llama-3-8B and Phi-3-mini, that are capable of both uncontrollable and controllable protein generation. For the uncontrollable generation task, our best model achieves an average pLDDT score of 69.75, demonstrating robust performance in generating viable protein structures. For the controllable generation task, in which the model generates proteins according to properties specified in the prompt, we achieve a remarkable average TM-Score of 0.84, indicating high structural similarity to target proteins. We chose 10 properties, including six classes of enzymes, to extend the capabilities of prior protein language models. Our approach utilizes the Low-Rank Adaptor (LoRA) technique, reducing trainable parameters to just 4% of the original model size, lowering computational requirements. By using a subset of the UniRef50 dataset and small models, we reduced the overall training time by 70% without compromising performance. Notably, Phi-3-mini reduced trainable parameters by 60%, decreasing training cost by 30% compared to Llama 3. Consequently, Phi-3 achieved a comparable TM-Score of 0.81, demonstrating that smaller models can match the performance of larger ones, like Llama 3. We also demonstrate the deployment of our models on the energy efficient ET-SoC-1 chip, significantly improving the TPS/W by a factor of 3.

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

Multimodal large language models acquire their instruction-following capabilities through a two-stage training process: pre-training on image-text pairs and fine-tuning on supervised vision-language instruction data. Recent studies have shown that large language models can achieve satisfactory results even with a limited amount of high-quality instruction-following data. In this paper, we introduce InstructionGPT-4, which is fine-tuned on a small dataset comprising only 200 examples, amounting to approximately 6% of the instruction-following data used in the alignment dataset for MiniGPT-4. We first propose several metrics to access the quality of multimodal instruction data. Based on these metrics, we present a simple and effective data selector to automatically identify and filter low-quality vision-language data. By employing this method, InstructionGPT-4 outperforms the original MiniGPT-4 on various evaluations (e.g., visual question answering, GPT-4 preference). Overall, our findings demonstrate that less but high-quality instruction tuning data is efficient to enable multimodal large language models to generate better output.

Learning high-quality feature embeddings efficiently and effectively is critical for the performance of web-scale machine learning systems. A typical model ingests hundreds of features with vocabularies on the order of millions to billions of tokens. The standard approach is to represent each feature value as a d-dimensional embedding, introducing hundreds of billions of parameters for extremely high-cardinality features. This bottleneck has led to substantial progress in alternative embedding algorithms. Many of these methods, however, make the assumption that each feature uses an independent embedding table. This work introduces a simple yet highly effective framework, Feature Multiplexing, where one single representation space is used across many different categorical features. Our theoretical and empirical analysis reveals that multiplexed embeddings can be decomposed into components from each constituent feature, allowing models to distinguish between features. We show that multiplexed representations lead to Pareto-optimal parameter-accuracy tradeoffs for three public benchmark datasets. Further, we propose a highly practical approach called Unified Embedding with three major benefits: simplified feature configuration, strong adaptation to dynamic data distributions, and compatibility with modern hardware. Unified embedding gives significant improvements in offline and online metrics compared to highly competitive baselines across five web-scale search, ads, and recommender systems, where it serves billions of users across the world in industry-leading products.

Recently, large language model (LLM) based text-to-speech (TTS) systems have gradually become the mainstream in the industry due to their high naturalness and powerful zero-shot voice cloning capabilities.Here, we introduce the IndexTTS system, which is mainly based on the XTTS and Tortoise model. We add some novel improvements. Specifically, in Chinese scenarios, we adopt a hybrid modeling method that combines characters and pinyin, making the pronunciations of polyphonic characters and long-tail characters controllable. We also performed a comparative analysis of the Vector Quantization (VQ) with Finite-Scalar Quantization (FSQ) for codebook utilization of acoustic speech tokens. To further enhance the effect and stability of voice cloning, we introduce a conformer-based speech conditional encoder and replace the speechcode decoder with BigVGAN2. Compared with XTTS, it has achieved significant improvements in naturalness, content consistency, and zero-shot voice cloning. As for the popular TTS systems in the open-source, such as Fish-Speech, CosyVoice2, FireRedTTS and F5-TTS, IndexTTS has a relatively simple training process, more controllable usage, and faster inference speed. Moreover, its performance surpasses that of these systems. Our demos are available at https://index-tts.github.io.

Although instruction-tuned large language models (LLMs) have exhibited remarkable capabilities across various NLP tasks, their effectiveness on other data modalities beyond text has not been fully studied. In this work, we propose Macaw-LLM, a novel multi-modal LLM that seamlessly integrates visual, audio, and textual information. Macaw-LLM consists of three main components: a modality module for encoding multi-modal data, a cognitive module for harnessing pretrained LLMs, and an alignment module for harmonizing diverse representations. Our novel alignment module seamlessly bridges multi-modal features to textual features, simplifying the adaptation process from the modality modules to the cognitive module. In addition, we construct a large-scale multi-modal instruction dataset in terms of multi-turn dialogue, including 69K image instances and 50K video instances. We have made our data, code and model publicly available, which we hope can pave the way for future research in multi-modal LLMs and expand the capabilities of LLMs to handle diverse data modalities and address complex real-world scenarios.

This work presents a novel framework for training Arabic nested embedding models through Matryoshka Embedding Learning, leveraging multilingual, Arabic-specific, and English-based models, to highlight the power of nested embeddings models in various Arabic NLP downstream tasks. Our innovative contribution includes the translation of various sentence similarity datasets into Arabic, enabling a comprehensive evaluation framework to compare these models across different dimensions. We trained several nested embedding models on the Arabic Natural Language Inference triplet dataset and assessed their performance using multiple evaluation metrics, including Pearson and Spearman correlations for cosine similarity, Manhattan distance, Euclidean distance, and dot product similarity. The results demonstrate the superior performance of the Matryoshka embedding models, particularly in capturing semantic nuances unique to the Arabic language. Results demonstrated that Arabic Matryoshka embedding models have superior performance in capturing semantic nuances unique to the Arabic language, significantly outperforming traditional models by up to 20-25\% across various similarity metrics. These results underscore the effectiveness of language-specific training and highlight the potential of Matryoshka models in enhancing semantic textual similarity tasks for Arabic NLP.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

We present Marian, an efficient and self-contained Neural Machine Translation framework with an integrated automatic differentiation engine based on dynamic computation graphs. Marian is written entirely in C++. We describe the design of the encoder-decoder framework and demonstrate that a research-friendly toolkit can achieve high training and translation speed.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Ternary and binary neural networks enable multiplication-free computation and promise multiple orders of magnitude efficiency gains over full-precision networks if implemented on specialized hardware. However, since both the parameter and the output space are highly discretized, such networks have proven very difficult to optimize. The difficulties are compounded for the class of transformer text generation models due to the sensitivity of the attention operation to quantization and the noise-compounding effects of autoregressive decoding in the high-cardinality output space. We approach the problem with a mix of statistics-based quantization for the weights and elastic quantization of the activations and demonstrate the first ternary and binary transformer models on the downstream tasks of summarization and machine translation. Our ternary BART base achieves an R1 score of 41 on the CNN/DailyMail benchmark, which is merely 3.9 points behind the full model while being 16x more efficient. Our binary model, while less accurate, achieves a highly non-trivial score of 35.6. For machine translation, we achieved BLEU scores of 21.7 and 17.6 on the WMT16 En-Ro benchmark, compared with a full precision mBART model score of 26.8. We also compare our approach in the 8-bit activation setting, where our ternary and even binary weight models can match or outperform the best existing 8-bit weight models in the literature. Our code and models are available at: https://github.com/facebookresearch/Ternary_Binary_Transformer

Recently, most handwritten mathematical expression recognition (HMER) methods adopt the encoder-decoder networks, which directly predict the markup sequences from formula images with the attention mechanism. However, such methods may fail to accurately read formulas with complicated structure or generate long markup sequences, as the attention results are often inaccurate due to the large variance of writing styles or spatial layouts. To alleviate this problem, we propose an unconventional network for HMER named Counting-Aware Network (CAN), which jointly optimizes two tasks: HMER and symbol counting. Specifically, we design a weakly-supervised counting module that can predict the number of each symbol class without the symbol-level position annotations, and then plug it into a typical attention-based encoder-decoder model for HMER. Experiments on the benchmark datasets for HMER validate that both joint optimization and counting results are beneficial for correcting the prediction errors of encoder-decoder models, and CAN consistently outperforms the state-of-the-art methods. In particular, compared with an encoder-decoder model for HMER, the extra time cost caused by the proposed counting module is marginal. The source code is available at https://github.com/LBH1024/CAN.

