Daily Papers

The development of domain-specific language models has significantly advanced natural language processing applications in various specialized fields, particularly in biomedicine. However, the focus has largely been on English-language models, leaving a gap for less-resourced languages such as Italian. This paper introduces Igea, the first decoder-only language model designed explicitly for biomedical text generation in Italian. Built on the Minerva model and continually pretrained on a diverse corpus of Italian medical texts, Igea is available in three model sizes: 350 million, 1 billion, and 3 billion parameters. The models aim to balance computational efficiency and performance, addressing the challenges of managing the peculiarities of medical terminology in Italian. We evaluate Igea using a mix of in-domain biomedical corpora and general-purpose benchmarks, highlighting its efficacy and retention of general knowledge even after the domain-specific training. This paper discusses the model's development and evaluation, providing a foundation for future advancements in Italian biomedical NLP.

In the era of digital healthcare, the huge volumes of textual information generated every day in hospitals constitute an essential but underused asset that could be exploited with task-specific, fine-tuned biomedical language representation models, improving patient care and management. For such specialized domains, previous research has shown that fine-tuning models stemming from broad-coverage checkpoints can largely benefit additional training rounds over large-scale in-domain resources. However, these resources are often unreachable for less-resourced languages like Italian, preventing local medical institutions to employ in-domain adaptation. In order to reduce this gap, our work investigates two accessible approaches to derive biomedical language models in languages other than English, taking Italian as a concrete use-case: one based on neural machine translation of English resources, favoring quantity over quality; the other based on a high-grade, narrow-scoped corpus natively written in Italian, thus preferring quality over quantity. Our study shows that data quantity is a harder constraint than data quality for biomedical adaptation, but the concatenation of high-quality data can improve model performance even when dealing with relatively size-limited corpora. The models published from our investigations have the potential to unlock important research opportunities for Italian hospitals and academia. Finally, the set of lessons learned from the study constitutes valuable insights towards a solution to build biomedical language models that are generalizable to other less-resourced languages and different domain settings.

The introduction of computerized medical records in hospitals has reduced burdensome operations like manual writing and information fetching. However, the data contained in medical records are still far underutilized, primarily because extracting them from unstructured textual medical records takes time and effort. Information Extraction, a subfield of Natural Language Processing, can help clinical practitioners overcome this limitation, using automated text-mining pipelines. In this work, we created the first Italian neuropsychiatric Named Entity Recognition dataset, PsyNIT, and used it to develop a Large Language Model for this task. Moreover, we conducted several experiments with three external independent datasets to implement an effective multicenter model, with overall F1-score 84.77%, Precision 83.16%, Recall 86.44%. The lessons learned are: (i) the crucial role of a consistent annotation process and (ii) a fine-tuning strategy that combines classical methods with a "few-shot" approach. This allowed us to establish methodological guidelines that pave the way for future implementations in this field and allow Italian hospitals to tap into important research opportunities.

Research on language technology for the development of medical applications is currently a hot topic in Natural Language Understanding and Generation. Thus, a number of large language models (LLMs) have recently been adapted to the medical domain, so that they can be used as a tool for mediating in human-AI interaction. While these LLMs display competitive performance on automated medical texts benchmarks, they have been pre-trained and evaluated with a focus on a single language (English mostly). This is particularly true of text-to-text models, which typically require large amounts of domain-specific pre-training data, often not easily accessible for many languages. In this paper, we address these shortcomings by compiling, to the best of our knowledge, the largest multilingual corpus for the medical domain in four languages, namely English, French, Italian and Spanish. This new corpus has been used to train Medical mT5, the first open-source text-to-text multilingual model for the medical domain. Additionally, we present two new evaluation benchmarks for all four languages with the aim of facilitating multilingual research in this domain. A comprehensive evaluation shows that Medical mT5 outperforms both encoders and similarly sized text-to-text models for the Spanish, French, and Italian benchmarks, while being competitive with current state-of-the-art LLMs in English.

Traditional approaches to Named Entity Recognition (NER) frame the task into a BIO sequence labeling problem. Although these systems often excel in the downstream task at hand, they require extensive annotated data and struggle to generalize to out-of-distribution input domains and unseen entity types. On the contrary, Large Language Models (LLMs) have demonstrated strong zero-shot capabilities. While several works address Zero-Shot NER in English, little has been done in other languages. In this paper, we define an evaluation framework for Zero-Shot NER, applying it to the Italian language. Furthermore, we introduce SLIMER-IT, the Italian version of SLIMER, an instruction-tuning approach for zero-shot NER leveraging prompts enriched with definition and guidelines. Comparisons with other state-of-the-art models, demonstrate the superiority of SLIMER-IT on never-seen-before entity tags.

Motivation: A perennial challenge for biomedical researchers and clinical practitioners is to stay abreast with the rapid growth of publications and medical notes. Natural language processing (NLP) has emerged as a promising direction for taming information overload. In particular, large neural language models facilitate transfer learning by pretraining on unlabeled text, as exemplified by the successes of BERT models in various NLP applications. However, fine-tuning such models for an end task remains challenging, especially with small labeled datasets, which are common in biomedical NLP. Results: We conduct a systematic study on fine-tuning stability in biomedical NLP. We show that finetuning performance may be sensitive to pretraining settings, especially in low-resource domains. Large models have potential to attain better performance, but increasing model size also exacerbates finetuning instability. We thus conduct a comprehensive exploration of techniques for addressing fine-tuning instability. We show that these techniques can substantially improve fine-tuning performance for lowresource biomedical NLP applications. Specifically, freezing lower layers is helpful for standard BERT-BASE models, while layerwise decay is more effective for BERT-LARGE and ELECTRA models. For low-resource text similarity tasks such as BIOSSES, reinitializing the top layer is the optimal strategy. Overall, domainspecific vocabulary and pretraining facilitate more robust models for fine-tuning. Based on these findings, we establish new state of the art on a wide range of biomedical NLP applications. Availability and implementation: To facilitate progress in biomedical NLP, we release our state-of-the-art pretrained and fine-tuned models: https://aka.ms/BLURB.

The T5 model and its unified text-to-text paradigm contributed in advancing the state-of-the-art for many natural language processing tasks. While some multilingual variants of the T5 model have recently been introduced, their performances were found to provide suboptimal performances for languages other than English if compared to monolingual variants. We are motivated by these findings to introduce IT5, the first family of encoder-decoder transformer models pretrained specifically on Italian. We perform a thorough cleaning of a web-crawled Italian corpus including more than 40 billion words and use it to pretrain three IT5 models of different sizes. The performance of IT5 models and their multilingual counterparts is then evaluated on a broad range of natural language understanding and generation benchmarks for Italian. We find the monolingual IT5 models to provide the best scale-to-performance ratio across tested models, consistently outperforming their multilingual counterparts and setting a new state-of-the-art for most Italian conditional language generation tasks.

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more effectively treat specific domains. In this paper, we propose an original study of PLMs in the medical domain on French language. We compare, for the first time, the performance of PLMs trained on both public data from the web and private data from healthcare establishments. We also evaluate different learning strategies on a set of biomedical tasks. In particular, we show that we can take advantage of already existing biomedical PLMs in a foreign language by further pre-train it on our targeted data. Finally, we release the first specialized PLMs for the biomedical field in French, called DrBERT, as well as the largest corpus of medical data under free license on which these models are trained.

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity Recognition (NER). Recent research in biomedical language processing has offered a number of biomedical LMs pre-trained using different methods and techniques that advance results on many BioNLP tasks, including NER. However, there is still a lack of a comprehensive comparison of pre-training approaches that would work more optimally in the biomedical domain. This paper aims to investigate different pre-training methods, such as pre-training the biomedical LM from scratch and pre-training it in a continued fashion. We compare existing methods with our proposed pre-training method of initializing weights for new tokens by distilling existing weights from the BERT model inside the context where the tokens were found. The method helps to speed up the pre-training stage and improve performance on NER. In addition, we compare how masking rate, corruption strategy, and masking strategies impact the performance of the biomedical LM. Finally, using the insights from our experiments, we introduce a new biomedical LM (BIOptimus), which is pre-trained using Curriculum Learning (CL) and contextualized weight distillation method. Our model sets new states of the art on several biomedical Named Entity Recognition (NER) tasks. We release our code and all pre-trained models

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.

