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Mar 14

Pop Quiz! Do Pre-trained Code Models Possess Knowledge of Correct API Names?

Recent breakthroughs in pre-trained code models, such as CodeBERT and Codex, have shown their superior performance in various downstream tasks. The correctness and unambiguity of API usage among these code models are crucial for achieving desirable program functionalities, requiring them to learn various API fully qualified names structurally and semantically. Recent studies reveal that even state-of-the-art pre-trained code models struggle with suggesting the correct APIs during code generation. However, the reasons for such poor API usage performance are barely investigated. To address this challenge, we propose using knowledge probing as a means of interpreting code models, which uses cloze-style tests to measure the knowledge stored in models. Our comprehensive study examines a code model's capability of understanding API fully qualified names from two different perspectives: API call and API import. Specifically, we reveal that current code models struggle with understanding API names, with pre-training strategies significantly affecting the quality of API name learning. We demonstrate that natural language context can assist code models in locating Python API names and generalize Python API name knowledge to unseen data. Our findings provide insights into the limitations and capabilities of current pre-trained code models, and suggest that incorporating API structure into the pre-training process can improve automated API usage and code representations. This work provides significance for advancing code intelligence practices and direction for future studies. All experiment results, data and source code used in this work are available at https://doi.org/10.5281/zenodo.7902072.

APIGen: Generative API Method Recommendation

Automatic API method recommendation is an essential task of code intelligence, which aims to suggest suitable APIs for programming queries. Existing approaches can be categorized into two primary groups: retrieval-based and learning-based approaches. Although these approaches have achieved remarkable success, they still come with notable limitations. The retrieval-based approaches rely on the text representation capabilities of embedding models, while the learning-based approaches require extensive task-specific labeled data for training. To mitigate the limitations, we propose APIGen, a generative API recommendation approach through enhanced in-context learning (ICL). APIGen involves two main components: (1) Diverse Examples Selection. APIGen searches for similar posts to the programming queries from the lexical, syntactical, and semantic perspectives, providing more informative examples for ICL. (2) Guided API Recommendation. APIGen enables large language models (LLMs) to perform reasoning before generating API recommendations, where the reasoning involves fine-grained matching between the task intent behind the queries and the factual knowledge of the APIs. With the reasoning process, APIGen makes recommended APIs better meet the programming requirement of queries and also enhances the interpretability of results. We compare APIGen with four existing approaches on two publicly available benchmarks. Experiments show that APIGen outperforms the best baseline CLEAR by 105.8% in method-level API recommendation and 54.3% in class-level API recommendation in terms of SuccessRate@1. Besides, APIGen achieves an average 49.87% increase compared to the zero-shot performance of popular LLMs such as GPT-4 in method-level API recommendation regarding the SuccessRate@3 metric.

ToolCoder: Teach Code Generation Models to use API search tools

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs

Despite the advancements of open-source large language models (LLMs) and their variants, e.g., LLaMA and Vicuna, they remain significantly limited in performing higher-level tasks, such as following human instructions to use external tools (APIs). This is because current instruction tuning largely focuses on basic language tasks instead of the tool-use domain. This is in contrast to state-of-the-art (SOTA) LLMs, e.g., ChatGPT, which have demonstrated excellent tool-use capabilities but are unfortunately closed source. To facilitate tool-use capabilities within open-source LLMs, we introduce ToolLLM, a general tool-use framework of data construction, model training and evaluation. We first present ToolBench, an instruction-tuning dataset for tool use, which is created automatically using ChatGPT. Specifically, we collect 16,464 real-world RESTful APIs spanning 49 categories from RapidAPI Hub, then prompt ChatGPT to generate diverse human instructions involving these APIs, covering both single-tool and multi-tool scenarios. Finally, we use ChatGPT to search for a valid solution path (chain of API calls) for each instruction. To make the searching process more efficient, we develop a novel depth-first search-based decision tree (DFSDT), enabling LLMs to evaluate multiple reasoning traces and expand the search space. We show that DFSDT significantly enhances the planning and reasoning capabilities of LLMs. For efficient tool-use assessment, we develop an automatic evaluator: ToolEval. We fine-tune LLaMA on ToolBench and obtain ToolLLaMA. Our ToolEval reveals that ToolLLaMA demonstrates a remarkable ability to execute complex instructions and generalize to unseen APIs, and exhibits comparable performance to ChatGPT. To make the pipeline more practical, we devise a neural API retriever to recommend appropriate APIs for each instruction, negating the need for manual API selection.

Contextual API Completion for Unseen Repositories Using LLMs

Large language models have made substantial progress in addressing diverse code-related tasks. However, their adoption is hindered by inconsistencies in generating output due to the lack of real-world, domain-specific information, such as for intra-repository API calls for unseen software projects. We introduce a novel technique to mitigate hallucinations by leveraging global and local contextual information within a code repository for API completion tasks. Our approach is tailored to refine code completion tasks, with a focus on optimizing local API completions. We examine relevant import statements during API completion to derive insights into local APIs, drawing from their method signatures. For API token completion, we analyze the inline variables and correlate them with the appropriate imported modules, thereby allowing our approach to rank the most contextually relevant suggestions from the available local APIs. Further, for conversational API completion, we gather APIs that are most relevant to the developer query with a retrieval-based search across the project. We employ our tool, LANCE, within the framework of our proposed benchmark, APIEval, encompassing two different programming languages. Our evaluation yields an average accuracy of 82.6% for API token completion and 76.9% for conversational API completion tasks. On average, LANCE surpasses Copilot by 143% and 142% for API token completion and conversational API completion, respectively. The implications of our findings are substantial for developers, suggesting that our lightweight context analysis can be applied to multilingual environments without language-specific training or fine-tuning, allowing for efficient implementation with minimal examples and effort.

Private-Library-Oriented Code Generation with Large Language Models

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.

API2Com: On the Improvement of Automatically Generated Code Comments Using API Documentations

Code comments can help in program comprehension and are considered as important artifacts to help developers in software maintenance. However, the comments are mostly missing or are outdated, specially in complex software projects. As a result, several automatic comment generation models are developed as a solution. The recent models explore the integration of external knowledge resources such as Unified Modeling Language class diagrams to improve the generated comments. In this paper, we propose API2Com, a model that leverages the Application Programming Interface Documentations (API Docs) as a knowledge resource for comment generation. The API Docs include the description of the methods in more details and therefore, can provide better context in the generated comments. The API Docs are used along with the code snippets and Abstract Syntax Trees in our model. We apply the model on a large Java dataset of over 130,000 methods and evaluate it using both Transformer and RNN-base architectures. Interestingly, when API Docs are used, the performance increase is negligible. We therefore run different experiments to reason about the results. For methods that only contain one API, adding API Docs improves the results by 4% BLEU score on average (BLEU score is an automatic evaluation metric used in machine translation). However, as the number of APIs that are used in a method increases, the performance of the model in generating comments decreases due to long documentations used in the input. Our results confirm that the API Docs can be useful in generating better comments, but, new techniques are required to identify the most informative ones in a method rather than using all documentations simultaneously.

GraphCodeBERT: Pre-training Code Representations with Data Flow

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

PAC Prediction Sets for Large Language Models of Code

Prediction sets have recently been shown to be a promising strategy for quantifying the uncertainty of deep neural networks in a way that provides theoretical guarantees. However, existing techniques have largely targeted settings where the space of labels is simple, so prediction sets can be arbitrary subsets of labels. For structured prediction problems where the space of labels is exponential in size, even prediction sets containing a small fraction of all labels can be exponentially large. In the context of code generation, we propose a solution that considers a restricted set of prediction sets that can compactly be represented as partial programs, which are programs with portions replaced with holes. Given a trained code generation model, our algorithm leverages a programming language's abstract syntax tree to generate a set of programs such that the correct program is in the set with high-confidence. Valuable applications of our algorithm include a Codex-style code generator with holes in uncertain parts of the generated code, which provides a partial program with theoretical guarantees. We evaluate our approach on PICARD (a T5 model for SQL semantic parsing) and Codex (a GPT model for over a dozen programming languages, including Python), demonstrating that our approach generates compact PAC prediction sets. This is the first research contribution that generates PAC prediction sets for generative code models.

EpiCoder: Encompassing Diversity and Complexity in Code Generation

Effective instruction tuning is indispensable for optimizing code LLMs, aligning model behavior with user expectations and enhancing model performance in real-world applications. However, most existing methods focus on code snippets, which are limited to specific functionalities and rigid structures, restricting the complexity and diversity of the synthesized data. To address these limitations, we introduce a novel feature tree-based synthesis framework inspired by Abstract Syntax Trees (AST). Unlike AST, which captures syntactic structure of code, our framework models semantic relationships between code elements, enabling the generation of more nuanced and diverse data. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features. This process enables the identification of more complex patterns and relationships within the code. By sampling subtrees with controlled depth and breadth, our framework allows precise adjustments to the complexity of the generated code, supporting a wide range of tasks from simple function-level operations to intricate multi-file scenarios. We fine-tuned widely-used base models to create the EpiCoder series, achieving state-of-the-art performance at both the function and file levels across multiple benchmarks. Notably, empirical evidence indicates that our approach shows significant potential in synthesizing highly complex repository-level code data. Further analysis elucidates the merits of this approach by rigorously assessing data complexity and diversity through software engineering principles and LLM-as-a-judge method.