There has been a growing interest in developing multimodal machine translation (MMT) systems that enhance neural machine translation (NMT) with visual knowledge. This problem setup involves using images as auxiliary information during training, and more recently, eliminating their use during inference. Towards this end, previous works face a challenge in training powerful MMT models from scratch due to the scarcity of annotated multilingual vision-language data, especially for low-resource languages. Simultaneously, there has been an influx of multilingual pre-trained models for NMT and multimodal pre-trained models for vision-language tasks, primarily in English, which have shown exceptional generalisation ability. However, these are not directly applicable to MMT since they do not provide aligned multimodal multilingual features for generative tasks. To alleviate this issue, instead of designing complex modules for MMT, we propose CLIPTrans, which simply adapts the independently pre-trained multimodal M-CLIP and the multilingual mBART. In order to align their embedding spaces, mBART is conditioned on the M-CLIP features by a prefix sequence generated through a lightweight mapping network. We train this in a two-stage pipeline which warms up the model with image captioning before the actual translation task. Through experiments, we demonstrate the merits of this framework and consequently push forward the state-of-the-art across standard benchmarks by an average of +2.67 BLEU. The code can be found at www.github.com/devaansh100/CLIPTrans.

Spoken semantic parsing (SSP) involves generating machine-comprehensible parses from input speech. Training robust models for existing application domains represented in training data or extending to new domains requires corresponding triplets of speech-transcript-semantic parse data, which is expensive to obtain. In this paper, we address this challenge by examining methods that can use transcript-semantic parse data (unpaired text) without corresponding speech. First, when unpaired text is drawn from existing textual corpora, Joint Audio Text (JAT) and Text-to-Speech (TTS) are compared as ways to generate speech representations for unpaired text. Experiments on the STOP dataset show that unpaired text from existing and new domains improves performance by 2% and 30% in absolute Exact Match (EM) respectively. Second, we consider the setting when unpaired text is not available in existing textual corpora. We propose to prompt Large Language Models (LLMs) to generate unpaired text for existing and new domains. Experiments show that examples and words that co-occur with intents can be used to generate unpaired text with Llama 2.0. Using the generated text with JAT and TTS for spoken semantic parsing improves EM on STOP by 1.4% and 2.6% absolute for existing and new domains respectively.

We present M3P, a Multitask Multilingual Multimodal Pre-trained model that combines multilingual pre-training and multimodal pre-training into a unified framework via multitask pre-training. Our goal is to learn universal representations that can map objects occurred in different modalities or texts expressed in different languages into a common semantic space. In addition, to explicitly encourage fine-grained alignment between images and non-English languages, we also propose Multimodal Code-switched Training (MCT) to combine monolingual pre-training and multimodal pre-training via a code-switch strategy. Experiments are performed on the multilingual image retrieval task across two benchmark datasets, including MSCOCO and Multi30K. M3P can achieve comparable results for English and new state-of-the-art results for non-English languages.

Last year, multimodal architectures served up a revolution in AI-based approaches and solutions, extending the capabilities of large language models (LLM). We propose an OmniFusion model based on a pretrained LLM and adapters for visual modality. We evaluated and compared several architecture design principles for better text and visual data coupling: MLP and transformer adapters, various CLIP ViT-based encoders (SigLIP, InternVIT, etc.), and their fusing approach, image encoding method (whole image or tiles encoding) and two 7B LLMs (the proprietary one and open-source Mistral). Experiments on 8 visual-language benchmarks show the top score for the best OmniFusion setup in terms of different VQA tasks in comparison with open-source LLaVA-like solutions: VizWiz, Pope, MM-Vet, ScienceQA, MMBench, TextVQA, VQAv2, MMMU. We also propose a variety of situations, where OmniFusion provides highly-detailed answers in different domains: housekeeping, sightseeing, culture, medicine, handwritten and scanned equations recognition, etc. Mistral-based OmniFusion model is an open-source solution with weights, training and inference scripts available at https://github.com/AIRI-Institute/OmniFusion.

In recent years, large language models have achieved significant success in generative tasks (e.g., speech cloning and audio generation) related to speech, audio, music, and other signal domains. A crucial element of these models is the discrete acoustic codecs, which serves as an intermediate representation replacing the mel-spectrogram. However, there exist several gaps between discrete codecs and downstream speech language models. Specifically, 1) most codec models are trained on only 1,000 hours of data, whereas most speech language models are trained on 60,000 hours; 2) Achieving good reconstruction performance requires the utilization of numerous codebooks, which increases the burden on downstream speech language models; 3) The initial channel of the codebooks contains excessive information, making it challenging to directly generate acoustic tokens from weakly supervised signals such as text in downstream tasks. Consequently, leveraging the characteristics of speech language models, we propose Language-Codec. In the Language-Codec, we introduce a Mask Channel Residual Vector Quantization (MCRVQ) mechanism along with improved Fourier transform structures and larger training datasets to address the aforementioned gaps. We compare our method with competing audio compression algorithms and observe significant outperformance across extensive evaluations. Furthermore, we also validate the efficiency of the Language-Codec on downstream speech language models. The source code and pre-trained models can be accessed at https://github.com/jishengpeng/languagecodec .

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Understanding telecom standards involves sorting through numerous technical documents, such as those produced by the 3rd Generation Partnership Project (3GPP), which is time-consuming and labor-intensive. While large language models (LLMs) can assist with the extensive 3GPP knowledge base, an inclusive dataset is crucial for their effective pre-training and fine-tuning. In this paper, we introduce TSpec-LLM, an open-source comprehensive dataset covering all 3GPP documents from Release 8 to Release 19 (1999--2023). To evaluate its efficacy, we first select a representative sample of 3GPP documents, create corresponding technical questions, and assess the baseline performance of various LLMs. We then incorporate a retrieval-augmented generation (RAG) framework to enhance LLM capabilities by retrieving relevant context from the TSpec-LLM dataset. Our evaluation shows that using a naive-RAG framework on TSpec-LLM improves the accuracy of GPT-3.5, Gemini 1.0 Pro, and GPT-4 from 44\%, 46\%, and 51\% to 71\%, 75\%, and 72\%, respectively.

Large language models (LLMs), such as Codex and GPT-4, have recently showcased their remarkable code generation abilities, facilitating a significant boost in coding efficiency. This paper will delve into utilizing LLMs for code generation in private libraries, as they are widely employed in everyday programming. Despite their remarkable capabilities, generating such private APIs poses a formidable conundrum for LLMs, as they inherently lack exposure to these private libraries during pre-training. To address this challenge, we propose a novel framework that emulates the process of programmers writing private code. This framework comprises two modules: APIFinder first retrieves potentially useful APIs from API documentation; and APICoder then leverages these retrieved APIs to generate private code. Specifically, APIFinder employs vector retrieval techniques and allows user involvement in the retrieval process. For APICoder, it can directly utilize off-the-shelf code generation models. To further cultivate explicit proficiency in invoking APIs from prompts, we continuously pre-train a reinforced version of APICoder, named CodeGenAPI. Our goal is to train the above two modules on vast public libraries, enabling generalization to private ones. Meanwhile, we create four private library benchmarks, including TorchDataEval, TorchDataComplexEval, MonkeyEval, and BeatNumEval, and meticulously handcraft test cases for each benchmark to support comprehensive evaluations. Numerous experiments on the four benchmarks consistently affirm the effectiveness of our approach. Furthermore, deeper analysis is also conducted to glean additional insights.

We propose an innovative token representation and update method in a new ultra-small language model: the Wave network. Specifically, we use a complex vector to represent each token, encoding both global and local semantics of the input text. A complex vector consists of two components: a magnitude vector representing the global semantics of the input text, and a phase vector capturing the relationships between individual tokens and global semantics. Experiments on the AG News text classification task demonstrate that, when generating complex vectors from randomly initialized token embeddings, our single-layer Wave Network achieves 90.91\% accuracy with wave interference and 91.66\% with wave modulation -- outperforming a single Transformer layer using BERT pre-trained embeddings by 19.23\% and 19.98\%, respectively, and approaching the accuracy of the pre-trained and fine-tuned BERT base model (94.64\%). Additionally, compared to BERT base, the Wave Network reduces video memory usage and training time by 77.34\% and 85.62\% during wave modulation. In summary, we used a 2.4-million-parameter small language model to achieve accuracy comparable to a 100-million-parameter BERT model in text classification.

A crucial component of many deep learning applications (such as FAQ and RAG) is dense retrieval, in which embedding models are used to convert raw text to numerical vectors and then get the most similar text by MIPS (Maximum Inner Product Search). Some text embedding benchmarks (e.g. MTEB, BEIR, and AIR-Bench) have been established to evaluate embedding models accurately. Thanks to these benchmarks, we can use SOTA models; however, the deployment and application of these models in industry were hampered by their large vector dimensions and numerous parameters. To alleviate this problem, 1) we present a distillation technique that can enable a smaller student model to achieve good performance. 2) Inspired by MRL we present a training approach of reducing the vector dimensions based on its own vectors or its teacher vectors. 3) We do simple yet effective alignment training between images and text to make our model a multimodal encoder. We trained Stella and Jasper models using the technologies above and achieved high scores on the MTEB leaderboard. We release the model and data at Hugging Face Hub (https://huggingface.co/infgrad/jasper_en_vision_language_v1) and the training logs are at https://api.wandb.ai/links/dunnzhang0/z8jqoqpb.