In this paper we present a technique of NLP to tackle the problem of inference relation (NLI) between pairs of sentences in a target language of choice without a language-specific training dataset. We exploit a generic translation dataset, manually translated, along with two instances of the same pre-trained model - the first to generate sentence embeddings for the source language, and the second fine-tuned over the target language to mimic the first. This technique is known as Knowledge Distillation. The model has been evaluated over machine translated Stanford NLI test dataset, machine translated Multi-Genre NLI test dataset, and manually translated RTE3-ITA test dataset. We also test the proposed architecture over different tasks to empirically demonstrate the generality of the NLI task. The model has been evaluated over the native Italian ABSITA dataset, on the tasks of Sentiment Analysis, Aspect-Based Sentiment Analysis, and Topic Recognition. We emphasise the generality and exploitability of the Knowledge Distillation technique that outperforms other methodologies based on machine translation, even though the former was not directly trained on the data it was tested over.

Plug-and-play language models (PPLMs) enable topic-conditioned natural language generation by pairing large pre-trained generators with attribute models used to steer the predicted token distribution towards the selected topic. Despite their computational efficiency, PPLMs require large amounts of labeled texts to effectively balance generation fluency and proper conditioning, making them unsuitable for low-resource settings. We present ETC-NLG, an approach leveraging topic modeling annotations to enable fully-unsupervised End-to-end Topic-Conditioned Natural Language Generation over emergent topics in unlabeled document collections. We first test the effectiveness of our approach in a low-resource setting for Italian, evaluating the conditioning for both topic models and gold annotations. We then perform a comparative evaluation of ETC-NLG for Italian and English using a parallel corpus. Finally, we propose an automatic approach to estimate the effectiveness of conditioning on the generated utterances.

Most biomedical pretrained language models are monolingual and cannot handle the growing cross-lingual requirements. The scarcity of non-English domain corpora, not to mention parallel data, poses a significant hurdle in training multilingual biomedical models. Since knowledge forms the core of domain-specific corpora and can be translated into various languages accurately, we propose a model called KBioXLM, which transforms the multilingual pretrained model XLM-R into the biomedical domain using a knowledge-anchored approach. We achieve a biomedical multilingual corpus by incorporating three granularity knowledge alignments (entity, fact, and passage levels) into monolingual corpora. Then we design three corresponding training tasks (entity masking, relation masking, and passage relation prediction) and continue training on top of the XLM-R model to enhance its domain cross-lingual ability. To validate the effectiveness of our model, we translate the English benchmarks of multiple tasks into Chinese. Experimental results demonstrate that our model significantly outperforms monolingual and multilingual pretrained models in cross-lingual zero-shot and few-shot scenarios, achieving improvements of up to 10+ points. Our code is publicly available at https://github.com/ngwlh-gl/KBioXLM.

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

Biomedical literature often uses complex language and inaccessible professional terminologies. That is why simplification plays an important role in improving public health literacy. Applying Natural Language Processing (NLP) models to automate such tasks allows for quick and direct accessibility for lay readers. In this work, we investigate the ability of state-of-the-art large language models (LLMs) on the task of biomedical abstract simplification, using the publicly available dataset for plain language adaptation of biomedical abstracts (PLABA). The methods applied include domain fine-tuning and prompt-based learning (PBL) on: 1) Encoder-decoder models (T5, SciFive, and BART), 2) Decoder-only GPT models (GPT-3.5 and GPT-4) from OpenAI and BioGPT, and 3) Control-token mechanisms on BART-based models. We used a range of automatic evaluation metrics, including BLEU, ROUGE, SARI, and BERTscore, and also conducted human evaluations. BART-Large with Control Token (BART-L-w-CT) mechanisms reported the highest SARI score of 46.54 and T5-base reported the highest BERTscore 72.62. In human evaluation, BART-L-w-CTs achieved a better simplicity score over T5-Base (2.9 vs. 2.2), while T5-Base achieved a better meaning preservation score over BART-L-w-CTs (3.1 vs. 2.6). We also categorised the system outputs with examples, hoping this will shed some light for future research on this task. Our code, fine-tuned models, and data splits are available at https://github.com/HECTA-UoM/PLABA-MU

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy owing to factors such as embedding size, hidden dimension, and number of layers. The natural language processing (NLP) community has developed numerous strategies to compress these models utilising techniques such as pruning, quantisation, and knowledge distillation, resulting in models that are considerably faster, smaller, and subsequently easier to use in practice. By the same token, in this paper we introduce six lightweight models, namely, BioDistilBERT, BioTinyBERT, BioMobileBERT, DistilBioBERT, TinyBioBERT, and CompactBioBERT which are obtained either by knowledge distillation from a biomedical teacher or continual learning on the Pubmed dataset via the Masked Language Modelling (MLM) objective. We evaluate all of our models on three biomedical tasks and compare them with BioBERT-v1.1 to create efficient lightweight models that perform on par with their larger counterparts. All the models will be publicly available on our Huggingface profile at https://huggingface.co/nlpie and the codes used to run the experiments will be available at https://github.com/nlpie-research/Compact-Biomedical-Transformers.

Clinical data in hospitals are increasingly accessible for research through clinical data warehouses, however these documents are unstructured. It is therefore necessary to extract information from medical reports to conduct clinical studies. Transfer learning with BERT-like models such as CamemBERT has allowed major advances, especially for named entity recognition. However, these models are trained for plain language and are less efficient on biomedical data. This is why we propose a new French public biomedical dataset on which we have continued the pre-training of CamemBERT. Thus, we introduce a first version of CamemBERT-bio, a specialized public model for the French biomedical domain that shows 2.54 points of F1 score improvement on average on different biomedical named entity recognition tasks. Our findings demonstrate the success of continual pre-training from a French model and contrast with recent proposals on the same domain and language. One of our key contributions highlights the importance of using a standard evaluation protocol that enables a clear view of the current state-of-the-art for French biomedical models.

Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like Knowledge Distillation (KD), it is possible to create smaller versions that perform almost as well as their larger counterparts. In this work, we specifically focus on development of compact language models for processing clinical texts (i.e. progress notes, discharge summaries etc). We developed a number of efficient lightweight clinical transformers using knowledge distillation and continual learning, with the number of parameters ranging from 15 million to 65 million. These models performed comparably to larger models such as BioBERT and ClinicalBioBERT and significantly outperformed other compact models trained on general or biomedical data. Our extensive evaluation was done across several standard datasets and covered a wide range of clinical text-mining tasks, including Natural Language Inference, Relation Extraction, Named Entity Recognition, and Sequence Classification. To our knowledge, this is the first comprehensive study specifically focused on creating efficient and compact transformers for clinical NLP tasks. The models and code used in this study can be found on our Huggingface profile at https://huggingface.co/nlpie and Github page at https://github.com/nlpie-research/Lightweight-Clinical-Transformers, respectively, promoting reproducibility of our results.

Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific downstream tasks. In the biomedical domain, natural language generation (NLG) tasks are of critical importance, while understudied. Approaching natural language understanding (NLU) tasks as NLG achieves satisfying performance in the general domain through constrained language generation or language prompting. We emphasize the lack of in-domain generative language models and the unsystematic generative downstream benchmarks in the biomedical domain, hindering the development of the research community. In this work, we introduce the generative language model BioBART that adapts BART to the biomedical domain. We collate various biomedical language generation tasks including dialogue, summarization, entity linking, and named entity recognition. BioBART pretrained on PubMed abstracts has enhanced performance compared to BART and set strong baselines on several tasks. Furthermore, we conduct ablation studies on the pretraining tasks for BioBART and find that sentence permutation has negative effects on downstream tasks.

Clinical Natural Language Processing (NLP) has become an emerging technology in healthcare that leverages a large amount of free-text data in electronic health records (EHRs) to improve patient care, support clinical decisions, and facilitate clinical and translational science research. Recently, deep learning has achieved state-of-the-art performance in many clinical NLP tasks. However, training deep learning models usually requires large annotated datasets, which are normally not publicly available and can be time-consuming to build in clinical domains. Working with smaller annotated datasets is typical in clinical NLP and therefore, ensuring that deep learning models perform well is crucial for the models to be used in real-world applications. A widely adopted approach is fine-tuning existing Pre-trained Language Models (PLMs), but these attempts fall short when the training dataset contains only a few annotated samples. Few-Shot Learning (FSL) has recently been investigated to tackle this problem. Siamese Neural Network (SNN) has been widely utilized as an FSL approach in computer vision, but has not been studied well in NLP. Furthermore, the literature on its applications in clinical domains is scarce. In this paper, we propose two SNN-based FSL approaches for clinical NLP, including Pre-Trained SNN (PT-SNN) and SNN with Second-Order Embeddings (SOE-SNN). We evaluated the proposed approaches on two clinical tasks, namely clinical text classification and clinical named entity recognition. We tested three few-shot settings including 4-shot, 8-shot, and 16-shot learning. Both clinical NLP tasks were benchmarked using three PLMs, including BERT,BioBERT, and BioClinicalBERT. The experimental results verified the effectiveness of the proposed SNN-based FSL approaches in both NLP tasks.