DeepArchitect: Automatically Designing and Training Deep Architectures

In deep learning, performance is strongly affected by the choice of architecture and hyperparameters. While there has been extensive work on automatic hyperparameter optimization for simple spaces, complex spaces such as the space of deep architectures remain largely unexplored. As a result, the choice of architecture is done manually by the human expert through a slow trial and error process guided mainly by intuition. In this paper we describe a framework for automatically designing and training deep models. We propose an extensible and modular language that allows the human expert to compactly represent complex search spaces over architectures and their hyperparameters. The resulting search spaces are tree-structured and therefore easy to traverse. Models can be automatically compiled to computational graphs once values for all hyperparameters have been chosen. We can leverage the structure of the search space to introduce different model search algorithms, such as random search, Monte Carlo tree search (MCTS), and sequential model-based optimization (SMBO). We present experiments comparing the different algorithms on CIFAR-10 and show that MCTS and SMBO outperform random search. In addition, these experiments show that our framework can be used effectively for model discovery, as it is possible to describe expressive search spaces and discover competitive models without much effort from the human expert. Code for our framework and experiments has been made publicly available.

CRAFT: Customizing LLMs by Creating and Retrieving from Specialized Toolsets

Large language models (LLMs) are often augmented with tools to solve complex tasks. By generating code snippets and executing them through task-specific Application Programming Interfaces (APIs), they can offload certain functions to dedicated external modules, such as image encoding and performing calculations. However, most existing approaches to augment LLMs with tools are constrained by general-purpose APIs and lack the flexibility for tailoring them to specific tasks. In this work, we present CRAFT, a general tool creation and retrieval framework for LLMs. It creates toolsets specifically curated for the tasks and equips LLMs with a component that retrieves tools from these sets to enhance their capability to solve complex tasks. For each task, we collect specific code solutions by prompting GPT-4 to solve the training examples. Following a validation step ensuring the correctness, these solutions are abstracted into code snippets to enhance reusability, and deduplicated for higher quality. At inference time, the language model retrieves snippets from the toolsets and then executes them or generates the output conditioning on the retrieved snippets. Our method is designed to be flexible and offers a plug-and-play approach to adapt off-the-shelf LLMs to unseen domains and modalities, without any finetuning. Experiments on vision-language, tabular processing, and mathematical reasoning tasks show that our approach achieves substantial improvements compared to strong baselines. In addition, our in-depth analysis reveals that: (1) consistent performance improvement can be achieved by scaling up the number of tools and the capability of the backbone models; (2) each component of our approach contributes to the performance gains; (3) the created tools are well-structured and reliable with low complexity and atomicity. The code is available at https://github.com/lifan-yuan/CRAFT.

Automatically Extracting Web API Specifications from HTML Documentation

Web API specifications are machine-readable descriptions of APIs. These specifications, in combination with related tooling, simplify and support the consumption of APIs. However, despite the increased distribution of web APIs, specifications are rare and their creation and maintenance heavily relies on manual efforts by third parties. In this paper, we propose an automatic approach and an associated tool called D2Spec for extracting specifications from web API documentation pages. Given a seed online documentation page on an API, D2Spec first crawls all documentation pages on the API, and then uses a set of machine learning techniques to extract the base URL, path templates, and HTTP methods, which collectively describe the endpoints of an API. We evaluated whether D2Spec can accurately extract endpoints from documentation on 120 web APIs. The results showed that D2Spec achieved a precision of 87.5% in identifying base URLs, a precision of 81.3% and a recall of 80.6% in generating path templates, and a precision of 84.4% and a recall of 76.2% in extracting HTTP methods. In addition, we found that D2Spec was useful when applied to APIs with pre-existing API specifications: D2Spec revealed many inconsistencies between web API documentation and their corresponding publicly available specifications. Thus, D2Spec can be used by web API providers to keep documentation and specifications in synchronization.

Learning to Represent Programs with Heterogeneous Graphs

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Code Structure-Aware through Line-level Semantic Learning for Code Vulnerability Detection

Different from the flow semantics of natural languages, programming languages are inherently rigid in structure and grammar. Existing fine-tuning methodologies for code vulnerability detection generally treat code as long text sequences, stripping away structural elements such as newlines ('/n') and whitespace. However, this approach inadvertently results in the loss of crucial structural information, diminishing the distinct characteristics of code and impairing the accuracy of vulnerability detection. To address these challenges, we propose a novel network architecture method based on pre-trained code models, which incorporates structural information awareness. We propose an enhanced code text processing workflow that retains structural elements prior to modeling. This refinement allows the model to retain and exploit line-level structural information and semantic information during the modeling process. Furthermore, we introduce a new network architecture, the Code Structure-Aware Network through Line-level Semantic Learning (CSLS), which integrates three key components: global vulnerability awareness, line-structural awareness, and sensitive-line awareness. We have conducted comprehensive experiments using vulnerability detection datasets from real-world projects. Extensive experiments were conducted on vulnerability detection datasets derived from real-world projects. The results demonstrate that our new code pre-processing flow significantly improves existing baselines (e.g., a 3\% accuracy improvement on the Devign dataset when applied to popular models such as CoderBert and UniXcoder). The proposed network architecture also demonstrates superior accuracy in detecting vulnerabilities, surpassing newly established benchmarks. These findings underscore the importance of structural information in enhancing the efficacy of code vulnerability detection models.

Evaluating the Impact of Source Code Parsers on ML4SE Models

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

How Well Do LLMs Generate Code for Different Application Domains? Benchmark and Evaluation

Recently, an increasing number of AI-driven programming assistants powered by code LLMs have been integrated into various real-world software development environments, significantly boosting developer productivity. However, existing code generation benchmarks primarily focus on general-purpose scenarios, leaving the code generation performance of LLMs for specific application domains largely unknown. In this paper, we introduce a new benchmark, MultiCodeBench, to fill this gap. MultiCodeBench comprises 2,400 programming tasks, covering 12 popular software development domains and 15 programming languages. Specifically, we perform in-depth research to identify these 12 application domains. Given that each domain may involve multiple technical frameworks, and that different frameworks present distinct challenges in the coding process, we categorize the commonly used frameworks and platforms within each domain. We then sample programming problems from GitHub repositories related to these subdomains. To ensure the quality of the tasks and mitigate data leakage issues, we invite annotators to rewrite the docstrings for each task in MultiCodeBench. Additionally, we build a static analysis-based dependency parsing tool to extract the dependencies in the ground truth for each task, enabling deeper performance analysis. Through extensive experiments on MultiCodeBench with eleven representative mainstream LLMs, we reveal the code generation performance of the LLMs across different application domains, providing practical insights for developers in downstream fields when selecting LLMs. Furthermore, we analyze the reasons behind the models' failures in completing software application development tasks, offering guidance for model developers to enhance domain-specific code generation capabilities.

PYInfer: Deep Learning Semantic Type Inference for Python Variables

Python type inference is challenging in practice. Due to its dynamic properties and extensive dependencies on third-party libraries without type annotations, the performance of traditional static analysis techniques is limited. Although semantics in source code can help manifest intended usage for variables (thus help infer types), they are usually ignored by existing tools. In this paper, we propose PYInfer, an end-to-end learning-based type inference tool that automatically generates type annotations for Python variables. The key insight is that contextual code semantics is critical in inferring the type for a variable. For each use of a variable, we collect a few tokens within its contextual scope, and design a neural network to predict its type. One challenge is that it is difficult to collect a high-quality human-labeled training dataset for this purpose. To address this issue, we apply an existing static analyzer to generate the ground truth for variables in source code. Our main contribution is a novel approach to statically infer variable types effectively and efficiently. Formulating the type inference as a classification problem, we can handle user-defined types and predict type probabilities for each variable. Our model achieves 91.2% accuracy on classifying 11 basic types in Python and 81.2% accuracy on classifying 500 most common types. Our results substantially outperform the state-of-the-art type annotators. Moreover, PYInfer achieves 5.2X more code coverage and is 187X faster than a state-of-the-art learning-based tool. With similar time consumption, our model annotates 5X more variables than a state-of-the-art static analysis tool. Our model also outperforms a learning-based function-level annotator on annotating types for variables and function arguments. All our tools and datasets are publicly available to facilitate future research in this direction.

Guiding Language Models of Code with Global Context using Monitors

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 .