Key-value (KV) caching has become the de-facto to accelerate generation speed for large language models (LLMs) inference. However, the growing cache demand with increasing sequence length has transformed LLM inference to be a memory bound problem, significantly constraining the system throughput. Existing methods rely on dropping unimportant tokens or quantizing all entries uniformly. Such methods, however, often incur high approximation errors to represent the compressed matrices. The autoregressive decoding process further compounds the error of each step, resulting in critical deviation in model generation and deterioration of performance. To tackle this challenge, we propose GEAR, an efficient KV cache compression framework that achieves near-lossless high-ratio compression. GEAR first applies quantization to majority of entries of similar magnitudes to ultra-low precision. It then employs a low rank matrix to approximate the quantization error, and a sparse matrix to remedy individual errors from outlier entries. By adeptly integrating three techniques, GEAR is able to fully exploit their synergistic potentials. Our experiments demonstrate that compared to alternatives, GEAR achieves near-lossless 4-bit KV cache compression with up to 2.38x throughput improvement, while reducing peak-memory size up to 2.29x. Our code is publicly available at https://github.com/HaoKang-Timmy/GEAR.

The prerequisite of many approaches to authorship analysis is a representation of writing style. But despite decades of research, it still remains unclear to what extent commonly used and widely accepted representations like character trigram frequencies actually represent an author's writing style, in contrast to more domain-specific style components or even topic. We address this shortcoming for the first time in a novel experimental setup of fixed authors but swapped domains between training and testing. With this setup, we reveal that approaches using character trigram features are highly susceptible to favor domain information when applied without attention to domains, suffering drops of up to 55.4 percentage points in classification accuracy under domain swapping. We further propose a new remedy based on domain-adversarial learning and compare it to ones from the literature based on heuristic rules. Both can work well, reducing accuracy losses under domain swapping to 3.6% and 3.9%, respectively.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

In this paper, we give an in-depth analysis on the mathematical problem formulations and the probabilistic optimization explorations for some of the key components in Transformer model [33] in the field of generative AI. We explore and discuss some potential further enhancement for current state of the art methods for some key underlying technologies of generative AI models from algorithmic and probabilistic optimization perspective. In particular, we present an optimal solution for sub-word encoding (SWE) based on similar initial settings as that of byte-pair encoding (BPE) algorithm in [9] with similar objectives as that of WordPiece approach in [28, 31] to maximize the likelihood of the training data. We also present cross entropy optimization method to optimize hyperparameters for word2vec model [17]. In addition, we propose a factored combination of rotary positional encoding (RoPE) [32] and attention with linear biases (ALiBi) [23] with a harmonic series. We also present a probabilistic FlashAttention [6, 7] (PrFlashAttention) method with a probability distribution over block distances in the matrix to decide which block is likely to participate in a given round of attention computation while maintaining the lower triangle shape of the tensor for autoregressive language models by re-shaping the tensors. Finally, we present staircase adaptive quantization (SAQ) of key-value (KV) cache for multi-query attention (MQA) based on the framework presented in [16] to have gradual quantization degradation while achieving reasonable model quality and cost savings.

Competition-level code generation tasks pose significant challenges for current state-of-the-art large language models (LLMs). For example, on the LiveCodeBench-Hard dataset, models such as O1-Mini and O1-Preview achieve pass@1 rates of only 0.366 and 0.143, respectively. While tree search techniques have proven effective in domains like mathematics and general coding, their potential in competition-level code generation remains under-explored. In this work, we propose a novel token-level tree search method specifically designed for code generation. Leveraging Qwen2.5-Coder-32B-Instruct, our approach achieves a pass rate of 0.305 on LiveCodeBench-Hard, surpassing the pass@100 performance of GPT4o-0513 (0.245). Furthermore, by integrating Chain-of-Thought (CoT) prompting, we improve our method's performance to 0.351, approaching O1-Mini's pass@1 rate. To ensure reproducibility, we report the average number of generations required per problem by our tree search method on the test set. Our findings underscore the potential of tree search to significantly enhance performance on competition-level code generation tasks. This opens up new possibilities for large-scale synthesis of challenging code problems supervised fine-tuning (SFT) data, advancing competition-level code generation tasks.

While knowledge distillation (transfer) has been attracting attentions from the research community, the recent development in the fields has heightened the need for reproducible studies and highly generalized frameworks to lower barriers to such high-quality, reproducible deep learning research. Several researchers voluntarily published frameworks used in their knowledge distillation studies to help other interested researchers reproduce their original work. Such frameworks, however, are usually neither well generalized nor maintained, thus researchers are still required to write a lot of code to refactor/build on the frameworks for introducing new methods, models, datasets and designing experiments. In this paper, we present our developed open-source framework built on PyTorch and dedicated for knowledge distillation studies. The framework is designed to enable users to design experiments by declarative PyYAML configuration files, and helps researchers complete the recently proposed ML Code Completeness Checklist. Using the developed framework, we demonstrate its various efficient training strategies, and implement a variety of knowledge distillation methods. We also reproduce some of their original experimental results on the ImageNet and COCO datasets presented at major machine learning conferences such as ICLR, NeurIPS, CVPR and ECCV, including recent state-of-the-art methods. All the source code, configurations, log files and trained model weights are publicly available at https://github.com/yoshitomo-matsubara/torchdistill .

Code search is crucial for code reuse, enabling developers to efficiently locate relevant snippets. Current methods rely on encoder-based models, which suffer from limitations such as poor generalization and restricted input lengths. Decoder-only large language models (LLMs), with their extensive pre-training, larger size, and longer input capabilities, offer potential solutions to these issues, yet their effectiveness in code search remains underexplored. To fill this gap, our study presents the first systematic exploration of decoder-only LLMs for code search. We evaluate nine state-of-the-art decoder-only models using two fine-tuning methods, two datasets (CSN and CoSQA^+), and three model sizes. Our findings reveal that fine-tuned CodeGemma significantly outperforms encoder-only models like UniXcoder, achieving a 5.57% improvement in MRR on CSN and a 49.6% increase in MAP on CoSQA^+ compared to zero-shot UniXcoder. These results highlight the superior performance and adaptability of decoder-only models. Additionally, we provide valuable insights into optimizing these models for code search, covering aspects such as model selection, fine-tuning methods, training data, and model size, and discussing their strengths and limitations.

This paper examines the problems of severe image-text misalignment and high redundancy in the widely-used large-scale Vision-Language Pre-Training (VLP) datasets. To address these issues, we propose an efficient and straightforward Vision-Language learning algorithm called TL;DR, which aims to compress the existing large VLP data into a small, high-quality set. Our approach consists of two major steps. First, a codebook-based encoder-decoder captioner is developed to select representative samples. Second, a new caption is generated to complement the original captions for selected samples, mitigating the text-image misalignment problem while maintaining uniqueness. As the result, TL;DR enables us to reduce the large dataset into a small set of high-quality data, which can serve as an alternative pre-training dataset. This algorithm significantly speeds up the time-consuming pretraining process. Specifically, TL;DR can compress the mainstream VLP datasets at a high ratio, e.g., reduce well-cleaned CC3M dataset from 2.82M to 0.67M (sim24\%) and noisy YFCC15M from 15M to 2.5M (sim16.7\%). Extensive experiments with three popular VLP models over seven downstream tasks show that VLP model trained on the compressed dataset provided by TL;DR can perform similar or even better results compared with training on the full-scale dataset. The code will be made available at https://github.com/showlab/datacentric.vlp.

Pre-trained models for Natural Languages (NL) like BERT and GPT have been recently shown to transfer well to Programming Languages (PL) and largely benefit a broad set of code-related tasks. Despite their success, most current methods either rely on an encoder-only (or decoder-only) pre-training that is suboptimal for generation (resp. understanding) tasks or process the code snippet in the same way as NL, neglecting the special characteristics of PL such as token types. We present CodeT5, a unified pre-trained encoder-decoder Transformer model that better leverages the code semantics conveyed from the developer-assigned identifiers. Our model employs a unified framework to seamlessly support both code understanding and generation tasks and allows for multi-task learning. Besides, we propose a novel identifier-aware pre-training task that enables the model to distinguish which code tokens are identifiers and to recover them when they are masked. Furthermore, we propose to exploit the user-written code comments with a bimodal dual generation task for better NL-PL alignment. Comprehensive experiments show that CodeT5 significantly outperforms prior methods on understanding tasks such as code defect detection and clone detection, and generation tasks across various directions including PL-NL, NL-PL, and PL-PL. Further analysis reveals that our model can better capture semantic information from code. Our code and pre-trained models are released at https: //github.com/salesforce/CodeT5 .

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

In multi-source sequence-to-sequence tasks, the attention mechanism can be modeled in several ways. This topic has been thoroughly studied on recurrent architectures. In this paper, we extend the previous work to the encoder-decoder attention in the Transformer architecture. We propose four different input combination strategies for the encoder-decoder attention: serial, parallel, flat, and hierarchical. We evaluate our methods on tasks of multimodal translation and translation with multiple source languages. The experiments show that the models are able to use multiple sources and improve over single source baselines.