The advancement of natural language processing (NLP) in biology hinges on models' ability to interpret intricate biomedical literature. Traditional models often struggle with the complex and domain-specific language in this field. In this paper, we present BioMamba, a pre-trained model specifically designed for biomedical text mining. BioMamba builds upon the Mamba architecture and is pre-trained on an extensive corpus of biomedical literature. Our empirical studies demonstrate that BioMamba significantly outperforms models like BioBERT and general-domain Mamba across various biomedical tasks. For instance, BioMamba achieves a 100 times reduction in perplexity and a 4 times reduction in cross-entropy loss on the BioASQ test set. We provide an overview of the model architecture, pre-training process, and fine-tuning techniques. Additionally, we release the code and trained model to facilitate further research.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Large language models (LLMs) have shown potential in biomedical applications, leading to efforts to fine-tune them on domain-specific data. However, the effectiveness of this approach remains unclear. This study evaluates the performance of biomedically fine-tuned LLMs against their general-purpose counterparts on a variety of clinical tasks. We evaluated their performance on clinical case challenges from the New England Journal of Medicine (NEJM) and the Journal of the American Medical Association (JAMA) and on several clinical tasks (e.g., information extraction, document summarization, and clinical coding). Using benchmarks specifically chosen to be likely outside the fine-tuning datasets of biomedical models, we found that biomedical LLMs mostly perform inferior to their general-purpose counterparts, especially on tasks not focused on medical knowledge. While larger models showed similar performance on case tasks (e.g., OpenBioLLM-70B: 66.4% vs. Llama-3-70B-Instruct: 65% on JAMA cases), smaller biomedical models showed more pronounced underperformance (e.g., OpenBioLLM-8B: 30% vs. Llama-3-8B-Instruct: 64.3% on NEJM cases). Similar trends were observed across the CLUE (Clinical Language Understanding Evaluation) benchmark tasks, with general-purpose models often performing better on text generation, question answering, and coding tasks. Our results suggest that fine-tuning LLMs to biomedical data may not provide the expected benefits and may potentially lead to reduced performance, challenging prevailing assumptions about domain-specific adaptation of LLMs and highlighting the need for more rigorous evaluation frameworks in healthcare AI. Alternative approaches, such as retrieval-augmented generation, may be more effective in enhancing the biomedical capabilities of LLMs without compromising their general knowledge.

There has been an influx of biomedical domain-specific language models, showing language models pre-trained on biomedical text perform better on biomedical domain benchmarks than those trained on general domain text corpora such as Wikipedia and Books. Yet, most works do not study the factors affecting each domain language application deeply. Additionally, the study of model size on domain-specific models has been mostly missing. We empirically study and evaluate several factors that can affect performance on domain language applications, such as the sub-word vocabulary set, model size, pre-training corpus, and domain transfer. We show consistent improvements on benchmarks with our larger BioMegatron model trained on a larger domain corpus, contributing to our understanding of domain language model applications. We demonstrate noticeable improvements over the previous state-of-the-art (SOTA) on standard biomedical NLP benchmarks of named entity recognition, relation extraction, and question answering. Model checkpoints and code are available at [https://ngc.nvidia.com] and [https://github.com/NVIDIA/NeMo].

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment analysis, document classification and many others. In the biomedical domain, significant progress has been made in adapting this paradigm to NLP tasks that require the integration of domain-specific knowledge as well as statistical modelling of language. In particular, research in this area has focused on the question of how best to construct LMs that take into account not only the patterns of token distribution in medical text, but also the wealth of structured information contained in terminology resources such as the UMLS. This work contributes a data-centric paradigm for enriching the language representations of biomedical transformer-encoder LMs by extracting text sequences from the UMLS. This allows for graph-based learning objectives to be combined with masked-language pre-training. Preliminary results from experiments in the extension of pre-trained LMs as well as training from scratch show that this framework improves downstream performance on multiple biomedical and clinical Named Entity Recognition (NER) tasks.

Recent large-scale Spoken Language Understanding datasets focus predominantly on English and do not account for language-specific phenomena such as particular phonemes or words in different lects. We introduce ITALIC, the first large-scale speech dataset designed for intent classification in Italian. The dataset comprises 16,521 crowdsourced audio samples recorded by 70 speakers from various Italian regions and annotated with intent labels and additional metadata. We explore the versatility of ITALIC by evaluating current state-of-the-art speech and text models. Results on intent classification suggest that increasing scale and running language adaptation yield better speech models, monolingual text models outscore multilingual ones, and that speech recognition on ITALIC is more challenging than on existing Italian benchmarks. We release both the dataset and the annotation scheme to streamline the development of new Italian SLU models and language-specific datasets.

Recent advancements in large language models (LLMs) have shown promising results across a variety of natural language processing (NLP) tasks. The application of LLMs to specific domains, such as biomedicine, has achieved increased attention. However, most biomedical LLMs focus on enhancing performance in monolingual biomedical question answering and conversation tasks. To further investigate the effectiveness of the LLMs on diverse biomedical NLP tasks in different languages, we present Taiyi, a bilingual (English and Chinese) fine-tuned LLM for diverse biomedical tasks. In this work, we first curated a comprehensive collection of 140 existing biomedical text mining datasets across over 10 task types. Subsequently, a two-stage strategy is proposed for supervised fine-tuning to optimize the model performance across varied tasks. Experimental results on 13 test sets covering named entity recognition, relation extraction, text classification, question answering tasks demonstrate Taiyi achieves superior performance compared to general LLMs. The case study involving additional biomedical NLP tasks further shows Taiyi's considerable potential for bilingual biomedical multi-tasking. The source code, datasets, and model for Taiyi are freely available at https://github.com/DUTIR-BioNLP/Taiyi-LLM.

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our larger model BioGPT-Large achieves 81.0% on PubMedQA. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

The deployment of large language models (LLMs) within the healthcare sector has sparked both enthusiasm and apprehension. These models exhibit the remarkable capability to provide proficient responses to free-text queries, demonstrating a nuanced understanding of professional medical knowledge. This comprehensive survey delves into the functionalities of existing LLMs designed for healthcare applications, elucidating the trajectory of their development, starting from traditional Pretrained Language Models (PLMs) to the present state of LLMs in healthcare sector. First, we explore the potential of LLMs to amplify the efficiency and effectiveness of diverse healthcare applications, particularly focusing on clinical language understanding tasks. These tasks encompass a wide spectrum, ranging from named entity recognition and relation extraction to natural language inference, multi-modal medical applications, document classification, and question-answering. Additionally, we conduct an extensive comparison of the most recent state-of-the-art LLMs in the healthcare domain, while also assessing the utilization of various open-source LLMs and highlighting their significance in healthcare applications. Furthermore, we present the essential performance metrics employed to evaluate LLMs in the biomedical domain, shedding light on their effectiveness and limitations. Finally, we summarize the prominent challenges and constraints faced by large language models in the healthcare sector, offering a holistic perspective on their potential benefits and shortcomings. This review provides a comprehensive exploration of the current landscape of LLMs in healthcare, addressing their role in transforming medical applications and the areas that warrant further research and development.

Inspired by the success of the General Language Understanding Evaluation benchmark, we introduce the Biomedical Language Understanding Evaluation (BLUE) benchmark to facilitate research in the development of pre-training language representations in the biomedicine domain. The benchmark consists of five tasks with ten datasets that cover both biomedical and clinical texts with different dataset sizes and difficulties. We also evaluate several baselines based on BERT and ELMo and find that the BERT model pre-trained on PubMed abstracts and MIMIC-III clinical notes achieves the best results. We make the datasets, pre-trained models, and codes publicly available at https://github.com/ncbi-nlp/BLUE_Benchmark.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Natural Language Processing (NLP) research has traditionally been predominantly focused on English, driven by the availability of resources, the size of the research community, and market demands. Recently, there has been a noticeable shift towards multilingualism in NLP, recognizing the need for inclusivity and effectiveness across diverse languages and cultures. Monolingual surveys have the potential to complement the broader trend towards multilingualism in NLP by providing foundational insights and resources, necessary for effectively addressing the linguistic diversity of global communication. However, monolingual NLP surveys are extremely rare in the literature. This study introduces a generalizable methodology for creating systematic and comprehensive monolingual NLP surveys, aimed at optimizing the process of constructing such surveys and thoroughly addressing a language's NLP support. Our approach integrates a structured search protocol to avoid selection bias and ensure reproducibility, an NLP task taxonomy to organize the surveyed material coherently, and language resources (LRs) taxonomies to identify potential benchmarks and highlight opportunities for improving resource availability (e.g., through better maintenance or licensing). We apply this methodology to Greek NLP (2012-2023), providing a comprehensive overview of its current state and challenges. We discuss the progress of Greek NLP and outline the Greek LRs found, classified by availability and usability, assessing language support per NLP task. The presented systematic literature review of Greek NLP serves as an application of our method that showcases the benefits of monolingual NLP surveys more broadly. Similar applications could be considered for the myriads of languages whose progress in NLP lags behind that of well-supported languages.