GNN-Coder: Boosting Semantic Code Retrieval with Combined GNNs and Transformer

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

CodexGraph: Bridging Large Language Models and Code Repositories via Code Graph Databases

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

Generating Structured Outputs from Language Models: Benchmark and Studies

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

Transformer-Based Models Are Not Yet Perfect At Learning to Emulate Structural Recursion

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

ProteinBench: A Holistic Evaluation of Protein Foundation Models

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

Assemblage: Automatic Binary Dataset Construction for Machine Learning

Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpuses of malicious binaries, obtaining high-quality corpuses of benign binaries for modern systems has proven challenging (e.g., due to licensing issues). Consequently, machine learning based pipelines for binary analysis utilize either costly commercial corpuses (e.g., VirusTotal) or open-source binaries (e.g., coreutils) available in limited quantities. To address these issues, we present Assemblage: an extensible cloud-based distributed system that crawls, configures, and builds Windows PE binaries to obtain high-quality binary corpuses suitable for training state-of-the-art models in binary analysis. We have run Assemblage on AWS over the past year, producing 890k Windows PE and 428k Linux ELF binaries across 29 configurations. Assemblage is designed to be both reproducible and extensible, enabling users to publish "recipes" for their datasets, and facilitating the extraction of a wide array of features. We evaluated Assemblage by using its data to train modern learning-based pipelines for compiler provenance and binary function similarity. Our results illustrate the practical need for robust corpuses of high-quality Windows PE binaries in training modern learning-based binary analyses. Assemblage can be downloaded from https://assemblage-dataset.net

Turning Trash into Treasure: Accelerating Inference of Large Language Models with Token Recycling

The rapid growth in the parameters of large language models (LLMs) has made inference latency a fundamental bottleneck, limiting broader application of LLMs. Speculative decoding represents a lossless approach to accelerate inference through a guess-and-verify paradigm, leveraging the parallel capabilities of modern hardware. Some speculative decoding methods rely on additional structures to guess draft tokens, such as small models or parameter-efficient architectures, which need extra training before use. Alternatively, retrieval-based train-free techniques build libraries from pre-existing corpora or by n-gram generation. However, they face challenges like large storage requirements, time-consuming retrieval, and limited adaptability. Observing that candidate tokens generated during the decoding process are likely to reoccur in future sequences, we propose Token Recycling. This approach stores candidate tokens in an adjacency matrix and employs a breadth-first search (BFS)-like algorithm on the matrix to construct a draft tree. The tree is then validated through tree attention. New candidate tokens from the decoding process are then used to update the matrix. Token Recycling requires \textless2MB of additional storage and achieves approximately 2x speedup across all sizes of LLMs. It significantly outperforms existing train-free methods by 30\% and even a training method by 25\%. It can be directly applied to any existing LLMs and tasks without the need for adaptation.

Autoregressive Entity Retrieval

Entities are at the center of how we represent and aggregate knowledge. For instance, Encyclopedias such as Wikipedia are structured by entities (e.g., one per Wikipedia article). The ability to retrieve such entities given a query is fundamental for knowledge-intensive tasks such as entity linking and open-domain question answering. Current approaches can be understood as classifiers among atomic labels, one for each entity. Their weight vectors are dense entity representations produced by encoding entity meta information such as their descriptions. This approach has several shortcomings: (i) context and entity affinity is mainly captured through a vector dot product, potentially missing fine-grained interactions; (ii) a large memory footprint is needed to store dense representations when considering large entity sets; (iii) an appropriately hard set of negative data has to be subsampled at training time. In this work, we propose GENRE, the first system that retrieves entities by generating their unique names, left to right, token-by-token in an autoregressive fashion. This mitigates the aforementioned technical issues since: (i) the autoregressive formulation directly captures relations between context and entity name, effectively cross encoding both; (ii) the memory footprint is greatly reduced because the parameters of our encoder-decoder architecture scale with vocabulary size, not entity count; (iii) the softmax loss is computed without subsampling negative data. We experiment with more than 20 datasets on entity disambiguation, end-to-end entity linking and document retrieval tasks, achieving new state-of-the-art or very competitive results while using a tiny fraction of the memory footprint of competing systems. Finally, we demonstrate that new entities can be added by simply specifying their names. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins

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.

Binding Language Models in Symbolic Languages

Though end-to-end neural approaches have recently been dominating NLP tasks in both performance and ease-of-use, they lack interpretability and robustness. We propose Binder, a training-free neural-symbolic framework that maps the task input to a program, which (1) allows binding a unified API of language model (LM) functionalities to a programming language (e.g., SQL, Python) to extend its grammar coverage and thus tackle more diverse questions, (2) adopts an LM as both the program parser and the underlying model called by the API during execution, and (3) requires only a few in-context exemplar annotations. Specifically, we employ GPT-3 Codex as the LM. In the parsing stage, with only a few in-context exemplars, Codex is able to identify the part of the task input that cannot be answerable by the original programming language, correctly generate API calls to prompt Codex to solve the unanswerable part, and identify where to place the API calls while being compatible with the original grammar. In the execution stage, Codex can perform versatile functionalities (e.g., commonsense QA, information extraction) given proper prompts in the API calls. Binder achieves state-of-the-art results on WikiTableQuestions and TabFact datasets, with explicit output programs that benefit human debugging. Note that previous best systems are all finetuned on tens of thousands of task-specific samples, while Binder only uses dozens of annotations as in-context exemplars without any training. Our code is available at https://github.com/HKUNLP/Binder .

Evaluating Protein Transfer Learning with TAPE

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

On the Usage of Continual Learning for Out-of-Distribution Generalization in Pre-trained Language Models of Code

Pre-trained language models (PLMs) have become a prevalent technique in deep learning for code, utilizing a two-stage pre-training and fine-tuning procedure to acquire general knowledge about code and specialize in a variety of downstream tasks. However, the dynamic nature of software codebases poses a challenge to the effectiveness and robustness of PLMs. In particular, world-realistic scenarios potentially lead to significant differences between the distribution of the pre-training and test data, i.e., distribution shift, resulting in a degradation of the PLM's performance on downstream tasks. In this paper, we stress the need for adapting PLMs of code to software data whose distribution changes over time, a crucial problem that has been overlooked in previous works. The motivation of this work is to consider the PLM in a non-stationary environment, where fine-tuning data evolves over time according to a software evolution scenario. Specifically, we design a scenario where the model needs to learn from a stream of programs containing new, unseen APIs over time. We study two widely used PLM architectures, i.e., a GPT2 decoder and a RoBERTa encoder, on two downstream tasks, API call and API usage prediction. We demonstrate that the most commonly used fine-tuning technique from prior work is not robust enough to handle the dynamic nature of APIs, leading to the loss of previously acquired knowledge i.e., catastrophic forgetting. To address these issues, we implement five continual learning approaches, including replay-based and regularization-based methods. Our findings demonstrate that utilizing these straightforward methods effectively mitigates catastrophic forgetting in PLMs across both downstream tasks while achieving comparable or superior performance.

Educating LLMs like Human Students: Structure-aware Injection of Domain Knowledge

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

ShortcutsBench: A Large-Scale Real-world Benchmark for API-based Agents

Recent advancements in integrating large language models (LLMs) with application programming interfaces (APIs) have gained significant interest in both academia and industry. These API-based agents, leveraging the strong autonomy and planning capabilities of LLMs, can efficiently solve problems requiring multi-step actions. However, their ability to handle multi-dimensional difficulty levels, diverse task types, and real-world demands through APIs remains unknown. In this paper, we introduce ShortcutsBench, a large-scale benchmark for the comprehensive evaluation of API-based agents in solving tasks with varying levels of difficulty, diverse task types, and real-world demands. ShortcutsBench includes a wealth of real APIs from Apple Inc.'s operating systems, refined user queries from shortcuts, human-annotated high-quality action sequences from shortcut developers, and accurate parameter filling values about primitive parameter types, enum parameter types, outputs from previous actions, and parameters that need to request necessary information from the system or user. Our extensive evaluation of agents built with 5 leading open-source (size >= 57B) and 4 closed-source LLMs (e.g. Gemini-1.5-Pro and GPT-3.5) reveals significant limitations in handling complex queries related to API selection, parameter filling, and requesting necessary information from systems and users. These findings highlight the challenges that API-based agents face in effectively fulfilling real and complex user queries. All datasets, code, and experimental results will be available at https://github.com/eachsheep/shortcutsbench.

CodeTF: One-stop Transformer Library for State-of-the-art Code LLM

Code intelligence plays a key role in transforming modern software engineering. Recently, deep learning-based models, especially Transformer-based large language models (LLMs), have demonstrated remarkable potential in tackling these tasks by leveraging massive open-source code data and programming language features. However, the development and deployment of such models often require expertise in both machine learning and software engineering, creating a barrier for the model adoption. In this paper, we present CodeTF, an open-source Transformer-based library for state-of-the-art Code LLMs and code intelligence. Following the principles of modular design and extensible framework, we design CodeTF with a unified interface to enable rapid access and development across different types of models, datasets and tasks. Our library supports a collection of pretrained Code LLM models and popular code benchmarks, including a standardized interface to train and serve code LLMs efficiently, and data features such as language-specific parsers and utility functions for extracting code attributes. In this paper, we describe the design principles, the architecture, key modules and components, and compare with other related library tools. Finally, we hope CodeTF is able to bridge the gap between machine learning/generative AI and software engineering, providing a comprehensive open-source solution for developers, researchers, and practitioners.

EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

TRACED: Execution-aware Pre-training for Source Code

Most existing pre-trained language models for source code focus on learning the static code text, typically augmented with static code structures (abstract syntax tree, dependency graphs, etc.). However, program semantics will not be fully exposed before the real execution. Without an understanding of the program execution, statically pre-trained models fail to comprehensively capture the dynamic code properties, such as the branch coverage and the runtime variable values, and they are consequently less effective at code understanding tasks, such as retrieving semantic clones and detecting software vulnerabilities. To close the gap between the static nature of language models and the dynamic characteristics of programs, we introduce TRACED, an execution-aware pre-training strategy for source code. Specifically, we pre-train code language models with a combination of source code, executable inputs, and corresponding execution traces. Our goal is to teach code models the complicated execution logic during the pre-training, enabling the model to statically estimate the dynamic code properties without repeatedly executing code during task-specific fine-tuning. To illustrate the effectiveness of our proposed approach, we fine-tune and evaluate TRACED on three downstream tasks: static execution estimation, clone retrieval, and vulnerability detection. The empirical results show that TRACED relatively improves the statically pre-trained code models by 12.4% for complete execution path prediction and by 25.2% for runtime variable value predictions. TRACED also significantly outperforms statically pre-trained models in clone retrieval and vulnerability detection across four public benchmarks.

Syntax-Aware On-the-Fly Code Completion

Code completion aims to help improve developers' productivity by suggesting the next code tokens from a given context. Various approaches have been proposed to incorporate abstract syntax tree (AST) information for model training, ensuring that code completion is aware of the syntax of the programming languages. However, existing syntax-aware code completion approaches are not on-the-fly, as we found that for every two-thirds of characters that developers type, AST fails to be extracted because it requires the syntactically correct source code, limiting its practicality in real-world scenarios. On the other hand, existing on-the-fly code completion does not consider syntactic information yet. In this paper, we propose PyCoder to leverage token types, a kind of lightweight syntactic information, which is readily available and aligns with the natural order of source code. Our PyCoder is trained in a multi-task training manner so that by learning the supporting task of predicting token types during the training phase, the models achieve better performance on predicting tokens and lines of code without the need for token types in the inference phase. Comprehensive experiments show that PyCoder achieves the first rank on the CodeXGLUE leaderboard with an accuracy of 77.12% for the token-level predictions, which is 0.43%-24.25% more accurate than baselines. In addition, PyCoder achieves an exact match of 43.37% for the line-level predictions, which is 3.63%-84.73% more accurate than baselines. These results lead us to conclude that token type information (an alternative to syntactic information) that is rarely used in the past can greatly improve the performance of code completion approaches, without requiring the syntactically correct source code like AST-based approaches do. Our PyCoder is publicly available on HuggingFace.

ComPile: A Large IR Dataset from Production Sources

Code is increasingly becoming a core data modality of modern machine learning research impacting not only the way we write code with conversational agents like OpenAI's ChatGPT, Google's Bard, or Anthropic's Claude, the way we translate code from one language into another, but also the compiler infrastructure underlying the language. While modeling approaches may vary and representations differ, the targeted tasks often remain the same within the individual classes of models. Relying solely on the ability of modern models to extract information from unstructured code does not take advantage of 70 years of programming language and compiler development by not utilizing the structure inherent to programs in the data collection. This detracts from the performance of models working over a tokenized representation of input code and precludes the use of these models in the compiler itself. To work towards the first intermediate representation (IR) based models, we fully utilize the LLVM compiler infrastructure, shared by a number of languages, to generate a 182B token dataset of LLVM IR. We generated this dataset from programming languages built on the shared LLVM infrastructure, including Rust, Swift, Julia, and C/C++, by hooking into LLVM code generation either through the language's package manager or the compiler directly to extract the dataset of intermediate representations from production grade programs. Statistical analysis proves the utility of our dataset not only for large language model training, but also for the introspection into the code generation process itself with the dataset showing great promise for machine-learned compiler components.

Deep Learning based Vulnerability Detection: Are We There Yet?

Automated detection of software vulnerabilities is a fundamental problem in software security. Existing program analysis techniques either suffer from high false positives or false negatives. Recent progress in Deep Learning (DL) has resulted in a surge of interest in applying DL for automated vulnerability detection. Several recent studies have demonstrated promising results achieving an accuracy of up to 95% at detecting vulnerabilities. In this paper, we ask, "how well do the state-of-the-art DL-based techniques perform in a real-world vulnerability prediction scenario?". To our surprise, we find that their performance drops by more than 50%. A systematic investigation of what causes such precipitous performance drop reveals that existing DL-based vulnerability prediction approaches suffer from challenges with the training data (e.g., data duplication, unrealistic distribution of vulnerable classes, etc.) and with the model choices (e.g., simple token-based models). As a result, these approaches often do not learn features related to the actual cause of the vulnerabilities. Instead, they learn unrelated artifacts from the dataset (e.g., specific variable/function names, etc.). Leveraging these empirical findings, we demonstrate how a more principled approach to data collection and model design, based on realistic settings of vulnerability prediction, can lead to better solutions. The resulting tools perform significantly better than the studied baseline: up to 33.57% boost in precision and 128.38% boost in recall compared to the best performing model in the literature. Overall, this paper elucidates existing DL-based vulnerability prediction systems' potential issues and draws a roadmap for future DL-based vulnerability prediction research. In that spirit, we make available all the artifacts supporting our results: https://git.io/Jf6IA.

DPLM-2: A Multimodal Diffusion Protein Language Model

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.

xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein

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.

Neighborhood-aware Scalable Temporal Network Representation Learning

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

On the Tool Manipulation Capability of Open-source Large Language Models

Recent studies on software tool manipulation with large language models (LLMs) mostly rely on closed model APIs. The industrial adoption of these models is substantially constrained due to the security and robustness risks in exposing information to closed LLM API services. In this paper, we ask can we enhance open-source LLMs to be competitive to leading closed LLM APIs in tool manipulation, with practical amount of human supervision. By analyzing common tool manipulation failures, we first demonstrate that open-source LLMs may require training with usage examples, in-context demonstration and generation style regulation to resolve failures. These insights motivate us to revisit classical methods in LLM literature, and demonstrate that we can adapt them as model alignment with programmatic data generation, system prompts and in-context demonstration retrievers to enhance open-source LLMs for tool manipulation. To evaluate these techniques, we create the ToolBench, a tool manipulation benchmark consisting of diverse software tools for real-world tasks. We demonstrate that our techniques can boost leading open-source LLMs by up to 90% success rate, showing capabilities competitive to OpenAI GPT-4 in 4 out of 8 ToolBench tasks. We show that such enhancement typically requires about one developer day to curate data for each tool, rendering a recipe with practical amount of human supervision.

UniXcoder: Unified Cross-Modal Pre-training for Code Representation

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.

Model-Agnostic Syntactical Information for Pre-Trained Programming Language Models

Pre-trained Programming Language Models (PPLMs) achieved many recent states of the art results for many code-related software engineering tasks. Though some studies use data flow or propose tree-based models that utilize Abstract Syntax Tree (AST), most PPLMs do not fully utilize the rich syntactical information in source code. Still, the input is considered a sequence of tokens. There are two issues; the first is computational inefficiency due to the quadratic relationship between input length and attention complexity. Second, any syntactical information, when needed as an extra input to the current PPLMs, requires the model to be pre-trained from scratch, wasting all the computational resources already used for pre-training the current models. In this work, we propose Named Entity Recognition (NER) adapters, lightweight modules that can be inserted into Transformer blocks to learn type information extracted from the AST. These adapters can be used with current PPLMs such as CodeBERT, GraphCodeBERT, and CodeT5. We train the NER adapters using a novel Token Type Classification objective function (TTC). We insert our proposed work in CodeBERT, building CodeBERTER, and evaluate the performance on two tasks of code refinement and code summarization. CodeBERTER improves the accuracy of code refinement from 16.4 to 17.8 while using 20% of training parameter budget compared to the fully fine-tuning approach, and the BLEU score of code summarization from 14.75 to 15.90 while reducing 77% of training parameters compared to the fully fine-tuning approach.