Contrastive learning based vision-language joint pre-training has emerged as a successful representation learning strategy. In this paper, we present a prototype representation learning framework incorporating both global and local alignment between medical images and reports. In contrast to standard global multi-modality alignment methods, we employ a local alignment module for fine-grained representation. Furthermore, a cross-modality conditional reconstruction module is designed to interchange information across modalities in the training phase by reconstructing masked images and reports. For reconstructing long reports, a sentence-wise prototype memory bank is constructed, enabling the network to focus on low-level localized visual and high-level clinical linguistic features. Additionally, a non-auto-regressive generation paradigm is proposed for reconstructing non-sequential reports. Experimental results on five downstream tasks, including supervised classification, zero-shot classification, image-to-text retrieval, semantic segmentation, and object detection, show the proposed method outperforms other state-of-the-art methods across multiple datasets and under different dataset size settings. The code is available at https://github.com/QtacierP/PRIOR.

As the size of Large Multi-Modal Models (LMMs) increases consistently, the adaptation of these pre-trained models to specialized tasks has become a computationally and memory-intensive challenge. Traditional fine-tuning methods require isolated, exhaustive retuning for each new task, limiting the models' versatility. Moreover, current efficient adaptation techniques often overlook modality alignment, focusing only on the knowledge extraction of new tasks. To tackle these issues, we introduce Multiway-Adapter, an innovative framework incorporating an 'Alignment Enhancer' to deepen modality alignment, enabling high transferability without tuning pre-trained parameters. Our method adds fewer than 1.25\% of additional parameters to LMMs, exemplified by the BEiT-3 model in our study. This leads to superior zero-shot image-text retrieval performance compared to fully fine-tuned models, while achieving up to a 57\% reduction in fine-tuning time. Our approach offers a resource-efficient and effective adaptation pathway for LMMs, broadening their applicability. The source code is publicly available at: https://github.com/longkukuhi/MultiWay-Adapter.

Recently, there has been a growing interest in leveraging Large Language Models for Verilog code generation. However, the current quality of the generated Verilog code remains suboptimal. This is largely due to the absence of well-defined, well-organized datasets with high-quality samples, as well as a lack of innovative fine-tuning methods and models specifically trained on Verilog. In this paper, we introduce a novel open-source dataset and a corresponding fine-tuning technique, which utilizes a multi-layered structure that we refer to as PyraNet. Our experiments demonstrate that employing the proposed dataset and fine-tuning approach leads to a more accurate fine-tuned model, producing syntactically and functionally correct Verilog code. The evaluation results show improvements by up-to 32.6% in comparison to the CodeLlama-7B baseline model and up-to 16.7% in comparison to the state-of-the-art models using VerilogEval evaluation platform.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Recently, ChatGPT has emerged as a powerful NLP tool that can carry out several tasks. However, the range of languages ChatGPT can handle remains largely a mystery. In this work, we investigate ChatGPT's language identification abilities. For this purpose, we compile Babel-670, a benchmark comprising 670 languages representing 23 language families. Languages in Babel-670 run the gamut between the very high-resource to the very low-resource and are spoken in five continents. We then study ChatGPT's (both GPT-3.5 and GPT-4) ability to (i) identify both language names and language codes (ii) under both zero- and few-shot conditions (iii) with and without provision of label set. When compared to smaller finetuned language identification tools, we find that ChatGPT lags behind. Our empirical analysis shows the reality that ChatGPT still resides in a state of potential enhancement before it can sufficiently serve diverse communities.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Recent years have witnessed a big convergence of language, vision, and multi-modal pretraining. In this work, we present mPLUG-2, a new unified paradigm with modularized design for multi-modal pretraining, which can benefit from modality collaboration while addressing the problem of modality entanglement. In contrast to predominant paradigms of solely relying on sequence-to-sequence generation or encoder-based instance discrimination, mPLUG-2 introduces a multi-module composition network by sharing common universal modules for modality collaboration and disentangling different modality modules to deal with modality entanglement. It is flexible to select different modules for different understanding and generation tasks across all modalities including text, image, and video. Empirical study shows that mPLUG-2 achieves state-of-the-art or competitive results on a broad range of over 30 downstream tasks, spanning multi-modal tasks of image-text and video-text understanding and generation, and uni-modal tasks of text-only, image-only, and video-only understanding. Notably, mPLUG-2 shows new state-of-the-art results of 48.0 top-1 accuracy and 80.3 CIDEr on the challenging MSRVTT video QA and video caption tasks with a far smaller model size and data scale. It also demonstrates strong zero-shot transferability on vision-language and video-language tasks. Code and models will be released in https://github.com/alibaba/AliceMind.

Multimodal Large Language Models (MLLMs) demonstrate robust zero-shot capabilities across diverse vision-language tasks after training on mega-scale datasets. However, dense prediction tasks, such as semantic segmentation and keypoint detection, pose significant challenges for MLLMs when represented solely as text outputs. Simultaneously, current MLLMs utilizing latent embeddings for visual task decoding generally demonstrate limited adaptability to both multi-task learning and multi-granularity scenarios. In this work, we present REF-VLM, an end-to-end framework for unified training of various visual decoding tasks. To address complex visual decoding scenarios, we introduce the Triplet-Based Referring Paradigm (TRP), which explicitly decouples three critical dimensions in visual decoding tasks through a triplet structure: concepts, decoding types, and targets. TRP employs symbolic delimiters to enforce structured representation learning, enhancing the parsability and interpretability of model outputs. Additionally, we construct Visual-Task Instruction Following Dataset (VTInstruct), a large-scale multi-task dataset containing over 100 million multimodal dialogue samples across 25 task types. Beyond text inputs and outputs, VT-Instruct incorporates various visual prompts such as point, box, scribble, and mask, and generates outputs composed of text and visual units like box, keypoint, depth and mask. The combination of different visual prompts and visual units generates a wide variety of task types, expanding the applicability of REF-VLM significantly. Both qualitative and quantitative experiments demonstrate that our REF-VLM outperforms other MLLMs across a variety of standard benchmarks. The code, dataset, and demo available at https://github.com/MacavityT/REF-VLM.

Multi-modal Large Language Models (MLLMs) have recently exhibited impressive general-purpose capabilities by leveraging vision foundation models to encode the core concepts of images into representations. These are then combined with instructions and processed by the language model to generate high-quality responses. Despite significant progress in enhancing the language component, challenges persist in optimally fusing visual encodings within the language model for task-specific adaptability. Recent research has focused on improving this fusion through modality adaptation modules but at the cost of significantly increased model complexity and training data needs. In this paper, we propose EMMA (Efficient Multi-Modal Adaptation), a lightweight cross-modality module designed to efficiently fuse visual and textual encodings, generating instruction-aware visual representations for the language model. Our key contributions include: (1) an efficient early fusion mechanism that integrates vision and language representations with minimal added parameters (less than 0.2% increase in model size), (2) an in-depth interpretability analysis that sheds light on the internal mechanisms of the proposed method; (3) comprehensive experiments that demonstrate notable improvements on both specialized and general benchmarks for MLLMs. Empirical results show that EMMA boosts performance across multiple tasks by up to 9.3% while significantly improving robustness against hallucinations. Our code is available at https://github.com/SaraGhazanfari/EMMA

We present lambeq, the first high-level Python library for Quantum Natural Language Processing (QNLP). The open-source toolkit offers a detailed hierarchy of modules and classes implementing all stages of a pipeline for converting sentences to string diagrams, tensor networks, and quantum circuits ready to be used on a quantum computer. lambeq supports syntactic parsing, rewriting and simplification of string diagrams, ansatz creation and manipulation, as well as a number of compositional models for preparing quantum-friendly representations of sentences, employing various degrees of syntax sensitivity. We present the generic architecture and describe the most important modules in detail, demonstrating the usage with illustrative examples. Further, we test the toolkit in practice by using it to perform a number of experiments on simple NLP tasks, implementing both classical and quantum pipelines.

Zero-shot text-to-speech (TTS) has gained significant attention due to its powerful voice cloning capabilities, requiring only a few seconds of unseen speaker voice prompts. However, all previous work has been developed for cloud-based systems. Taking autoregressive models as an example, although these approaches achieve high-fidelity voice cloning, they fall short in terms of inference speed, model size, and robustness. Therefore, we propose MobileSpeech, which is a fast, lightweight, and robust zero-shot text-to-speech system based on mobile devices for the first time. Specifically: 1) leveraging discrete codec, we design a parallel speech mask decoder module called SMD, which incorporates hierarchical information from the speech codec and weight mechanisms across different codec layers during the generation process. Moreover, to bridge the gap between text and speech, we introduce a high-level probabilistic mask that simulates the progression of information flow from less to more during speech generation. 2) For speaker prompts, we extract fine-grained prompt duration from the prompt speech and incorporate text, prompt speech by cross attention in SMD. We demonstrate the effectiveness of MobileSpeech on multilingual datasets at different levels, achieving state-of-the-art results in terms of generating speed and speech quality. MobileSpeech achieves RTF of 0.09 on a single A100 GPU and we have successfully deployed MobileSpeech on mobile devices. Audio samples are available at https://mobilespeech.github.io/ .