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the continual influx of domain-specific terminologies in scholarly literature. Current research in Biomedical Method (BioMethod) NER suffers from a scarcity of resources, primarily attributed to the intricate nature of methodological concepts, which necessitate a profound understanding for precise delineation. In this study, we propose a novel dataset for biomedical method entity recognition, employing an automated BioMethod entity recognition and information retrieval system to assist human annotation. Furthermore, we comprehensively explore a range of conventional and contemporary open-domain NER methodologies, including the utilization of cutting-edge large-scale language models (LLMs) customised to our dataset. Our empirical findings reveal that the large parameter counts of language models surprisingly inhibit the effective assimilation of entity extraction patterns pertaining to biomedical methods. Remarkably, the approach, leveraging the modestly sized ALBERT model (only 11MB), in conjunction with conditional random fields (CRF), achieves state-of-the-art (SOTA) performance.

The integration of large language model (LLM) techniques in the field of medical analysis has brought about significant advancements, yet the scarcity of large, diverse, and well-annotated datasets remains a major challenge. Medical data and tasks, which vary in format, size, and other parameters, require extensive preprocessing and standardization for effective use in training LLMs. To address these challenges, we introduce MedINST, the Meta Dataset of Biomedical Instructions, a novel multi-domain, multi-task instructional meta-dataset. MedINST comprises 133 biomedical NLP tasks and over 7 million training samples, making it the most comprehensive biomedical instruction dataset to date. Using MedINST as the meta dataset, we curate MedINST32, a challenging benchmark with different task difficulties aiming to evaluate LLMs' generalization ability. We fine-tune several LLMs on MedINST and evaluate on MedINST32, showcasing enhanced cross-task generalization.

Etruscan is an ancient language spoken in Italy from the 7th century BC to the 1st century AD. There are no native speakers of the language at the present day, and its resources are scarce, as there exist only around 12,000 known inscriptions. To the best of our knowledge, there are no publicly available Etruscan corpora for natural language processing. Therefore, we propose a dataset for machine translation from Etruscan to English, which contains 2891 translated examples from existing academic sources. Some examples are extracted manually, while others are acquired in an automatic way. Along with the dataset, we benchmark different machine translation models observing that it is possible to achieve a BLEU score of 10.1 with a small transformer model. Releasing the dataset can help enable future research on this language, similar languages or other languages with scarce resources.

Machine translation is indispensable in healthcare for enabling the global dissemination of medical knowledge across languages. However, complex medical terminology poses unique challenges to achieving adequate translation quality and accuracy. This study introduces a novel "LLMs-in-the-loop" approach to develop supervised neural machine translation models optimized specifically for medical texts. While large language models (LLMs) have demonstrated powerful capabilities, this research shows that small, specialized models trained on high-quality in-domain (mostly synthetic) data can outperform even vastly larger LLMs. Custom parallel corpora in six languages were compiled from scientific articles, synthetically generated clinical documents, and medical texts. Our LLMs-in-the-loop methodology employs synthetic data generation, rigorous evaluation, and agent orchestration to enhance performance. We developed small medical translation models using the MarianMT base model. We introduce a new medical translation test dataset to standardize evaluation in this domain. Assessed using BLEU, METEOR, ROUGE, and BERT scores on this test set, our MarianMT-based models outperform Google Translate, DeepL, and GPT-4-Turbo. Results demonstrate that our LLMs-in-the-loop approach, combined with fine-tuning high-quality, domain-specific data, enables specialized models to outperform general-purpose and some larger systems. This research, part of a broader series on expert small models, paves the way for future healthcare-related AI developments, including deidentification and bio-medical entity extraction models. Our study underscores the potential of tailored neural translation models and the LLMs-in-the-loop methodology to advance the field through improved data generation, evaluation, agent, and modeling techniques.

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for better language representations. Interestingly, in the absence of enough clinical data to train a model from scratch, we applied mixed-domain pretraining and cross-domain transfer approaches to generate a performant bio-clinical model suitable for real-world clinical data. We evaluated our models on Named Entity Recognition (NER) tasks for biomedical documents and challenging hospital discharge reports. When compared against the competitive mBERT and BETO models, we outperform them in all NER tasks by a significant margin. Finally, we studied the impact of the model's vocabulary on the NER performances by offering an interesting vocabulary-centric analysis. The results confirm that domain-specific pretraining is fundamental to achieving higher performances in downstream NER tasks, even within a mid-resource scenario. To the best of our knowledge, we provide the first biomedical and clinical transformer-based pretrained language models for Spanish, intending to boost native Spanish NLP applications in biomedicine. Our best models are freely available in the HuggingFace hub: https://huggingface.co/BSC-TeMU.

The utilization of clinical reports for various secondary purposes, including health research and treatment monitoring, is crucial for enhancing patient care. Natural Language Processing (NLP) tools have emerged as valuable assets for extracting and processing relevant information from these reports. However, the availability of specialized language models for the clinical domain in Spanish has been limited. In this paper, we introduce EriBERTa, a bilingual domain-specific language model pre-trained on extensive medical and clinical corpora. We demonstrate that EriBERTa outperforms previous Spanish language models in the clinical domain, showcasing its superior capabilities in understanding medical texts and extracting meaningful information. Moreover, EriBERTa exhibits promising transfer learning abilities, allowing for knowledge transfer from one language to another. This aspect is particularly beneficial given the scarcity of Spanish clinical data.

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED

Developing the required technology to assist medical experts in their everyday activities is currently a hot topic in the Artificial Intelligence research field. Thus, a number of large language models (LLMs) and automated benchmarks have recently been proposed with the aim of facilitating information extraction in Evidence-Based Medicine (EBM) using natural language as a tool for mediating in human-AI interaction. The most representative benchmarks are limited to either multiple-choice or long-form answers and are available only in English. In order to address these shortcomings, in this paper we present a new dataset which, unlike previous work: (i) includes not only explanatory arguments for the correct answer, but also arguments to reason why the incorrect answers are not correct; (ii) the explanations are written originally by medical doctors to answer questions from the Spanish Residency Medical Exams. Furthermore, this new benchmark allows us to setup a novel extractive task which consists of identifying the explanation of the correct answer written by medical doctors. An additional benefit of our setting is that we can leverage the extractive QA paradigm to automatically evaluate performance of LLMs without resorting to costly manual evaluation by medical experts. Comprehensive experimentation with language models for Spanish shows that sometimes multilingual models fare better than monolingual ones, even outperforming models which have been adapted to the medical domain. Furthermore, results across the monolingual models are mixed, with supposedly smaller and inferior models performing competitively. In any case, the obtained results show that our novel dataset and approach can be an effective technique to help medical practitioners in identifying relevant evidence-based explanations for medical questions.

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

Recently, the increasing demand for superior medical services has highlighted the discrepancies in the medical infrastructure. With big data, especially texts, forming the foundation of medical services, there is an exigent need for effective natural language processing (NLP) solutions tailored to the healthcare domain. Conventional approaches leveraging pre-trained models present promising results in this domain and current large language models (LLMs) offer advanced foundation for medical text processing. However, most medical LLMs are trained only with supervised fine-tuning (SFT), even though it efficiently empowers LLMs to understand and respond to medical instructions but is ineffective in learning domain knowledge and aligning with human preference. Another engineering barrier that prevents current medical LLM from better text processing ability is their restricted context length (e.g., 2,048 tokens), making it hard for the LLMs to process long context, which is frequently required in the medical domain. In this work, we propose ChiMed-GPT, a new benchmark LLM designed explicitly for Chinese medical domain, with enlarged context length to 4,096 tokens and undergoes a comprehensive training regime with pre-training, SFT, and RLHF. Evaluations on real-world tasks including information extraction, question answering, and dialogue generation demonstrate ChiMed-GPT's superior performance over general domain LLMs. Furthermore, we analyze possible biases through prompting ChiMed-GPT to perform attitude scales regarding discrimination of patients, so as to contribute to further responsible development of LLMs in the medical domain. The code and model are released at https://github.com/synlp/ChiMed-GPT.