CoCoNUT: Structural Code Understanding does not fall out of a tree

Large Language Models (LLMs) have shown impressive performance across a wide array of tasks involving both structured and unstructured textual data. Recent results on various benchmarks for code generation, repair, or completion suggest that certain models have programming abilities comparable to or even surpass humans. In this work, we demonstrate that high performance on such benchmarks does not correlate to humans' innate ability to understand structural control flow in code. To this end, we extract solutions from the HumanEval benchmark, which the relevant models perform strongly on, and trace their execution path using function calls sampled from the respective test set. Using this dataset, we investigate the ability of seven state-of-the-art LLMs to match the execution trace and find that, despite their ability to generate semantically identical code, they possess limited ability to trace execution paths, especially for longer traces and specific control structures. We find that even the top-performing model, Gemini, can fully and correctly generate only 47% of HumanEval task traces. Additionally, we introduce a subset for three key structures not contained in HumanEval: Recursion, Parallel Processing, and Object-Oriented Programming, including concepts like Inheritance and Polymorphism. Besides OOP, we show that none of the investigated models achieve an accuracy over 5% on the relevant traces. Aggregating these specialized parts with HumanEval tasks, we present Benchmark CoCoNUT: Code Control Flow for Navigation Understanding and Testing, which measures a model's ability to trace execution of code upon relevant calls, including advanced structural components. We conclude that current LLMs need significant improvement to enhance code reasoning abilities. We hope our dataset helps researchers bridge this gap.

PyBench: Evaluating LLM Agent on various real-world coding tasks

The LLM Agent, equipped with a code interpreter, is capable of automatically solving real-world coding tasks, such as data analysis and image editing. However, existing benchmarks primarily focus on either simplistic tasks, such as completing a few lines of code, or on extremely complex and specific tasks at the repository level, neither of which are representative of various daily coding tasks. To address this gap, we introduce PyBench, a benchmark encompassing five main categories of real-world tasks, covering more than 10 types of files. Given a high-level user query and related files, the LLM Agent needs to reason and execute Python code via a code interpreter for a few turns before making a formal response to fulfill the user's requirements. Successfully addressing tasks in PyBench demands a robust understanding of various Python packages, superior reasoning capabilities, and the ability to incorporate feedback from executed code. Our evaluations indicate that current open-source LLMs are struggling with these tasks. Hence, we conduct analysis and experiments on four kinds of datasets proving that comprehensive abilities are needed for PyBench. Our fine-tuned 8B size model: PyLlama3 achieves an exciting performance on PyBench which surpasses many 33B and 70B size models. Our Benchmark, Training Dataset, and Model are available at: https://github.com/Mercury7353/PyBench{https://github.com/Mercury7353/PyBench}

Are Code Pre-trained Models Powerful to Learn Code Syntax and Semantics?

Analysis of pre-trained code models also has revealed that they can effectively learn program syntax. However, these works are limited in analyzing code syntax and their distance-based approaches are not accurate due to the curse of high dimensionality. Furthermore, the study of the learnt program semantics of these models is rarely discussed. To further understand the code features learnt by these models, in this paper, we target two well-known representative code pre-trained models (i.e., CodeBERT and GraphCodeBERT) and devise a set of probing tasks for the syntax and semantics analysis. Specifically, on one hand, we design two probing tasks (i.e., syntax pair node prediction and token tagging prediction) to manipulate AST for the understanding of learnt program syntax. On the other hand, we design two tasks (i.e., semantic relationship prediction and semantic propagation prediction(inGraph) ) on the constructed control flow graph (CFG), data dependency graph (DDG) and control dependency graph (CDG) for the learnt program semantic analysis. In addition, to understand which kind of program semantics these pre-trained models can comprehend well, we conduct the statistical analysis for attention weights learnt by different heads and layers. Through extensive analysis in terms of program syntax and semantics, we have the following findings: 1) Both CodeBERT and GraphCodeBERT can learn the program syntax well. 2) Both CodeBERT and GraphCodeBERT can learn program semantics to different extents. GraphCodeBERT is superior to CodeBERT in learning program control flow and data dependency information but has a similar capability to CodeBERT in learning control dependency information. 3) Both CodeBERT and GraphCodeBERT can capture program semantics in the final layer of representation, but different attention heads and layers exhibit different roles in learning program semantics.

Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Learning Type Inference for Enhanced Dataflow Analysis

Statically analyzing dynamically-typed code is a challenging endeavor, as even seemingly trivial tasks such as determining the targets of procedure calls are non-trivial without knowing the types of objects at compile time. Addressing this challenge, gradual typing is increasingly added to dynamically-typed languages, a prominent example being TypeScript that introduces static typing to JavaScript. Gradual typing improves the developer's ability to verify program behavior, contributing to robust, secure and debuggable programs. In practice, however, users only sparsely annotate types directly. At the same time, conventional type inference faces performance-related challenges as program size grows. Statistical techniques based on machine learning offer faster inference, but although recent approaches demonstrate overall improved accuracy, they still perform significantly worse on user-defined types than on the most common built-in types. Limiting their real-world usefulness even more, they rarely integrate with user-facing applications. We propose CodeTIDAL5, a Transformer-based model trained to reliably predict type annotations. For effective result retrieval and re-integration, we extract usage slices from a program's code property graph. Comparing our approach against recent neural type inference systems, our model outperforms the current state-of-the-art by 7.85% on the ManyTypes4TypeScript benchmark, achieving 71.27% accuracy overall. Furthermore, we present JoernTI, an integration of our approach into Joern, an open source static analysis tool, and demonstrate that the analysis benefits from the additional type information. As our model allows for fast inference times even on commodity CPUs, making our system available through Joern leads to high accessibility and facilitates security research.

FlexiBERT: Are Current Transformer Architectures too Homogeneous and Rigid?

The existence of a plethora of language models makes the problem of selecting the best one for a custom task challenging. Most state-of-the-art methods leverage transformer-based models (e.g., BERT) or their variants. Training such models and exploring their hyperparameter space, however, is computationally expensive. Prior work proposes several neural architecture search (NAS) methods that employ performance predictors (e.g., surrogate models) to address this issue; however, analysis has been limited to homogeneous models that use fixed dimensionality throughout the network. This leads to sub-optimal architectures. To address this limitation, we propose a suite of heterogeneous and flexible models, namely FlexiBERT, that have varied encoder layers with a diverse set of possible operations and different hidden dimensions. For better-posed surrogate modeling in this expanded design space, we propose a new graph-similarity-based embedding scheme. We also propose a novel NAS policy, called BOSHNAS, that leverages this new scheme, Bayesian modeling, and second-order optimization, to quickly train and use a neural surrogate model to converge to the optimal architecture. A comprehensive set of experiments shows that the proposed policy, when applied to the FlexiBERT design space, pushes the performance frontier upwards compared to traditional models. FlexiBERT-Mini, one of our proposed models, has 3% fewer parameters than BERT-Mini and achieves 8.9% higher GLUE score. A FlexiBERT model with equivalent performance as the best homogeneous model achieves 2.6x smaller size. FlexiBERT-Large, another proposed model, achieves state-of-the-art results, outperforming the baseline models by at least 5.7% on the GLUE benchmark.

Learning Performance-Improving Code Edits

The waning of Moore's Law has shifted the focus of the tech industry towards alternative methods for continued performance gains. While optimizing compilers are a standard tool to help increase program efficiency, programmers continue to shoulder much responsibility in crafting and refactoring code with better performance characteristics. In this paper, we investigate the ability of large language models (LLMs) to suggest functionally correct, performance improving code edits. We hypothesize that language models can suggest such edits in ways that would be impractical for static analysis alone. We investigate these questions by curating a large-scale dataset of Performance-Improving Edits, PIE. PIE contains trajectories of programs, where a programmer begins with an initial, slower version and iteratively makes changes to improve the program's performance. We use PIE to evaluate and improve the capacity of large language models. Specifically, use examples from PIE to fine-tune multiple variants of CODEGEN, a billion-scale Transformer-decoder model. Additionally, we use examples from PIE to prompt OpenAI's CODEX using a few-shot prompting. By leveraging PIE, we find that both CODEX and CODEGEN can generate performance-improving edits, with speedups of more than 2.5x for over 25% of the programs, for C++ and Python, even after the C++ programs were compiled using the O3 optimization level. Crucially, we show that PIE allows CODEGEN, an open-sourced and 10x smaller model than CODEX, to match the performance of CODEX on this challenging task. Overall, this work opens new doors for creating systems and methods that can help programmers write efficient code.

Unified Functional Hashing in Automatic Machine Learning

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design

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.

TokenFormer: Rethinking Transformer Scaling with Tokenized Model Parameters

Transformers have become the predominant architecture in foundation models due to their excellent performance across various domains. However, the substantial cost of scaling these models remains a significant concern. This problem arises primarily from their dependence on a fixed number of parameters within linear projections. When architectural modifications (e.g., channel dimensions) are introduced, the entire model typically requires retraining from scratch. As model sizes continue growing, this strategy results in increasingly high computational costs and becomes unsustainable. To overcome this problem, we introduce TokenFormer, a natively scalable architecture that leverages the attention mechanism not only for computations among input tokens but also for interactions between tokens and model parameters, thereby enhancing architectural flexibility. By treating model parameters as tokens, we replace all the linear projections in Transformers with our token-parameter attention layer, where input tokens act as queries and model parameters as keys and values. This reformulation allows for progressive and efficient scaling without necessitating retraining from scratch. Our model scales from 124M to 1.4B parameters by incrementally adding new key-value parameter pairs, achieving performance comparable to Transformers trained from scratch while greatly reducing training costs. Code and models are available at https://github.com/Haiyang-W/TokenFormer.

ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Observatory: Characterizing Embeddings of Relational Tables

Language models and specialized table embedding models have recently demonstrated strong performance on many tasks over tabular data. Researchers and practitioners are keen to leverage these models in many new application contexts; but limited understanding of the strengths and weaknesses of these models, and the table representations they generate, makes the process of finding a suitable model for a given task reliant on trial and error. There is an urgent need to gain a comprehensive understanding of these models to minimize inefficiency and failures in downstream usage. To address this need, we propose Observatory, a formal framework to systematically analyze embedding representations of relational tables. Motivated both by invariants of the relational data model and by statistical considerations regarding data distributions, we define eight primitive properties, and corresponding measures to quantitatively characterize table embeddings for these properties. Based on these properties, we define an extensible framework to evaluate language and table embedding models. We collect and synthesize a suite of datasets and use Observatory to analyze nine such models. Our analysis provides insights into the strengths and weaknesses of learned representations over tables. We find, for example, that some models are sensitive to table structure such as column order, that functional dependencies are rarely reflected in embeddings, and that specialized table embedding models have relatively lower sample fidelity. Such insights help researchers and practitioners better anticipate model behaviors and select appropriate models for their downstream tasks, while guiding researchers in the development of new models.

Integrating Knowledge Graph embedding and pretrained Language Models in Hypercomplex Spaces

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

PAT: Pruning-Aware Tuning for Large Language Models

Large language models (LLMs) excel in language tasks, especially with supervised fine-tuning after pre-training. However, their substantial memory and computational requirements hinder practical applications. Structural pruning, which reduces less significant weight dimensions, is one solution. Yet, traditional post-hoc pruning often leads to significant performance loss, with limited recovery from further fine-tuning due to reduced capacity. Since the model fine-tuning refines the general and chaotic knowledge in pre-trained models, we aim to incorporate structural pruning with the fine-tuning, and propose the Pruning-Aware Tuning (PAT) paradigm to eliminate model redundancy while preserving the model performance to the maximum extend. Specifically, we insert the innovative Hybrid Sparsification Modules (HSMs) between the Attention and FFN components to accordingly sparsify the upstream and downstream linear modules. The HSM comprises a lightweight operator and a globally shared trainable mask. The lightweight operator maintains a training overhead comparable to that of LoRA, while the trainable mask unifies the channels to be sparsified, ensuring structural pruning. Additionally, we propose the Identity Loss which decouples the transformation and scaling properties of the HSMs to enhance training robustness. Extensive experiments demonstrate that PAT excels in both performance and efficiency. For example, our Llama2-7b model with a 25\% pruning ratio achieves 1.33times speedup while outperforming the LoRA-finetuned model by up to 1.26\% in accuracy with a similar training cost. Code: https://github.com/kriskrisliu/PAT_Pruning-Aware-Tuning

Evaluating and Explaining Large Language Models for Code Using Syntactic Structures

Large Language Models (LLMs) for code are a family of high-parameter, transformer-based neural networks pre-trained on massive datasets of both natural and programming languages. These models are rapidly being employed in commercial AI-based developer tools, such as GitHub CoPilot. However, measuring and explaining their effectiveness on programming tasks is a challenging proposition, given their size and complexity. The methods for evaluating and explaining LLMs for code are inextricably linked. That is, in order to explain a model's predictions, they must be reliably mapped to fine-grained, understandable concepts. Once this mapping is achieved, new methods for detailed model evaluations are possible. However, most current explainability techniques and evaluation benchmarks focus on model robustness or individual task performance, as opposed to interpreting model predictions. To this end, this paper introduces ASTxplainer, an explainability method specific to LLMs for code that enables both new methods for LLM evaluation and visualizations of LLM predictions that aid end-users in understanding model predictions. At its core, ASTxplainer provides an automated method for aligning token predictions with AST nodes, by extracting and aggregating normalized model logits within AST structures. To demonstrate the practical benefit of ASTxplainer, we illustrate the insights that our framework can provide by performing an empirical evaluation on 12 popular LLMs for code using a curated dataset of the most popular GitHub projects. Additionally, we perform a user study examining the usefulness of an ASTxplainer-derived visualization of model predictions aimed at enabling model users to explain predictions. The results of these studies illustrate the potential for ASTxplainer to provide insights into LLM effectiveness, and aid end-users in understanding predictions.

How Far Can Camels Go? Exploring the State of Instruction Tuning on Open Resources

In this work we explore recent advances in instruction-tuning language models on a range of open instruction-following datasets. Despite recent claims that open models can be on par with state-of-the-art proprietary models, these claims are often accompanied by limited evaluation, making it difficult to compare models across the board and determine the utility of various resources. We provide a large set of instruction-tuned models from 6.7B to 65B parameters in size, trained on 12 instruction datasets ranging from manually curated (e.g., OpenAssistant) to synthetic and distilled (e.g., Alpaca) and systematically evaluate them on their factual knowledge, reasoning, multilinguality, coding, and open-ended instruction following abilities through a collection of automatic, model-based, and human-based metrics. We further introduce T\"ulu, our best performing instruction-tuned model suite finetuned on a combination of high-quality open resources. Our experiments show that different instruction-tuning datasets can uncover or enhance specific skills, while no single dataset (or combination) provides the best performance across all evaluations. Interestingly, we find that model and human preference-based evaluations fail to reflect differences in model capabilities exposed by benchmark-based evaluations, suggesting the need for the type of systemic evaluation performed in this work. Our evaluations show that the best model in any given evaluation reaches on average 83% of ChatGPT performance, and 68% of GPT-4 performance, suggesting that further investment in building better base models and instruction-tuning data is required to close the gap. We release our instruction-tuned models, including a fully finetuned 65B T\"ulu, along with our code, data, and evaluation framework at https://github.com/allenai/open-instruct to facilitate future research.

Learning to Mine Aligned Code and Natural Language Pairs from Stack Overflow

For tasks like code synthesis from natural language, code retrieval, and code summarization, data-driven models have shown great promise. However, creating these models require parallel data between natural language (NL) and code with fine-grained alignments. Stack Overflow (SO) is a promising source to create such a data set: the questions are diverse and most of them have corresponding answers with high-quality code snippets. However, existing heuristic methods (e.g., pairing the title of a post with the code in the accepted answer) are limited both in their coverage and the correctness of the NL-code pairs obtained. In this paper, we propose a novel method to mine high-quality aligned data from SO using two sets of features: hand-crafted features considering the structure of the extracted snippets, and correspondence features obtained by training a probabilistic model to capture the correlation between NL and code using neural networks. These features are fed into a classifier that determines the quality of mined NL-code pairs. Experiments using Python and Java as test beds show that the proposed method greatly expands coverage and accuracy over existing mining methods, even when using only a small number of labeled examples. Further, we find that reasonable results are achieved even when training the classifier on one language and testing on another, showing promise for scaling NL-code mining to a wide variety of programming languages beyond those for which we are able to annotate data.

Comments as Natural Logic Pivots: Improve Code Generation via Comment Perspective

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.

DocTer: Documentation Guided Fuzzing for Testing Deep Learning API Functions

Input constraints are useful for many software development tasks. For example, input constraints of a function enable the generation of valid inputs, i.e., inputs that follow these constraints, to test the function deeper. API functions of deep learning (DL) libraries have DL specific input constraints, which are described informally in the free form API documentation. Existing constraint extraction techniques are ineffective for extracting DL specific input constraints. To fill this gap, we design and implement a new technique, DocTer, to analyze API documentation to extract DL specific input constraints for DL API functions. DocTer features a novel algorithm that automatically constructs rules to extract API parameter constraints from syntactic patterns in the form of dependency parse trees of API descriptions. These rules are then applied to a large volume of API documents in popular DL libraries to extract their input parameter constraints. To demonstrate the effectiveness of the extracted constraints, DocTer uses the constraints to enable the automatic generation of valid and invalid inputs to test DL API functions. Our evaluation on three popular DL libraries (TensorFlow, PyTorch, and MXNet) shows that the precision of DocTer in extracting input constraints is 85.4%. DocTer detects 94 bugs from 174 API functions, including one previously unknown security vulnerability that is now documented in the CVE database, while a baseline technique without input constraints detects only 59 bugs. Most (63) of the 94 bugs are previously unknown, 54 of which have been fixed or confirmed by developers after we report them. In addition, DocTer detects 43 inconsistencies in documents, 39 of which are fixed or confirmed.

Protein Multimer Structure Prediction via Prompt Learning

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.