We introduce AnyGPT, an any-to-any multimodal language model that utilizes discrete representations for the unified processing of various modalities, including speech, text, images, and music. AnyGPT can be trained stably without any alterations to the current large language model (LLM) architecture or training paradigms. Instead, it relies exclusively on data-level preprocessing, facilitating the seamless integration of new modalities into LLMs, akin to the incorporation of new languages. We build a multimodal text-centric dataset for multimodal alignment pre-training. Utilizing generative models, we synthesize the first large-scale any-to-any multimodal instruction dataset. It consists of 108k samples of multi-turn conversations that intricately interweave various modalities, thus equipping the model to handle arbitrary combinations of multimodal inputs and outputs. Experimental results demonstrate that AnyGPT is capable of facilitating any-to-any multimodal conversation while achieving performance comparable to specialized models across all modalities, proving that discrete representations can effectively and conveniently unify multiple modalities within a language model. Demos are shown in https://junzhan2000.github.io/AnyGPT.github.io/

A range of recent works addresses the problem of compression of sequence of tokens into a shorter sequence of real-valued vectors to be used as inputs instead of token embeddings or key-value cache. These approaches allow to reduce the amount of compute in existing language models. Despite relying on powerful models as encoders, the maximum attainable lossless compression ratio is typically not higher than x10. This fact is highly intriguing because, in theory, the maximum information capacity of large real-valued vectors is far beyond the presented rates even for 16-bit precision and a modest vector size. In this work, we explore the limits of compression by replacing the encoder with a per-sample optimization procedure. We show that vectors with compression ratios up to x1500 exist, which highlights two orders of magnitude gap between existing and practically attainable solutions. Furthermore, we empirically show that the compression limits are determined not by the length of the input but by the amount of uncertainty to be reduced, namely, the cross-entropy loss on this sequence without any conditioning. The obtained limits highlight the substantial gap between the theoretical capacity of input embeddings and their practical utilization, suggesting significant room for optimization in model design.

Code editing encompasses a variety of pragmatic tasks that developers deal with daily. Despite its relevance and practical usefulness, automatic code editing remains an underexplored area in the evolution of deep learning models, partly due to data scarcity. In this work, we explore the use of large language models (LLMs) to edit code based on user instructions, covering a broad range of implicit tasks such as comment insertion, code optimization, and code refactoring. To facilitate this, we introduce InstructCoder, the first dataset designed to adapt LLMs for general-purpose code editing, containing highdiversity code-editing tasks. It consists of over 114,000 instruction-input-output triplets and covers multiple distinct code editing scenarios. The dataset is systematically expanded through an iterative process that commences with code editing data sourced from GitHub commits as seed tasks. Seed and generated tasks are used subsequently to prompt ChatGPT for more task data. Our experiments demonstrate that open-source LLMs fine-tuned on InstructCoder can edit code correctly based on users' instructions most of the time, exhibiting unprecedented code-editing performance levels. Such results suggest that proficient instruction-finetuning can lead to significant amelioration in code editing abilities. The dataset and the source code are available at https://github.com/qishenghu/CodeInstruct.

We present a direct speech-to-speech translation (S2ST) model that translates speech from one language to speech in another language without relying on intermediate text generation. We tackle the problem by first applying a self-supervised discrete speech encoder on the target speech and then training a sequence-to-sequence speech-to-unit translation (S2UT) model to predict the discrete representations of the target speech. When target text transcripts are available, we design a joint speech and text training framework that enables the model to generate dual modality output (speech and text) simultaneously in the same inference pass. Experiments on the Fisher Spanish-English dataset show that the proposed framework yields improvement of 6.7 BLEU compared with a baseline direct S2ST model that predicts spectrogram features. When trained without any text transcripts, our model performance is comparable to models that predict spectrograms and are trained with text supervision, showing the potential of our system for translation between unwritten languages. Audio samples are available at https://facebookresearch.github.io/speech_translation/direct_s2st_units/index.html .

Language models (LMs) have recently flourished in natural language processing and computer vision, generating high-fidelity texts or images in various tasks. In contrast, the current speech generative models are still struggling regarding speech quality and task generalization. This paper presents Vec-Tok Speech, an extensible framework that resembles multiple speech generation tasks, generating expressive and high-fidelity speech. Specifically, we propose a novel speech codec based on speech vectors and semantic tokens. Speech vectors contain acoustic details contributing to high-fidelity speech reconstruction, while semantic tokens focus on the linguistic content of speech, facilitating language modeling. Based on the proposed speech codec, Vec-Tok Speech leverages an LM to undertake the core of speech generation. Moreover, Byte-Pair Encoding (BPE) is introduced to reduce the token length and bit rate for lower exposure bias and longer context coverage, improving the performance of LMs. Vec-Tok Speech can be used for intra- and cross-lingual zero-shot voice conversion (VC), zero-shot speaking style transfer text-to-speech (TTS), speech-to-speech translation (S2ST), speech denoising, and speaker de-identification and anonymization. Experiments show that Vec-Tok Speech, built on 50k hours of speech, performs better than other SOTA models. Code will be available at https://github.com/BakerBunker/VecTok .

Recent advancements in large language models have facilitated the execution of complex language tasks, not only in English but also in non-English languages. However, the tokenizers of most language models, such as Llama, trained on English-centric corpora, tend to excessively fragment tokens in non-English languages. This issue is especially pronounced in non-roman alphabetic languages, which are often divided at a character or even Unicode level, leading to slower text generation. To address this, our study introduces a novel framework designed to expedite text generation in these languages. This framework predicts larger linguistic units than those of conventional multilingual tokenizers and is specifically tailored to the target language, thereby reducing the number of decoding steps required. Our empirical results demonstrate that the proposed framework increases the generation speed by a factor of 1.9 compared to standard decoding while maintaining the performance of a pre-trained multilingual model on monolingual tasks.

The training of large language models (LLMs) necessitates substantial data and computational resources, and updating outdated LLMs entails significant efforts and resources. While numerous model editing techniques (METs) have emerged to efficiently update model outputs without retraining, their effectiveness in multilingual LLMs, where knowledge is stored in diverse languages, remains an underexplored research area. This research paper introduces the cross-lingual model editing (XME) paradigm, wherein a fact is edited in one language, and the subsequent update propagation is observed across other languages. To investigate the XME paradigm, we conducted experiments using BLOOM, mBERT, and XLM-RoBERTa using the two writing scripts: Latin (English, French, and Spanish) and Indic (Hindi, Gujarati, and Bengali). The results reveal notable performance limitations of state-of-the-art METs under the XME setting, mainly when the languages involved belong to two distinct script families. These findings highlight the need for further research and development of XME techniques to address these challenges. For more comprehensive information, the dataset used in this research and the associated code are publicly available at the following URLhttps://github.com/lingo-iitgn/XME.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Tokenization methods like Byte-Pair Encoding (BPE) enhance computational efficiency in large language models (LLMs) but often obscure internal character structures within tokens. This limitation hinders LLMs' ability to predict precise character positions, which is crucial in tasks like Chinese Spelling Correction (CSC) where identifying the positions of misspelled characters accelerates correction processes. We propose Token Internal Position Awareness (TIPA), a method that significantly improves models' ability to capture character positions within tokens by training them on reverse character prediction tasks using the tokenizer's vocabulary. Experiments demonstrate that TIPA enhances position prediction accuracy in LLMs, enabling more precise identification of target characters in original text. Furthermore, when applied to downstream tasks that do not require exact position prediction, TIPA still boosts performance in tasks needing character-level information, validating its versatility and effectiveness.

Positional Encodings (PEs) are a critical component of Transformer-based Large Language Models (LLMs), providing the attention mechanism with important sequence-position information. One of the most popular types of encoding used today in LLMs are Rotary Positional Encodings (RoPE), that rotate the queries and keys based on their relative distance. A common belief is that RoPE is useful because it helps to decay token dependency as relative distance increases. In this work, we argue that this is unlikely to be the core reason. We study the internals of a trained Gemma 7B model to understand how RoPE is being used at a mechanical level. We find that Gemma learns to use RoPE to construct robust "positional" attention patterns by exploiting the highest frequencies. We also find that, in general, Gemma greatly prefers to use the lowest frequencies of RoPE, which we suspect are used to carry semantic information. We mathematically prove interesting behaviours of RoPE and conduct experiments to verify our findings, proposing a modification of RoPE that fixes some highlighted issues and improves performance. We believe that this work represents an interesting step in better understanding PEs in LLMs, which we believe holds crucial value for scaling LLMs to large sizes and context lengths.