Pre-training large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as bidirectional encoder representations from transformers (BERT), the performance of information extraction from a free text by NLP has significantly improved for both the general domain and medical domain; however, it is difficult to train specific BERT models that perform well for domains in which there are few publicly available databases of high quality and large size. We hypothesized that this problem can be addressed by up-sampling a domain-specific corpus and using it for pre-training with a larger corpus in a balanced manner. Our proposed method consists of a single intervention with one option: simultaneous pre-training after up-sampling and amplified vocabulary. We conducted three experiments and evaluated the resulting products. We confirmed that our Japanese medical BERT outperformed conventional baselines and the other BERT models in terms of the medical document classification task and that our English BERT pre-trained using both the general and medical-domain corpora performed sufficiently well for practical use in terms of the biomedical language understanding evaluation (BLUE) benchmark. Moreover, our enhanced biomedical BERT model, in which clinical notes were not used during pre-training, showed that both the clinical and biomedical scores of the BLUE benchmark were 0.3 points above that of the ablation model trained without our proposed method. Well-balanced pre-training by up-sampling instances derived from a corpus appropriate for the target task allows us to construct a high-performance BERT model.

This paper introduces LatinCy, a set of trained general purpose Latin-language "core" pipelines for use with the spaCy natural language processing framework. The models are trained on a large amount of available Latin data, including all five of the Latin Universal Dependency treebanks, which have been preprocessed to be compatible with each other. The result is a set of general models for Latin with good performance on a number of natural language processing tasks (e.g. the top-performing model yields POS tagging, 97.41% accuracy; lemmatization, 94.66% accuracy; morphological tagging 92.76% accuracy). The paper describes the model training, including its training data and parameterization, and presents the advantages to Latin-language researchers of having a spaCy model available for NLP work.

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can struggle in specialized domains such as medicine, where unique domain-specific terminologies, domain-specific abbreviations, and varying document structures are common. This paper explores strategies for adapting these models to domain-specific requirements, primarily through continuous pre-training on domain-specific data. We pre-trained several German medical language models on 2.4B tokens derived from translated public English medical data and 3B tokens of German clinical data. The resulting models were evaluated on various German downstream tasks, including named entity recognition (NER), multi-label classification, and extractive question answering. Our results suggest that models augmented by clinical and translation-based pre-training typically outperform general domain models in medical contexts. We conclude that continuous pre-training has demonstrated the ability to match or even exceed the performance of clinical models trained from scratch. Furthermore, pre-training on clinical data or leveraging translated texts have proven to be reliable methods for domain adaptation in medical NLP tasks.

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.

Large Language Models (LLMs) have the potential of facilitating the development of Artificial Intelligence technology to assist medical experts for interactive decision support, which has been demonstrated by their competitive performances in Medical QA. However, while impressive, the required quality bar for medical applications remains far from being achieved. Currently, LLMs remain challenged by outdated knowledge and by their tendency to generate hallucinated content. Furthermore, most benchmarks to assess medical knowledge lack reference gold explanations which means that it is not possible to evaluate the reasoning of LLMs predictions. Finally, the situation is particularly grim if we consider benchmarking LLMs for languages other than English which remains, as far as we know, a totally neglected topic. In order to address these shortcomings, in this paper we present MedExpQA, the first multilingual benchmark based on medical exams to evaluate LLMs in Medical Question Answering. To the best of our knowledge, MedExpQA includes for the first time reference gold explanations written by medical doctors which can be leveraged to establish various gold-based upper-bounds for comparison with LLMs performance. Comprehensive multilingual experimentation using both the gold reference explanations and Retrieval Augmented Generation (RAG) approaches show that performance of LLMs still has large room for improvement, especially for languages other than English. Furthermore, and despite using state-of-the-art RAG methods, our results also demonstrate the difficulty of obtaining and integrating readily available medical knowledge that may positively impact results on downstream evaluations for Medical Question Answering. So far the benchmark is available in four languages, but we hope that this work may encourage further development to other languages.

Recent advances in NLP have led to the creation of powerful language models for many languages including Ancient Greek and Latin. While prior work on Classical languages unanimously uses BERT, in this work we create four language models for Ancient Greek that vary along two dimensions to study their versatility for tasks of interest for Classical languages: we explore (i) encoder-only and encoder-decoder architectures using RoBERTa and T5 as strong model types, and create for each of them (ii) a monolingual Ancient Greek and a multilingual instance that includes Latin and English. We evaluate all models on morphological and syntactic tasks, including lemmatization, which demonstrates the added value of T5's decoding abilities. We further define two probing tasks to investigate the knowledge acquired by models pre-trained on Classical texts. Our experiments provide the first benchmarking analysis of existing models of Ancient Greek. Results show that our models provide significant improvements over the SoTA. The systematic analysis of model types can inform future research in designing language models for Classical languages, including the development of novel generative tasks. We make all our models available as community resources, along with a large curated pre-training corpus for Ancient Greek, to support the creation of a larger, comparable model zoo for Classical Philology. Our models and resources are available at https://github.com/Heidelberg-NLP/ancient-language-models.

Natural Language Processing (NLP) has seen remarkable advances in recent years, particularly with the emergence of Large Language Models that have achieved unprecedented performance across many tasks. However, these developments have mainly benefited a small number of high-resource languages such as English. The majority of languages still face significant challenges due to the scarcity of training data and computational resources. To address this issue, this thesis focuses on cross-lingual transfer learning, a research area aimed at leveraging data and models from high-resource languages to improve NLP performance for low-resource languages. Specifically, we focus on Sequence Labeling tasks such as Named Entity Recognition, Opinion Target Extraction, and Argument Mining. The research is structured around three main objectives: (1) advancing data-based cross-lingual transfer learning methods through improved translation and annotation projection techniques, (2) developing enhanced model-based transfer learning approaches utilizing state-of-the-art multilingual models, and (3) applying these methods to real-world problems while creating open-source resources that facilitate future research in low-resource NLP. More specifically, this thesis presents a new method to improve data-based transfer with T-Projection, a state-of-the-art annotation projection method that leverages text-to-text multilingual models and machine translation systems. T-Projection significantly outperforms previous annotation projection methods by a wide margin. For model-based transfer, we introduce a constrained decoding algorithm that enhances cross-lingual Sequence Labeling in zero-shot settings using text-to-text models. Finally, we develop Medical mT5, the first multilingual text-to-text medical model, demonstrating the practical impact of our research on real-world applications.

Evaluating Natural Language Generation (NLG) systems is a challenging task. Firstly, the metric should ensure that the generated hypothesis reflects the reference's semantics. Secondly, it should consider the grammatical quality of the generated sentence. Thirdly, it should be robust enough to handle various surface forms of the generated sentence. Thus, an effective evaluation metric has to be multifaceted. In this paper, we propose an automatic evaluation metric incorporating several core aspects of natural language understanding (language competence, syntactic and semantic variation). Our proposed metric, RoMe, is trained on language features such as semantic similarity combined with tree edit distance and grammatical acceptability, using a self-supervised neural network to assess the overall quality of the generated sentence. Moreover, we perform an extensive robustness analysis of the state-of-the-art methods and RoMe. Empirical results suggest that RoMe has a stronger correlation to human judgment over state-of-the-art metrics in evaluating system-generated sentences across several NLG tasks.

Natural language processing (NLP) is an area of artificial intelligence that applies information technologies to process the human language, understand it to a certain degree, and use it in various applications. This area has rapidly developed in the last few years and now employs modern variants of deep neural networks to extract relevant patterns from large text corpora. The main objective of this work is to survey the recent use of NLP in the field of pharmacology. As our work shows, NLP is a highly relevant information extraction and processing approach for pharmacology. It has been used extensively, from intelligent searches through thousands of medical documents to finding traces of adversarial drug interactions in social media. We split our coverage into five categories to survey modern NLP methodology, commonly addressed tasks, relevant textual data, knowledge bases, and useful programming libraries. We split each of the five categories into appropriate subcategories, describe their main properties and ideas, and summarize them in a tabular form. The resulting survey presents a comprehensive overview of the area, useful to practitioners and interested observers.