Scaling Sparse Fine-Tuning to Large Language Models

Large Language Models (LLMs) are difficult to fully fine-tune (e.g., with instructions or human feedback) due to their sheer number of parameters. A family of parameter-efficient sparse fine-tuning (SFT) methods have proven promising in terms of performance but their memory requirements increase proportionally to the size of the LLMs. In this work, we scale sparse fine-tuning to state-of-the-art LLMs like LLaMA 2 7B and 13B. At any given time, for a desired density level, we maintain an array of parameter indices and the deltas of these parameters relative to their pretrained values. We iterate among: (a) updating the active deltas, (b) pruning indices (based on the change of magnitude of their deltas) and (c) regrowth of indices. For regrowth, we explore two criteria based on either the accumulated gradients of a few candidate parameters or their approximate momenta estimated using the efficient SM3 optimizer. We experiment with instruction-tuning of LLMs on standard dataset mixtures, finding that SFT is often superior to popular parameter-efficient fine-tuning methods like LoRA (low-rank adaptation) in terms of performance and comparable in terms of run time. We additionally show that SFT is compatible with both quantization and efficient optimizers, to facilitate scaling to ever-larger model sizes. We release the code for SFT at https://github.com/AlanAnsell/peft and for the instruction-tuning experiments at https://github.com/ducdauge/sft-llm.

Towards Efficient Fine-tuning of Pre-trained Code Models: An Experimental Study and Beyond

Recently, fine-tuning pre-trained code models such as CodeBERT on downstream tasks has achieved great success in many software testing and analysis tasks. While effective and prevalent, fine-tuning the pre-trained parameters incurs a large computational cost. In this paper, we conduct an extensive experimental study to explore what happens to layer-wise pre-trained representations and their encoded code knowledge during fine-tuning. We then propose efficient alternatives to fine-tune the large pre-trained code model based on the above findings. Our experimental study shows that (1) lexical, syntactic and structural properties of source code are encoded in the lower, intermediate, and higher layers, respectively, while the semantic property spans across the entire model. (2) The process of fine-tuning preserves most of the code properties. Specifically, the basic code properties captured by lower and intermediate layers are still preserved during fine-tuning. Furthermore, we find that only the representations of the top two layers change most during fine-tuning for various downstream tasks. (3) Based on the above findings, we propose Telly to efficiently fine-tune pre-trained code models via layer freezing. The extensive experimental results on five various downstream tasks demonstrate that training parameters and the corresponding time cost are greatly reduced, while performances are similar or better. Replication package including source code, datasets, and online Appendix is available at: https://github.com/DeepSoftwareAnalytics/Telly.

Class-Level Code Generation from Natural Language Using Iterative, Tool-Enhanced Reasoning over Repository

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

Hardware and Software Platform Inference

It is now a common business practice to buy access to large language model (LLM) inference rather than self-host, because of significant upfront hardware infrastructure and energy costs. However, as a buyer, there is no mechanism to verify the authenticity of the advertised service including the serving hardware platform, e.g. that it is actually being served using an NVIDIA H100. Furthermore, there are reports suggesting that model providers may deliver models that differ slightly from the advertised ones, often to make them run on less expensive hardware. That way, a client pays premium for a capable model access on more expensive hardware, yet ends up being served by a (potentially less capable) cheaper model on cheaper hardware. In this paper we introduce \textbf{hardware and software platform inference (HSPI)} -- a method for identifying the underlying architecture and software stack of a (black-box) machine learning model solely based on its input-output behavior. Our method leverages the inherent differences of various architectures and compilers to distinguish between different types and software stacks. By analyzing the numerical patterns in the model's outputs, we propose a classification framework capable of accurately identifying the used for model inference as well as the underlying software configuration. Our findings demonstrate the feasibility of inferring type from black-box models. We evaluate HSPI against models served on different real hardware and find that in a white-box setting we can distinguish between different s with between 83.9% and 100% accuracy. Even in a black-box setting we are able to achieve results that are up to three times higher than random guess accuracy.

Data-Efficient Massive Tool Retrieval: A Reinforcement Learning Approach for Query-Tool Alignment with Language Models

Recent advancements in large language models (LLMs) integrated with external tools and APIs have successfully addressed complex tasks by using in-context learning or fine-tuning. Despite this progress, the vast scale of tool retrieval remains challenging due to stringent input length constraints. In response, we propose a pre-retrieval strategy from an extensive repository, effectively framing the problem as the massive tool retrieval (MTR) task. We introduce the MTRB (massive tool retrieval benchmark) to evaluate real-world tool-augmented LLM scenarios with a large number of tools. This benchmark is designed for low-resource scenarios and includes a diverse collection of tools with descriptions refined for consistency and clarity. It consists of three subsets, each containing 90 test samples and 10 training samples. To handle the low-resource MTR task, we raise a new query-tool alignment (QTA) framework leverages LLMs to enhance query-tool alignment by rewriting user queries through ranking functions and the direct preference optimization (DPO) method. This approach consistently outperforms existing state-of-the-art models in top-5 and top-10 retrieval tasks across the MTRB benchmark, with improvements up to 93.28% based on the metric Sufficiency@k, which measures the adequacy of tool retrieval within the first k results. Furthermore, ablation studies validate the efficacy of our framework, highlighting its capacity to optimize performance even with limited annotated samples. Specifically, our framework achieves up to 78.53% performance improvement in Sufficiency@k with just a single annotated sample. Additionally, QTA exhibits strong cross-dataset generalizability, emphasizing its potential for real-world applications.

CoderEval: A Benchmark of Pragmatic Code Generation with Generative Pre-trained Models

Code generation models based on the pre-training and fine-tuning paradigm have been increasingly attempted by both academia and industry, resulting in well-known industrial models such as Codex, CodeGen, and PanGu-Coder. To evaluate the effectiveness of these models, multiple existing benchmarks are proposed, including only cases of generating a standalone function, i.e., a function that may invoke or access only built-in functions and standard libraries. However, non-standalone functions, which typically are not included in the existing benchmarks, constitute more than 70% of the functions in popular open-source projects, and evaluating models' effectiveness on standalone functions cannot reflect these models' effectiveness on pragmatic code generation scenarios. To help bridge the preceding gap, in this paper, we propose a benchmark named CoderEval, consisting of 230 Python and 230 Java code generation tasks carefully curated from popular real-world open-source projects and a self-contained execution platform to automatically assess the functional correctness of generated code. CoderEval supports code generation tasks from six levels of context dependency, where context refers to code elements such as types, APIs, variables, and consts defined outside the function under generation but within the dependent third-party libraries, current class, file, or project. CoderEval can be used to evaluate the effectiveness of models in generating code beyond only standalone functions. By evaluating three code generation models on CoderEval, we find that the effectiveness of these models in generating standalone functions is substantially higher than that in generating non-standalone functions. Our analysis highlights the current progress and pinpoints future directions to further improve a model's effectiveness by leveraging contextual information for pragmatic code generation.

COMEX: A Tool for Generating Customized Source Code Representations

Learning effective representations of source code is critical for any Machine Learning for Software Engineering (ML4SE) system. Inspired by natural language processing, large language models (LLMs) like Codex and CodeGen treat code as generic sequences of text and are trained on huge corpora of code data, achieving state of the art performance on several software engineering (SE) tasks. However, valid source code, unlike natural language, follows a strict structure and pattern governed by the underlying grammar of the programming language. Current LLMs do not exploit this property of the source code as they treat code like a sequence of tokens and overlook key structural and semantic properties of code that can be extracted from code-views like the Control Flow Graph (CFG), Data Flow Graph (DFG), Abstract Syntax Tree (AST), etc. Unfortunately, the process of generating and integrating code-views for every programming language is cumbersome and time consuming. To overcome this barrier, we propose our tool COMEX - a framework that allows researchers and developers to create and combine multiple code-views which can be used by machine learning (ML) models for various SE tasks. Some salient features of our tool are: (i) it works directly on source code (which need not be compilable), (ii) it currently supports Java and C#, (iii) it can analyze both method-level snippets and program-level snippets by using both intra-procedural and inter-procedural analysis, and (iv) it is easily extendable to other languages as it is built on tree-sitter - a widely used incremental parser that supports over 40 languages. We believe this easy-to-use code-view generation and customization tool will give impetus to research in source code representation learning methods and ML4SE. Tool: https://pypi.org/project/comex - GitHub: https://github.com/IBM/tree-sitter-codeviews - Demo: https://youtu.be/GER6U87FVbU

SymbolicAI: A framework for logic-based approaches combining generative models and solvers

We introduce SymbolicAI, a versatile and modular framework employing a logic-based approach to concept learning and flow management in generative processes. SymbolicAI enables the seamless integration of generative models with a diverse range of solvers by treating large language models (LLMs) as semantic parsers that execute tasks based on both natural and formal language instructions, thus bridging the gap between symbolic reasoning and generative AI. We leverage probabilistic programming principles to tackle complex tasks, and utilize differentiable and classical programming paradigms with their respective strengths. The framework introduces a set of polymorphic, compositional, and self-referential operations for data stream manipulation, aligning LLM outputs with user objectives. As a result, we can transition between the capabilities of various foundation models endowed with zero- and few-shot learning capabilities and specialized, fine-tuned models or solvers proficient in addressing specific problems. In turn, the framework facilitates the creation and evaluation of explainable computational graphs. We conclude by introducing a quality measure and its empirical score for evaluating these computational graphs, and propose a benchmark that compares various state-of-the-art LLMs across a set of complex workflows. We refer to the empirical score as the "Vector Embedding for Relational Trajectory Evaluation through Cross-similarity", or VERTEX score for short. The framework codebase and benchmark are linked below.