Large language models (LLMs) have shown surprisingly good performance in multilingual neural machine translation (MNMT) even when trained without parallel data. Yet, despite the fact that the amount of training data is gigantic, they still struggle with translating rare words, particularly for low-resource languages. Even worse, it is usually unrealistic to retrieve relevant demonstrations for in-context learning with low-resource languages on LLMs, which restricts the practical use of LLMs for translation -- how should we mitigate this problem? To this end, we present a novel method, CoD, which augments LLMs with prior knowledge with the chains of multilingual dictionaries for a subset of input words to elicit translation abilities for LLMs. Extensive experiments indicate that augmenting ChatGPT with CoD elicits large gains by up to 13x ChrF++ points for MNMT (3.08 to 42.63 for English to Serbian written in Cyrillic script) on FLORES-200 full devtest set. We further demonstrate the importance of chaining the multilingual dictionaries, as well as the superiority of CoD to few-shot demonstration for low-resource languages.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

In this paper, we introduce SCALE, a collaborative framework that connects compact Specialized Translation Models (STMs) and general-purpose Large Language Models (LLMs) as one unified translation engine. By introducing translation from STM into the triplet in-context demonstrations, SCALE unlocks refinement and pivoting ability of LLM, thus mitigating language bias of LLM and parallel data bias of STM, enhancing LLM speciality without sacrificing generality, and facilitating continual learning without expensive LLM fine-tuning. Our comprehensive experiments show that SCALE significantly outperforms both few-shot LLMs (GPT-4) and specialized models (NLLB) in challenging low-resource settings. Moreover, in Xhosa to English translation, SCALE experiences consistent improvement by a 4 BLEURT score without tuning LLM and surpasses few-shot GPT-4 by 2.5 COMET score and 3.8 BLEURT score when equipped with a compact model consisting of merely 600M parameters. SCALE could also effectively exploit the existing language bias of LLMs by using an English-centric STM as a pivot for translation between any language pairs, outperforming few-shot GPT-4 by an average of 6 COMET points across eight translation directions. Furthermore we provide an in-depth analysis of SCALE's robustness, translation characteristics, and latency costs, providing solid foundation for future studies exploring the potential synergy between LLMs and more specialized, task-specific models.

This paper presents NT-Java-1.1B, an open-source specialized code language model built on StarCoderBase-1.1B, designed for coding tasks in Java programming. NT-Java-1.1B achieves state-of-the-art performance, surpassing its base model and majority of other models of similar size on MultiPL-E Java code benchmark. While there have been studies on extending large, generic pre-trained models to improve proficiency in specific programming languages like Python, similar investigations on small code models for other programming languages are lacking. Large code models require specialized hardware like GPUs for inference, highlighting the need for research into building small code models that can be deployed on developer desktops. This paper addresses this research gap by focusing on the development of a small Java code model, NT-Java-1.1B, and its quantized versions, which performs comparably to open models around 1.1B on MultiPL-E Java code benchmarks, making them ideal for desktop deployment. This paper establishes the foundation for specialized models across languages and sizes for a family of NT Models.

In this work, we study how the performance of a given direction changes with its sampling ratio in Multilingual Neural Machine Translation (MNMT). By training over 200 multilingual models with various model sizes, data sizes, and language directions, we find it interesting that the performance of certain translation direction does not always improve with the increase of its weight in the multi-task optimization objective. Accordingly, scalarization method leads to a multitask trade-off front that deviates from the traditional Pareto front when there exists data imbalance in the training corpus, which poses a great challenge to improve the overall performance of all directions. Based on our observations, we propose the Double Power Law to predict the unique performance trade-off front in MNMT, which is robust across various languages, data adequacy, and the number of tasks. Finally, we formulate the sample ratio selection problem in MNMT as an optimization problem based on the Double Power Law. In our experiments, it achieves better performance than temperature searching and gradient manipulation methods with only 1/5 to 1/2 of the total training budget. We release the code at https://github.com/pkunlp-icler/ParetoMNMT for reproduction.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Layout-aware pre-trained models has achieved significant progress on document image question answering. They introduce extra learnable modules into existing language models to capture layout information within document images from text bounding box coordinates obtained by OCR tools. However, extra modules necessitate pre-training on extensive document images. This prevents these methods from directly utilizing off-the-shelf instruction-tuning language foundation models, which have recently shown promising potential in zero-shot learning. Instead, in this paper, we find that instruction-tuning language models like Claude and ChatGPT can understand layout by spaces and line breaks. Based on this observation, we propose the LAyout and Task aware Instruction Prompt (LATIN-Prompt), which consists of layout-aware document content and task-aware instruction. Specifically, the former uses appropriate spaces and line breaks to recover the layout information among text segments obtained by OCR tools, and the latter ensures that generated answers adhere to formatting requirements. Moreover, we propose the LAyout and Task aware Instruction Tuning (LATIN-Tuning) to improve the performance of small instruction-tuning models like Alpaca. Experimental results show that LATIN-Prompt enables zero-shot performance of Claude and ChatGPT to be comparable to the fine-tuning performance of SOTAs on document image question answering, and LATIN-Tuning enhances the zero-shot performance of Alpaca significantly. For example, LATIN-Prompt improves the performance of Claude and ChatGPT on DocVQA by 263% and 20% respectively. LATIN-Tuning improves the performance of Alpaca on DocVQA by 87.7%. Quantitative and qualitative analyses demonstrate the effectiveness of LATIN-Prompt and LATIN-Tuning. We provide the code in supplementary and will release it to facilitate future research.

We propose expanding the shared Transformer module to produce and initialize Transformers of varying depths, enabling adaptation to diverse resource constraints. Drawing an analogy to genetic expansibility, we term such module as learngene. To identify the expansion mechanism, we delve into the relationship between the layer's position and its corresponding weight value, and find that linear function appropriately approximates this relationship. Building on this insight, we present Transformer as Linear Expansion of learnGene (TLEG), a novel approach for flexibly producing and initializing Transformers of diverse depths. Specifically, to learn learngene, we firstly construct an auxiliary Transformer linearly expanded from learngene, after which we train it through employing soft distillation. Subsequently, we can produce and initialize Transformers of varying depths via linearly expanding the well-trained learngene, thereby supporting diverse downstream scenarios. Extensive experiments on ImageNet-1K demonstrate that TLEG achieves comparable or better performance in contrast to many individual models trained from scratch, while reducing around 2x training cost. When transferring to several downstream classification datasets, TLEG surpasses existing initialization methods by a large margin (e.g., +6.87% on iNat 2019 and +7.66% on CIFAR-100). Under the situation where we need to produce models of varying depths adapting for different resource constraints, TLEG achieves comparable results while reducing around 19x parameters stored to initialize these models and around 5x pre-training costs, in contrast to the pre-training and fine-tuning approach. When transferring a fixed set of parameters to initialize different models, TLEG presents better flexibility and competitive performance while reducing around 2.9x parameters stored to initialize, compared to the pre-training approach.

Neural machine translation (NMT) is nowadays commonly applied at the subword level, using byte-pair encoding. A promising alternative approach focuses on character-level translation, which simplifies processing pipelines in NMT considerably. This approach, however, must consider relatively longer sequences, rendering the training process prohibitively expensive. In this paper, we discuss a novel, Transformer-based approach, that we compare, both in speed and in quality to the Transformer at subword and character levels, as well as previously developed character-level models. We evaluate our models on 4 language pairs from WMT'15: DE-EN, CS-EN, FI-EN and RU-EN. The proposed novel architecture can be trained on a single GPU and is 34% percent faster than the character-level Transformer; still, the obtained results are at least on par with it. In addition, our proposed model outperforms the subword-level model in FI-EN and shows close results in CS-EN. To stimulate further research in this area and close the gap with subword-level NMT, we make all our code and models publicly available.

Pre-trained vision-language models~(VLMs) are the de-facto foundation models for various downstream tasks. However, scene text recognition methods still prefer backbones pre-trained on a single modality, namely, the visual modality, despite the potential of VLMs to serve as powerful scene text readers. For example, CLIP can robustly identify regular (horizontal) and irregular (rotated, curved, blurred, or occluded) text in images. With such merits, we transform CLIP into a scene text reader and introduce CLIP4STR, a simple yet effective STR method built upon image and text encoders of CLIP. It has two encoder-decoder branches: a visual branch and a cross-modal branch. The visual branch provides an initial prediction based on the visual feature, and the cross-modal branch refines this prediction by addressing the discrepancy between the visual feature and text semantics. To fully leverage the capabilities of both branches, we design a dual predict-and-refine decoding scheme for inference. We scale CLIP4STR in terms of the model size, pre-training data, and training data, achieving state-of-the-art performance on 11 STR benchmarks. Additionally, a comprehensive empirical study is provided to enhance the understanding of the adaptation of CLIP to STR. We believe our method establishes a simple yet strong baseline for future STR research with VLMs.