Biomedical data and benchmarks are highly valuable yet very limited in low-resource languages other than English such as Vietnamese. In this paper, we make use of a state-of-the-art translation model in English-Vietnamese to translate and produce both pretrained as well as supervised data in the biomedical domains. Thanks to such large-scale translation, we introduce ViPubmedT5, a pretrained Encoder-Decoder Transformer model trained on 20 million translated abstracts from the high-quality public PubMed corpus. ViPubMedT5 demonstrates state-of-the-art results on two different biomedical benchmarks in summarization and acronym disambiguation. Further, we release ViMedNLI - a new NLP task in Vietnamese translated from MedNLI using the recently public En-vi translation model and carefully refined by human experts, with evaluations of existing methods against ViPubmedT5.

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.

This paper presents several BERT-based models for Russian language biomedical text mining (RuBioBERT, RuBioRoBERTa). The models are pre-trained on a corpus of freely available texts in the Russian biomedical domain. With this pre-training, our models demonstrate state-of-the-art results on RuMedBench - Russian medical language understanding benchmark that covers a diverse set of tasks, including text classification, question answering, natural language inference, and named entity recognition.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

To enhance the performance of large language models (LLMs) in biomedical natural language processing (BioNLP) by introducing a domain-specific instruction dataset and examining its impact when combined with multi-task learning principles. We created the BioInstruct, comprising 25,005 instructions to instruction-tune LLMs(LLaMA 1 & 2, 7B & 13B version). The instructions were created by prompting the GPT-4 language model with three-seed samples randomly drawn from an 80 human curated instructions. We employed Low-Rank Adaptation(LoRA) for parameter-efficient fine-tuning. We then evaluated these instruction-tuned LLMs on several BioNLP tasks, which can be grouped into three major categories: question answering(QA), information extraction(IE), and text generation(GEN). We also examined whether categories(e.g., QA, IE, and generation) of instructions impact model performance. Comparing with LLMs without instruction-tuned, our instruction-tuned LLMs demonstrated marked performance gains: 17.3% in QA, 5.7% in IE, and 96% in Generation tasks. Our 7B-parameter instruction-tuned LLaMA 1 model was competitive or even surpassed other LLMs in the biomedical domain that were also fine-tuned from LLaMA 1 with vast domain-specific data or a variety of tasks. Our results also show that the performance gain is significantly higher when instruction fine-tuning is conducted with closely related tasks. Our findings align with the observations of multi-task learning, suggesting the synergies between two tasks. The BioInstruct dataset serves as a valuable resource and instruction tuned LLMs lead to the best performing BioNLP applications.

This study introduces a novel approach for generating high-quality, language-specific chat corpora using a self-chat mechanism. We combine a generator LLM for creating new samples and an embedder LLM to ensure diversity. A new Masked Language Modelling (MLM) model-based quality assessment metric is proposed for evaluating and filtering the corpora. Utilizing the llama2-70b as the generator and a multilingual sentence transformer as embedder, we generate an Italian chat corpus and refine the Fauno corpus, which is based on translated English ChatGPT self-chat data. The refinement uses structural assertions and Natural Language Processing techniques. Both corpora undergo a comprehensive quality evaluation using the proposed MLM model-based quality metric. The Italian LLM fine-tuned with these corpora demonstrates significantly enhanced language comprehension and question-answering skills. The resultant model, cerbero-7b, establishes a new state-of-the-art for Italian LLMs. This approach marks a substantial advancement in the development of language-specific LLMs, with a special emphasis on augmenting corpora for underrepresented languages like Italian.

Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses additional challenges in vision--language modelling compared to the general domain, and previous work has used insufficiently adapted models that lack domain-specific language understanding. In this paper, we show that principled textual semantic modelling can substantially improve contrastive learning in self-supervised vision--language processing. We release a language model that achieves state-of-the-art results in radiology natural language inference through its improved vocabulary and novel language pretraining objective leveraging semantics and discourse characteristics in radiology reports. Further, we propose a self-supervised joint vision--language approach with a focus on better text modelling. It establishes new state of the art results on a wide range of publicly available benchmarks, in part by leveraging our new domain-specific language model. We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing. A broad evaluation, including on this new dataset, shows that our contrastive learning approach, aided by textual-semantic modelling, outperforms prior methods in segmentation tasks, despite only using a global-alignment objective.

Gender-fair language aims at promoting gender equality by using terms and expressions that include all identities and avoid reinforcing gender stereotypes. Implementing gender-fair strategies is particularly challenging in heavily gender-marked languages, such as Italian. To address this, the Gender-Fair Generation challenge intends to help shift toward gender-fair language in written communication. The challenge, designed to assess and monitor the recognition and generation of gender-fair language in both mono- and cross-lingual scenarios, includes three tasks: (1) the detection of gendered expressions in Italian sentences, (2) the reformulation of gendered expressions into gender-fair alternatives, and (3) the generation of gender-fair language in automatic translation from English to Italian. The challenge relies on three different annotated datasets: the GFL-it corpus, which contains Italian texts extracted from administrative documents provided by the University of Brescia; GeNTE, a bilingual test set for gender-neutral rewriting and translation built upon a subset of the Europarl dataset; and Neo-GATE, a bilingual test set designed to assess the use of non-binary neomorphemes in Italian for both fair formulation and translation tasks. Finally, each task is evaluated with specific metrics: average of F1-score obtained by means of BERTScore computed on each entry of the datasets for task 1, an accuracy measured with a gender-neutral classifier, and a coverage-weighted accuracy for tasks 2 and 3.

Large Language Models (LLMs) have demonstrated remarkable versatility in recent years, offering potential applications across specialized domains such as healthcare and medicine. Despite the availability of various open-source LLMs tailored for health contexts, adapting general-purpose LLMs to the medical domain presents significant challenges. In this paper, we introduce BioMistral, an open-source LLM tailored for the biomedical domain, utilizing Mistral as its foundation model and further pre-trained on PubMed Central. We conduct a comprehensive evaluation of BioMistral on a benchmark comprising 10 established medical question-answering (QA) tasks in English. We also explore lightweight models obtained through quantization and model merging approaches. Our results demonstrate BioMistral's superior performance compared to existing open-source medical models and its competitive edge against proprietary counterparts. Finally, to address the limited availability of data beyond English and to assess the multilingual generalization of medical LLMs, we automatically translated and evaluated this benchmark into 7 other languages. This marks the first large-scale multilingual evaluation of LLMs in the medical domain. Datasets, multilingual evaluation benchmarks, scripts, and all the models obtained during our experiments are freely released.

Natural language tasks like Named Entity Recognition (NER) in the clinical domain on non-English texts can be very time-consuming and expensive due to the lack of annotated data. Cross-lingual transfer (CLT) is a way to circumvent this issue thanks to the ability of multilingual large language models to be fine-tuned on a specific task in one language and to provide high accuracy for the same task in another language. However, other methods leveraging translation models can be used to perform NER without annotated data in the target language, by either translating the training set or test set. This paper compares cross-lingual transfer with these two alternative methods, to perform clinical NER in French and in German without any training data in those languages. To this end, we release MedNERF a medical NER test set extracted from French drug prescriptions and annotated with the same guidelines as an English dataset. Through extensive experiments on this dataset and on a German medical dataset (Frei and Kramer, 2021), we show that translation-based methods can achieve similar performance to CLT but require more care in their design. And while they can take advantage of monolingual clinical language models, those do not guarantee better results than large general-purpose multilingual models, whether with cross-lingual transfer or translation.

Recent developments in Japanese large language models (LLMs) primarily focus on general domains, with fewer advancements in Japanese biomedical LLMs. One obstacle is the absence of a comprehensive, large-scale benchmark for comparison. Furthermore, the resources for evaluating Japanese biomedical LLMs are insufficient. To advance this field, we propose a new benchmark including eight LLMs across four categories and 20 Japanese biomedical datasets across five tasks. Experimental results indicate that: (1) LLMs with a better understanding of Japanese and richer biomedical knowledge achieve better performance in Japanese biomedical tasks, (2) LLMs that are not mainly designed for Japanese biomedical domains can still perform unexpectedly well, and (3) there is still much room for improving the existing LLMs in certain Japanese biomedical tasks. Moreover, we offer insights that could further enhance development in this field. Our evaluation tools tailored to our benchmark as well as the datasets are publicly available in https://huggingface.co/datasets/Coldog2333/JMedBench to facilitate future research.