Program Synthesis with Large Language Models

This paper explores the limits of the current generation of large language models for program synthesis in general purpose programming languages. We evaluate a collection of such models (with between 244M and 137B parameters) on two new benchmarks, MBPP and MathQA-Python, in both the few-shot and fine-tuning regimes. Our benchmarks are designed to measure the ability of these models to synthesize short Python programs from natural language descriptions. The Mostly Basic Programming Problems (MBPP) dataset contains 974 programming tasks, designed to be solvable by entry-level programmers. The MathQA-Python dataset, a Python version of the MathQA benchmark, contains 23914 problems that evaluate the ability of the models to synthesize code from more complex text. On both datasets, we find that synthesis performance scales log-linearly with model size. Our largest models, even without finetuning on a code dataset, can synthesize solutions to 59.6 percent of the problems from MBPP using few-shot learning with a well-designed prompt. Fine-tuning on a held-out portion of the dataset improves performance by about 10 percentage points across most model sizes. On the MathQA-Python dataset, the largest fine-tuned model achieves 83.8 percent accuracy. Going further, we study the model's ability to engage in dialog about code, incorporating human feedback to improve its solutions. We find that natural language feedback from a human halves the error rate compared to the model's initial prediction. Additionally, we conduct an error analysis to shed light on where these models fall short and what types of programs are most difficult to generate. Finally, we explore the semantic grounding of these models by fine-tuning them to predict the results of program execution. We find that even our best models are generally unable to predict the output of a program given a specific input.

ArchGym: An Open-Source Gymnasium for Machine Learning Assisted Architecture Design

Machine learning is a prevalent approach to tame the complexity of design space exploration for domain-specific architectures. Using ML for design space exploration poses challenges. First, it's not straightforward to identify the suitable algorithm from an increasing pool of ML methods. Second, assessing the trade-offs between performance and sample efficiency across these methods is inconclusive. Finally, lack of a holistic framework for fair, reproducible, and objective comparison across these methods hinders progress of adopting ML-aided architecture design space exploration and impedes creating repeatable artifacts. To mitigate these challenges, we introduce ArchGym, an open-source gym and easy-to-extend framework that connects diverse search algorithms to architecture simulators. To demonstrate utility, we evaluate ArchGym across multiple vanilla and domain-specific search algorithms in designing custom memory controller, deep neural network accelerators, and custom SoC for AR/VR workloads, encompassing over 21K experiments. Results suggest that with unlimited samples, ML algorithms are equally favorable to meet user-defined target specification if hyperparameters are tuned; no solution is necessarily better than another (e.g., reinforcement learning vs. Bayesian methods). We coin the term hyperparameter lottery to describe the chance for a search algorithm to find an optimal design provided meticulously selected hyperparameters. The ease of data collection and aggregation in ArchGym facilitates research in ML-aided architecture design space exploration. As a case study, we show this advantage by developing a proxy cost model with an RMSE of 0.61% that offers a 2,000-fold reduction in simulation time. Code and data for ArchGym is available at https://bit.ly/ArchGym.

xTrimoABFold: De novo Antibody Structure Prediction without MSA

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

The Good, the Bad, and the Missing: Neural Code Generation for Machine Learning Tasks

Machine learning (ML) has been increasingly used in a variety of domains, while solving ML programming tasks poses unique challenges because of the fundamentally different nature and construction from general programming tasks, especially for developers who do not have ML backgrounds. Automatic code generation that produces a code snippet from a natural language description can be a promising technique to accelerate ML programming tasks. In recent years, although many deep learning-based neural code generation models have been proposed with high accuracy, the fact that most of them are mainly evaluated on general programming tasks calls into question their effectiveness and usefulness in ML programming tasks. In this paper, we set out to investigate the effectiveness of existing neural code generation models on ML programming tasks. For our analysis, we select six state-of-the-art neural code generation models, and evaluate their performance on four widely used ML libraries, with newly-created 83K pairs of natural-language described ML programming tasks. Our empirical study reveals some good, bad, and missing aspects of neural code generation models on ML tasks, with a few major ones listed below. (Good) Neural code generation models perform significantly better on ML tasks than on non-ML tasks. (Bad) Most of the generated code is semantically incorrect. (Bad) Code generation models cannot significantly improve developers' completion time. (Good) The generated code can help developers write more correct code by providing developers with clues for using correct APIs. (Missing) The observation from our user study reveals the missing aspects of code generation for ML tasks, e.g., decomposing code generation for divide-and-conquer into two tasks: API sequence identification and API usage generation.

DySpec: Faster Speculative Decoding with Dynamic Token Tree Structure

While speculative decoding has recently appeared as a promising direction for accelerating the inference of large language models (LLMs), the speedup and scalability are strongly bounded by the token acceptance rate. Prevalent methods usually organize predicted tokens as independent chains or fixed token trees, which fails to generalize to diverse query distributions. In this paper, we propose DySpec, a faster speculative decoding algorithm with a novel dynamic token tree structure. We begin by bridging the draft distribution and acceptance rate from intuitive and empirical clues, and successfully show that the two variables are strongly correlated. Based on this, we employ a greedy strategy to dynamically expand the token tree at run time. Theoretically, we show that our method can achieve optimal results under mild assumptions. Empirically, DySpec yields a higher acceptance rate and speedup than fixed trees. DySpec can drastically improve the throughput and reduce the latency of token generation across various data distribution and model sizes, which significantly outperforms strong competitors, including Specinfer and Sequoia. Under low temperature setting, DySpec can improve the throughput up to 9.1times and reduce the latency up to 9.4times on Llama2-70B. Under high temperature setting, DySpec can also improve the throughput up to 6.21times, despite the increasing difficulty of speculating more than one token per step for draft model.

Optimizing Speculative Decoding for Serving Large Language Models Using Goodput

Reducing the inference latency of large language models (LLMs) is crucial, and speculative decoding (SD) stands out as one of the most effective techniques. Rather than letting the LLM generate all tokens directly, speculative decoding employs effective proxies to predict potential outputs, which are then verified by the LLM without compromising the generation quality. Yet, deploying SD in real online LLM serving systems (with continuous batching) does not always yield improvement -- under higher request rates or low speculation accuracy, it paradoxically increases latency. Furthermore, there is no best speculation length work for all workloads under different system loads. Based on the observations, we develop a dynamic framework SmartSpec. SmartSpec dynamically determines the best speculation length for each request (from 0, i.e., no speculation, to many tokens) -- hence the associated speculative execution costs -- based on a new metric called goodput, which characterizes the current observed load of the entire system and the speculation accuracy. We show that SmartSpec consistently reduces average request latency by up to 3.2x compared to non-speculative decoding baselines across different sizes of target models, draft models, request rates, and datasets. Moreover, SmartSpec can be applied to different styles of speculative decoding, including traditional, model-based approaches as well as model-free methods like prompt lookup and tree-style decoding.

Peptide Sequencing Via Protein Language Models

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Layer-wise Importance Matters: Less Memory for Better Performance in Parameter-efficient Fine-tuning of Large Language Models

Parameter-Efficient Fine-Tuning (PEFT) methods have gained significant popularity for adapting pre-trained Large Language Models (LLMs) to downstream tasks, primarily due to their potential to significantly reduce memory and computational overheads. However, a common limitation in most PEFT approaches is their application of a uniform architectural design across all layers. This uniformity involves identical trainable modules and ignores the varying importance of each layer, leading to sub-optimal fine-tuning results. To overcome the above limitation and obtain better performance, we develop a novel approach, Importance-aware Sparse Tuning (IST), to fully utilize the inherent sparsity and select the most important subset of full layers with effective layer-wise importance scoring. The proposed IST is a versatile and plug-and-play technique compatible with various PEFT methods that operate on a per-layer basis. By leveraging the estimated importance scores, IST dynamically updates these selected layers in PEFT modules, leading to reduced memory demands. We further provide theoretical proof of convergence and empirical evidence of superior performance to demonstrate the advantages of IST over uniform updating strategies. Extensive experiments on a range of LLMs, PEFTs, and downstream tasks substantiate the effectiveness of our proposed method, showcasing IST's capacity to enhance existing layer-based PEFT methods. Our code is available at https://github.com/Kaiseem/IST.