The field of vision and language has witnessed a proliferation of pre-trained foundation models. Most existing methods are independently pre-trained with contrastive objective like CLIP, image-to-text generative objective like PaLI, or text-to-image generative objective like Parti. However, the three objectives can be pre-trained on the same data, image-text pairs, and intuitively they complement each other as contrasting provides global alignment capacity and generation grants fine-grained understanding. In this work, we present a Contrastive Bi-directional Image-Text generation model (CoBIT), which attempts to unify the three pre-training objectives in one framework. Specifically, CoBIT employs a novel unicoder-decoder structure, consisting of an image unicoder, a text unicoder and a cross-modal decoder. The image/text unicoders can switch between encoding and decoding in different tasks, enabling flexibility and shared knowledge that benefits both image-to-text and text-to-image generations. CoBIT achieves superior performance in image understanding, image-text understanding (Retrieval, Captioning, VQA, SNLI-VE) and text-based content creation, particularly in zero-shot scenarios. For instance, 82.7% in zero-shot ImageNet classification, 9.37 FID score in zero-shot text-to-image generation and 44.8 CIDEr in zero-shot captioning.

We describe GEMBA, a GPT-based metric for assessment of translation quality, which works both with a reference translation and without. In our evaluation, we focus on zero-shot prompting, comparing four prompt variants in two modes, based on the availability of the reference. We investigate nine versions of GPT models, including ChatGPT and GPT-4. We show that our method for translation quality assessment only works with GPT~3.5 and larger models. Comparing to results from WMT22's Metrics shared task, our method achieves state-of-the-art accuracy in both modes when compared to MQM-based human labels. Our results are valid on the system level for all three WMT22 Metrics shared task language pairs, namely English into German, English into Russian, and Chinese into English. This provides a first glimpse into the usefulness of pre-trained, generative large language models for quality assessment of translations. We publicly release all our code and prompt templates used for the experiments described in this work, as well as all corresponding scoring results, to allow for external validation and reproducibility.

Vector Symbolic Architectures (VSAs) give a way to represent a complex object as a single fixed-length vector, so that similar objects have similar vector representations. These vector representations then become easy to use for machine learning or nearest-neighbor search. We review a previously proposed VSA method, MBAT (Matrix Binding of Additive Terms), which uses multiplication by random matrices for binding related terms. However, multiplying by such matrices introduces instabilities which can harm performance. Making the random matrices be orthogonal matrices provably fixes this problem. With respect to larger scale applications, we see how to apply MBAT vector representations for any data expressed in JSON. JSON is used in numerous programming languages to express complex data, but its native format appears highly unsuited for machine learning. Expressing JSON as a fixed-length vector makes it readily usable for machine learning and nearest-neighbor search. Creating such JSON vectors also shows that a VSA needs to employ binding operations that are non-commutative. VSAs are now ready to try with full-scale practical applications, including healthcare, pharmaceuticals, and genomics. Keywords: MBAT (Matrix Binding of Additive Terms), VSA (Vector Symbolic Architecture), HDC (Hyperdimensional Computing), Distributed Representations, Binding, Orthogonal Matrices, Recurrent Connections, Machine Learning, Search, JSON, VSA Applications

Parameter-efficient fine-tuning (PEFT) methods seek to adapt large models via updates to a small number of weights. However, much prior interpretability work has shown that representations encode rich semantic information, suggesting that editing representations might be a more powerful alternative. Here, we pursue this hypothesis by developing a family of Representation Finetuning (ReFT) methods. ReFT methods operate on a frozen base model and learn task-specific interventions on hidden representations. We define a strong instance of the ReFT family, Low-rank Linear Subspace ReFT (LoReFT). LoReFT is a drop-in replacement for existing PEFTs and learns interventions that are 10x-50x more parameter-efficient than prior state-of-the-art PEFTs. We showcase LoReFT on eight commonsense reasoning tasks, four arithmetic reasoning tasks, Alpaca-Eval v1.0, and GLUE. In all these evaluations, LoReFT delivers the best balance of efficiency and performance, and almost always outperforms state-of-the-art PEFTs. We release a generic ReFT training library publicly at https://github.com/stanfordnlp/pyreft.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

We study lossless acceleration for seq2seq generation with a novel decoding algorithm -- Aggressive Decoding. Unlike the previous efforts (e.g., non-autoregressive decoding) speeding up seq2seq generation at the cost of quality loss, our approach aims to yield the identical (or better) generation compared with autoregressive decoding but in a significant speedup, achieved by innovative cooperation of aggressive decoding and verification that are both efficient due to parallel computing. We propose two Aggressive Decoding paradigms for 2 kinds of seq2seq tasks: 1) For the seq2seq tasks whose inputs and outputs are highly similar (e.g., Grammatical Error Correction), we propose Input-guided Aggressive Decoding (IAD) that aggressively copies from the input sentence as drafted decoded tokens to verify in parallel; 2) For other general seq2seq tasks (e.g., Machine Translation), we propose Generalized Aggressive Decoding (GAD) that first employs an additional non-autoregressive decoding model for aggressive decoding and then verifies in parallel in the autoregressive manner. We test Aggressive Decoding on the most popular 6-layer Transformer model on GPU in multiple seq2seq tasks: 1) For IAD, we show that it can introduce a 7x-9x speedup for the Transformer in Grammatical Error Correction and Text Simplification tasks with the identical results as greedy decoding; 2) For GAD, we observe a 3x-5x speedup with the identical or even better quality in two important seq2seq tasks: Machine Translation and Abstractive Summarization. Moreover, Aggressive Decoding can benefit even more from stronger computing devices that are better at parallel computing. Given the lossless quality as well as significant and promising speedup, we believe Aggressive Decoding may potentially evolve into a de facto standard for efficient and lossless seq2seq generation in the near future.

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

The cascade of 2D geometric transformations were exploited to model relations between entities in a knowledge graph (KG), leading to an effective KG embedding (KGE) model, CompoundE. Furthermore, the rotation in the 3D space was proposed as a new KGE model, Rotate3D, by leveraging its non-commutative property. Inspired by CompoundE and Rotate3D, we leverage 3D compound geometric transformations, including translation, rotation, scaling, reflection, and shear and propose a family of KGE models, named CompoundE3D, in this work. CompoundE3D allows multiple design variants to match rich underlying characteristics of a KG. Since each variant has its own advantages on a subset of relations, an ensemble of multiple variants can yield superior performance. The effectiveness and flexibility of CompoundE3D are experimentally verified on four popular link prediction datasets.

Proof-oriented programs mix computational content with proofs of program correctness. However, the human effort involved in programming and proving is still substantial, despite the use of Satisfiability Modulo Theories (SMT) solvers to automate proofs in languages such as F*. Seeking to spur research on using AI to automate the construction of proof-oriented programs, we curate a dataset of 600K lines of open-source F* programs and proofs, including software used in production systems ranging from Windows and Linux, to Python and Firefox. Our dataset includes around 32K top-level F* definitions, each representing a type-directed program and proof synthesis problem -- producing a definition given a formal specification expressed as an F* type. We provide a program-fragment checker that queries F* to check the correctness of candidate solutions. We believe this is the largest corpus of SMT-assisted program proofs coupled with a reproducible program-fragment checker. Grounded in this dataset, we investigate the use of AI to synthesize programs and their proofs in F*, with promising results. Our main finding in that the performance of fine-tuned smaller language models (such as Phi-2 or StarCoder) compare favorably with large language models (such as GPT-4), at a much lower computational cost. We also identify various type-based retrieval augmentation techniques and find that they boost performance significantly. With detailed error analysis and case studies, we identify potential strengths and weaknesses of models and techniques and suggest directions for future improvements.

In this report, we present DNA 1.0 8B Instruct, a state-of-the-art bilingual language model optimized for Korean and English language tasks. By applying continual pre-training (CPT) with high-quality Korean datasets to Llama 3.1 8B and subsequent supervised fine-tuning (SFT), we create an instruction-following model with enhanced Korean language capabilities. This model is then merged with Llama 3.1 8B Instruct via spherical linear interpolation (SLERP) and undergoes further optimization through direct preference optimization (DPO) and knowledge distillation (KD). DNA 1.0 8B Instruct achieves state-of-the-art results on Korean-specific tasks, including KMMLU (53.26%), KoBEST (83.40%), and BELEBELE (57.99%), while maintaining strong English capabilities on MMLU (66.64%), MMLU-Pro (43.05%) and GSM8K (80.52%). As an open model, DNA 1.0 8B Instruct represents a significant advancement in bilingual language modeling. As an open model, DNA 1.0 8B Instruct is freely available through https://huggingface.co/dnotitia/Llama-DNA-1.0-8B-Instruct . For commercial licensing inquiries or feedback, please contact us at https://www.dnotitia.com/contact/post-form