Recently, pretrained language models based on BERT have been introduced for the French biomedical domain. Although these models have achieved state-of-the-art results on biomedical and clinical NLP tasks, they are constrained by a limited input sequence length of 512 tokens, which poses challenges when applied to clinical notes. In this paper, we present a comparative study of three adaptation strategies for long-sequence models, leveraging the Longformer architecture. We conducted evaluations of these models on 16 downstream tasks spanning both biomedical and clinical domains. Our findings reveal that further pre-training an English clinical model with French biomedical texts can outperform both converting a French biomedical BERT to the Longformer architecture and pre-training a French biomedical Longformer from scratch. The results underscore that long-sequence French biomedical models improve performance across most downstream tasks regardless of sequence length, but BERT based models remain the most efficient for named entity recognition tasks.

Italy exhibits rich linguistic diversity across its territory due to the distinct regional languages spoken in different areas. Recent advances in self-supervised learning provide new opportunities to analyze Italy's linguistic varieties using speech data alone. This includes the potential to leverage representations learned from large amounts of data to better examine nuances between closely related linguistic varieties. In this study, we focus on automatically identifying the geographic region of origin of speech samples drawn from Italy's diverse language varieties. We leverage self-supervised learning models to tackle this task and analyze differences and similarities between Italy's regional languages. In doing so, we also seek to uncover new insights into the relationships among these diverse yet closely related varieties, which may help linguists understand their interconnected evolution and regional development over time and space. To improve the discriminative ability of learned representations, we evaluate several supervised contrastive learning objectives, both as pre-training steps and additional fine-tuning objectives. Experimental evidence shows that pre-trained self-supervised models can effectively identify regions from speech recording. Additionally, incorporating contrastive objectives during fine-tuning improves classification accuracy and yields embeddings that distinctly separate regional varieties, demonstrating the value of combining self-supervised pre-training and contrastive learning for this task.

This paper explores the impact of different back-translation approaches on machine translation for Ladin, specifically the Val Badia variant. Given the limited amount of parallel data available for this language (only 18k Ladin-Italian sentence pairs), we investigate the performance of a multilingual neural machine translation model fine-tuned for Ladin-Italian. In addition to the available authentic data, we synthesise further translations by using three different models: a fine-tuned neural model, a rule-based system developed specifically for this language pair, and a large language model. Our experiments show that all approaches achieve comparable translation quality in this low-resource scenario, yet round-trip translations highlight differences in model performance.

We present a statistical model for German medical natural language processing trained for named entity recognition (NER) as an open, publicly available model. The work serves as a refined successor to our first GERNERMED model which is substantially outperformed by our work. We demonstrate the effectiveness of combining multiple techniques in order to achieve strong results in entity recognition performance by the means of transfer-learning on pretrained deep language models (LM), word-alignment and neural machine translation. Due to the sparse situation on open, public medical entity recognition models for German texts, this work offers benefits to the German research community on medical NLP as a baseline model. Since our model is based on public English data, its weights are provided without legal restrictions on usage and distribution. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED-pp

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model - GatorTron - using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on 5 clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve 5 clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

With 17,000 pairs of Sicilian-English translated sentences, Arba Sicula developed the first neural machine translator for the Sicilian language. Using small subword vocabularies, we trained small Transformer models with high dropout parameters and achieved BLEU scores in the upper 20s. Then we supplemented our dataset with backtranslation and multilingual translation and pushed our scores into the mid 30s. We also attribute our success to incorporating theoretical information in our dataset. Prior to training, we biased the subword vocabulary towards the desinences one finds in a textbook. And we included textbook exercises in our dataset.

This paper investigates the challenges of developing large language models (LLMs) proficient in both multilingual understanding and medical knowledge. We demonstrate that simply translating medical data does not guarantee strong performance on clinical tasks in the target language. Our experiments reveal that the optimal language mix in training data varies significantly across different medical tasks. We find that larger models with carefully calibrated language ratios achieve superior performance on native-language clinical tasks. Furthermore, our results suggest that relying solely on fine-tuning may not be the most effective approach for incorporating new language knowledge into LLMs. Instead, data and computationally intensive pretraining methods may still be necessary to achieve optimal performance in multilingual medical settings. These findings provide valuable guidance for building effective and inclusive medical AI systems for diverse linguistic communities.

Large Language Models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), enabling new ways to analyze data, treat patients, and conduct research. This bibliometric review aims to provide a panoramic view of how LLMs have been used in BHI by examining research articles and collaboration networks from 2022 to 2023. It further explores how LLMs can improve Natural Language Processing (NLP) applications in various BHI areas like medical diagnosis, patient engagement, electronic health record management, and personalized medicine. To do this, our bibliometric review identifies key trends, maps out research networks, and highlights major developments in this fast-moving field. Lastly, it discusses the ethical concerns and practical challenges of using LLMs in BHI, such as data privacy and reliable medical recommendations. Looking ahead, we consider how LLMs could further transform biomedical research as well as healthcare delivery and patient outcomes. This bibliometric review serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI.

One of the biggest challenges that prohibit the use of many current NLP methods in clinical settings is the availability of public datasets. In this work, we present MeDAL, a large medical text dataset curated for abbreviation disambiguation, designed for natural language understanding pre-training in the medical domain. We pre-trained several models of common architectures on this dataset and empirically showed that such pre-training leads to improved performance and convergence speed when fine-tuning on downstream medical tasks.

We present Latin BERT, a contextual language model for the Latin language, trained on 642.7 million words from a variety of sources spanning the Classical era to the 21st century. In a series of case studies, we illustrate the affordances of this language-specific model both for work in natural language processing for Latin and in using computational methods for traditional scholarship: we show that Latin BERT achieves a new state of the art for part-of-speech tagging on all three Universal Dependency datasets for Latin and can be used for predicting missing text (including critical emendations); we create a new dataset for assessing word sense disambiguation for Latin and demonstrate that Latin BERT outperforms static word embeddings; and we show that it can be used for semantically-informed search by querying contextual nearest neighbors. We publicly release trained models to help drive future work in this space.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

Recent advancements in the field of natural language processing (NLP) and especially large language models (LLMs) and their numerous applications have brought research attention to design of different document processing tools and enhancements in the process of document archiving, search and retrieval. Domain of official, legal documents is especially interesting due to vast amount of data generated on the daily basis, as well as the significant community of interested practitioners (lawyers, law offices, administrative workers, state institutions and citizens). Providing efficient ways for automation of everyday work involving legal documents is therefore expected to have significant impact in different fields. In this work we present one LLM based solution for Named Entity Recognition (NER) in the case of legal documents written in Serbian language. It leverages on the pre-trained bidirectional encoder representations from transformers (BERT), which had been carefully adapted to the specific task of identifying and classifying specific data points from textual content. Besides novel dataset development for Serbian language (involving public court rulings), presented system design and applied methodology, the paper also discusses achieved performance metrics and their implications for objective assessment of the proposed solution. Performed cross-validation tests on the created manually labeled dataset with mean F_1 score of 0.96 and additional results on the examples of intentionally modified text inputs confirm applicability of the proposed system design and robustness of the developed NER solution.

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

In natural language processing (NLP), there is a need for more resources in Portuguese, since much of the data used in the state-of-the-art research is in other languages. In this paper, we pretrain a T5 model on the BrWac corpus, an extensive collection of web pages in Portuguese, and evaluate its performance against other Portuguese pretrained models and multilingual models on three different tasks. We show that our Portuguese pretrained models have significantly better performance over the original T5 models. Moreover, we demonstrate the positive impact of using a Portuguese vocabulary. Our code and models are available at https://github.com/unicamp-dl/PTT5.