Recent advancements in audio generation have been significantly propelled by the capabilities of Large Language Models (LLMs). The existing research on audio LLM has primarily focused on enhancing the architecture and scale of audio language models, as well as leveraging larger datasets, and generally, acoustic codecs, such as EnCodec, are used for audio tokenization. However, these codecs were originally designed for audio compression, which may lead to suboptimal performance in the context of audio LLM. Our research aims to address the shortcomings of current audio LLM codecs, particularly their challenges in maintaining semantic integrity in generated audio. For instance, existing methods like VALL-E, which condition acoustic token generation on text transcriptions, often suffer from content inaccuracies and elevated word error rates (WER) due to semantic misinterpretations of acoustic tokens, resulting in word skipping and errors. To overcome these issues, we propose a straightforward yet effective approach called X-Codec. X-Codec incorporates semantic features from a pre-trained semantic encoder before the Residual Vector Quantization (RVQ) stage and introduces a semantic reconstruction loss after RVQ. By enhancing the semantic ability of the codec, X-Codec significantly reduces WER in speech synthesis tasks and extends these benefits to non-speech applications, including music and sound generation. Our experiments in text-to-speech, music continuation, and text-to-sound tasks demonstrate that integrating semantic information substantially improves the overall performance of language models in audio generation. Our code and demo are available (Demo: https://x-codec-audio.github.io Code: https://github.com/zhenye234/xcodec)

Length generalization, the ability to generalize from small training context sizes to larger ones, is a critical challenge in the development of Transformer-based language models. Positional encoding (PE) has been identified as a major factor influencing length generalization, but the exact impact of different PE schemes on extrapolation in downstream tasks remains unclear. In this paper, we conduct a systematic empirical study comparing the length generalization performance of decoder-only Transformers with five different position encoding approaches including Absolute Position Embedding (APE), T5's Relative PE, ALiBi, and Rotary, in addition to Transformers without positional encoding (NoPE). Our evaluation encompasses a battery of reasoning and mathematical tasks. Our findings reveal that the most commonly used positional encoding methods, such as ALiBi, Rotary, and APE, are not well suited for length generalization in downstream tasks. More importantly, NoPE outperforms other explicit positional encoding methods while requiring no additional computation. We theoretically demonstrate that NoPE can represent both absolute and relative PEs, but when trained with SGD, it mostly resembles T5's relative PE attention patterns. Finally, we find that scratchpad is not always helpful to solve length generalization and its format highly impacts the model's performance. Overall, our work suggests that explicit position embeddings are not essential for decoder-only Transformers to generalize well to longer sequences.

We present two end-to-end models: Audio-to-Byte (A2B) and Byte-to-Audio (B2A), for multilingual speech recognition and synthesis. Prior work has predominantly used characters, sub-words or words as the unit of choice to model text. These units are difficult to scale to languages with large vocabularies, particularly in the case of multilingual processing. In this work, we model text via a sequence of Unicode bytes, specifically, the UTF-8 variable length byte sequence for each character. Bytes allow us to avoid large softmaxes in languages with large vocabularies, and share representations in multilingual models. We show that bytes are superior to grapheme characters over a wide variety of languages in monolingual end-to-end speech recognition. Additionally, our multilingual byte model outperform each respective single language baseline on average by 4.4% relatively. In Japanese-English code-switching speech, our multilingual byte model outperform our monolingual baseline by 38.6% relatively. Finally, we present an end-to-end multilingual speech synthesis model using byte representations which matches the performance of our monolingual baselines.

This paper presents the outcomes of fine-tuning Mistral 7B, a general-purpose large language model (LLM), for adaptive machine translation (MT). The fine-tuning process involves utilising a combination of zero-shot and one-shot translation prompts within the medical domain. The primary objective is to enhance real-time adaptive MT capabilities of Mistral 7B, enabling it to adapt translations to the required domain at inference time. The results, particularly for Spanish-to-English MT, showcase the efficacy of the fine-tuned model, demonstrating quality improvements in both zero-shot and one-shot translation scenarios, surpassing Mistral 7B's baseline performance. Notably, the fine-tuned Mistral outperforms ChatGPT "gpt-3.5-turbo" in zero-shot translation while achieving comparable one-shot translation quality. Moreover, the zero-shot translation of the fine-tuned Mistral matches NLLB 3.3B's performance, and its one-shot translation quality surpasses that of NLLB 3.3B. These findings emphasise the significance of fine-tuning efficient LLMs like Mistral 7B to yield high-quality zero-shot translations comparable to task-oriented models like NLLB 3.3B. Additionally, the adaptive gains achieved in one-shot translation are comparable to those of commercial LLMs such as ChatGPT. Our experiments demonstrate that, with a relatively small dataset of 20,000 segments that incorporate a mix of zero-shot and one-shot prompts, fine-tuning significantly enhances Mistral's in-context learning ability, especially for real-time adaptive MT.

Deploying NMT models on mobile devices is essential for privacy, low latency, and offline scenarios. For high model capacity, NMT models are rather large. Running these models on devices is challenging with limited storage, memory, computation, and power consumption. Existing work either only focuses on a single metric such as FLOPs or general engine which is not good at auto-regressive decoding. In this paper, we present MobileNMT, a system that can translate in 15MB and 30ms on devices. We propose a series of principles for model compression when combined with quantization. Further, we implement an engine that is friendly to INT8 and decoding. With the co-design of model and engine, compared with the existing system, we speed up 47.0x and save 99.5% of memory with only 11.6% loss of BLEU. The code is publicly available at https://github.com/zjersey/Lightseq-ARM.

A naive application of state-of-the-art bidirectional encoders for streaming sequence tagging would require encoding each token from scratch for each new token in an incremental streaming input (like transcribed speech). The lack of re-usability of previous computation leads to a higher number of Floating Point Operations (or FLOPs) and higher number of unnecessary label flips. Increased FLOPs consequently lead to higher wall-clock time and increased label flipping leads to poorer streaming performance. In this work, we present a Hybrid Encoder with Adaptive Restart (HEAR) that addresses these issues while maintaining the performance of bidirectional encoders over the offline (or complete) inputs while improving performance on streaming (or incomplete) inputs. HEAR has a Hybrid unidirectional-bidirectional encoder architecture to perform sequence tagging, along with an Adaptive Restart Module (ARM) to selectively guide the restart of bidirectional portion of the encoder. Across four sequence tagging tasks, HEAR offers FLOP savings in streaming settings upto 71.1% and also outperforms bidirectional encoders for streaming predictions by upto +10% streaming exact match.

As the text-to-image (T2I) domain progresses, generating text that seamlessly integrates with visual content has garnered significant attention. However, even with accurate text generation, the inability to control font and color can greatly limit certain applications, and this issue remains insufficiently addressed. This paper introduces AnyText2, a novel method that enables precise control over multilingual text attributes in natural scene image generation and editing. Our approach consists of two main components. First, we propose a WriteNet+AttnX architecture that injects text rendering capabilities into a pre-trained T2I model. Compared to its predecessor, AnyText, our new approach not only enhances image realism but also achieves a 19.8% increase in inference speed. Second, we explore techniques for extracting fonts and colors from scene images and develop a Text Embedding Module that encodes these text attributes separately as conditions. As an extension of AnyText, this method allows for customization of attributes for each line of text, leading to improvements of 3.3% and 9.3% in text accuracy for Chinese and English, respectively. Through comprehensive experiments, we demonstrate the state-of-the-art performance of our method. The code and model will be made open-source in https://github.com/tyxsspa/AnyText2.

General-purpose multilingual vector representations, used in retrieval, regression and classification, are traditionally obtained from bidirectional encoder models. Despite their wide applicability, encoders have been recently overshadowed by advances in generative decoder-only models. However, many innovations driving this progress are not inherently tied to decoders. In this paper, we revisit the development of multilingual encoders through the lens of these advances, and introduce EuroBERT, a family of multilingual encoders covering European and widely spoken global languages. Our models outperform existing alternatives across a diverse range of tasks, spanning multilingual capabilities, mathematics, and coding, and natively supporting sequences of up to 8,192 tokens. We also examine the design decisions behind EuroBERT, offering insights into our dataset composition and training pipeline. We publicly release the EuroBERT models, including intermediate training checkpoints, together with our training framework.

When describing an image, reading text in the visual scene is crucial to understand the key information. Recent work explores the TextCaps task, i.e. image captioning with reading Optical Character Recognition (OCR) tokens, which requires models to read text and cover them in generated captions. Existing approaches fail to generate accurate descriptions because of their (1) poor reading ability; (2) inability to choose the crucial words among all extracted OCR tokens; (3) repetition of words in predicted captions. To this end, we propose a Confidence-aware Non-repetitive Multimodal Transformers (CNMT) to tackle the above challenges. Our CNMT consists of a reading, a reasoning and a generation modules, in which Reading Module employs better OCR systems to enhance text reading ability and a confidence embedding to select the most noteworthy tokens. To address the issue of word redundancy in captions, our Generation Module includes a repetition mask to avoid predicting repeated word in captions. Our model outperforms state-of-the-art models on TextCaps dataset, improving from 81.0 to 93.0 in CIDEr. Our source code is publicly available.