In this paper, we aim to develop an open-source, multilingual language model for medicine, that the benefits a wider, linguistically diverse audience from different regions. In general, we present the contribution from the following aspects: first, for multilingual medical-specific adaptation, we construct a new multilingual medical corpus, that contains approximately 25.5B tokens encompassing 6 main languages, termed as MMedC, that enables auto-regressive training for existing general LLMs. second, to monitor the development of multilingual LLMs in medicine, we propose a new multilingual medical multi-choice question-answering benchmark with rationale, termed as MMedBench; third, we have assessed a number of popular, opensource large language models (LLMs) on our benchmark, along with those further auto-regressive trained on MMedC, as a result, our final model, termed as MMedLM 2, with only 7B parameters, achieves superior performance compared to all other open-source models, even rivaling GPT-4 on MMedBench. We will make the resources publicly available, including code, model weights, and datasets.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

This study evaluates the performance of large language models (LLMs) as medical agents in Portuguese, aiming to develop a reliable and relevant virtual assistant for healthcare professionals. The HealthCareMagic-100k-en and MedQuAD datasets, translated from English using GPT-3.5, were used to fine-tune the ChatBode-7B model using the PEFT-QLoRA method. The InternLM2 model, with initial training on medical data, presented the best overall performance, with high precision and adequacy in metrics such as accuracy, completeness and safety. However, DrBode models, derived from ChatBode, exhibited a phenomenon of catastrophic forgetting of acquired medical knowledge. Despite this, these models performed frequently or even better in aspects such as grammaticality and coherence. A significant challenge was low inter-rater agreement, highlighting the need for more robust assessment protocols. This work paves the way for future research, such as evaluating multilingual models specific to the medical field, improving the quality of training data, and developing more consistent evaluation methodologies for the medical field.

This paper provides a comprehensive survey of the latest research on multilingual large language models (MLLMs). MLLMs not only are able to understand and generate language across linguistic boundaries, but also represent an important advancement in artificial intelligence. We first discuss the architecture and pre-training objectives of MLLMs, highlighting the key components and methodologies that contribute to their multilingual capabilities. We then discuss the construction of multilingual pre-training and alignment datasets, underscoring the importance of data quality and diversity in enhancing MLLM performance. An important focus of this survey is on the evaluation of MLLMs. We present a detailed taxonomy and roadmap covering the assessment of MLLMs' cross-lingual knowledge, reasoning, alignment with human values, safety, interpretability and specialized applications. Specifically, we extensively discuss multilingual evaluation benchmarks and datasets, and explore the use of LLMs themselves as multilingual evaluators. To enhance MLLMs from black to white boxes, we also address the interpretability of multilingual capabilities, cross-lingual transfer and language bias within these models. Finally, we provide a comprehensive review of real-world applications of MLLMs across diverse domains, including biology, medicine, computer science, mathematics and law. We showcase how these models have driven innovation and improvements in these specialized fields while also highlighting the challenges and opportunities in deploying MLLMs within diverse language communities and application scenarios. We listed the paper related in this survey and publicly available at https://github.com/tjunlp-lab/Awesome-Multilingual-LLMs-Papers.

Recently, Large Language Models (LLMs) have showcased remarkable capabilities in natural language understanding. While demonstrating proficiency in everyday conversations and question-answering situations, these models frequently struggle in domains that require precision, such as medical applications, due to their lack of domain-specific knowledge. In this paper, we describe the procedure for building a powerful, open-source language model specifically designed for medicine applications, termed as PMC-LLaMA. Our contributions are threefold: (i) we systematically investigate the process of adapting a general-purpose foundation language model towards medical domain, this involves data-centric knowledge injection through the integration of 4.8M biomedical academic papers and 30K medical textbooks, as well as comprehensive fine-tuning for alignment with domain-specific instructions; (ii) we contribute a large-scale, comprehensive dataset for instruction tuning. This dataset encompasses medical question-answering (QA), rationale for reasoning, and conversational dialogues, comprising a total of 202M tokens; (iii) we conduct thorough ablation studies to demonstrate the effectiveness of each proposed component. While evaluating on various public medical question-answering benchmarks, our lightweight PMCLLaMA, which consists of only 13 billion parameters, exhibits superior performance, even surpassing ChatGPT. All models, codes, datasets can be found in https://github.com/chaoyi-wu/PMC-LLaMA.

Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires abundant query-article annotations that are difficult to obtain in biomedicine. As a result, most biomedical IR systems only conduct lexical matching. In response, we introduce BioCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot biomedical IR. To train BioCPT, we collected an unprecedented scale of 255 million user click logs from PubMed. With such data, we use contrastive learning to train a pair of closely-integrated retriever and re-ranker. Experimental results show that BioCPT sets new state-of-the-art performance on five biomedical IR tasks, outperforming various baselines including much larger models such as GPT-3-sized cpt-text-XL. In addition, BioCPT also generates better biomedical article and sentence representations for semantic evaluations. As such, BioCPT can be readily applied to various real-world biomedical IR tasks. BioCPT API and code are publicly available at https://github.com/ncbi/BioCPT.

The paper describes the open Russian medical language understanding benchmark covering several task types (classification, question answering, natural language inference, named entity recognition) on a number of novel text sets. Given the sensitive nature of the data in healthcare, such a benchmark partially closes the problem of Russian medical dataset absence. We prepare the unified format labeling, data split, and evaluation metrics for new tasks. The remaining tasks are from existing datasets with a few modifications. A single-number metric expresses a model's ability to cope with the benchmark. Moreover, we implement several baseline models, from simple ones to neural networks with transformer architecture, and release the code. Expectedly, the more advanced models yield better performance, but even a simple model is enough for a decent result in some tasks. Furthermore, for all tasks, we provide a human evaluation. Interestingly the models outperform humans in the large-scale classification tasks. However, the advantage of natural intelligence remains in the tasks requiring more knowledge and reasoning.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

Pre-trained language models (PLMs), such as BERT and GPT, have revolutionized the field of NLP, not only in the general domain but also in the biomedical domain. Most prior efforts in building biomedical PLMs have resorted simply to domain adaptation and focused mainly on English. In this work we introduce eHealth, a Chinese biomedical PLM built from scratch with a new pre-training framework. This new framework pre-trains eHealth as a discriminator through both token- and sequence-level discrimination. The former is to detect input tokens corrupted by a generator and recover their original identities from plausible candidates, while the latter is to further distinguish corruptions of a same original sequence from those of others. As such, eHealth can learn language semantics at both token and sequence levels. Extensive experiments on 11 Chinese biomedical language understanding tasks of various forms verify the effectiveness and superiority of our approach. We release the pre-trained model at https://github.com/PaddlePaddle/Research/tree/master/KG/eHealth and will also release the code later.

Explaining Artificial Intelligence (AI) decisions is a major challenge nowadays in AI, in particular when applied to sensitive scenarios like medicine and law. However, the need to explain the rationale behind decisions is a main issue also for human-based deliberation as it is important to justify why a certain decision has been taken. Resident medical doctors for instance are required not only to provide a (possibly correct) diagnosis, but also to explain how they reached a certain conclusion. Developing new tools to aid residents to train their explanation skills is therefore a central objective of AI in education. In this paper, we follow this direction, and we present, to the best of our knowledge, the first multilingual dataset for Medical Question Answering where correct and incorrect diagnoses for a clinical case are enriched with a natural language explanation written by doctors. These explanations have been manually annotated with argument components (i.e., premise, claim) and argument relations (i.e., attack, support), resulting in the Multilingual CasiMedicos-Arg dataset which consists of 558 clinical cases in four languages (English, Spanish, French, Italian) with explanations, where we annotated 5021 claims, 2313 premises, 2431 support relations, and 1106 attack relations. We conclude by showing how competitive baselines perform over this challenging dataset for the argument mining task.

In this work, we study the task of classifying legal texts written in the Greek language. We introduce and make publicly available a novel dataset based on Greek legislation, consisting of more than 47 thousand official, categorized Greek legislation resources. We experiment with this dataset and evaluate a battery of advanced methods and classifiers, ranging from traditional machine learning and RNN-based methods to state-of-the-art Transformer-based methods. We show that recurrent architectures with domain-specific word embeddings offer improved overall performance while being competitive even to transformer-based models. Finally, we show that cutting-edge multilingual and monolingual transformer-based models brawl on the top of the classifiers' ranking, making us question the necessity of training monolingual transfer learning models as a rule of thumb. To the best of our knowledge, this is the first time the task of Greek legal text classification is considered in an open research project, while also Greek is a language with very limited NLP resources in general.

Despite the vast repository of global medical knowledge predominantly being in English, local languages are crucial for delivering tailored healthcare services, particularly in areas with limited medical resources. To extend the reach of medical AI advancements to a broader population, we aim to develop medical LLMs across the six most widely spoken languages, encompassing a global population of 6.1 billion. This effort culminates in the creation of the ApolloCorpora multilingual medical dataset and the XMedBench benchmark. In the multilingual medical benchmark, the released Apollo models, at various relatively-small sizes (i.e., 0.5B, 1.8B, 2B, 6B, and 7B), achieve the best performance among models of equivalent size. Especially, Apollo-7B is the state-of-the-art multilingual medical LLMs up to 70B. Additionally, these lite models could be used to improve the multi-lingual medical capabilities of larger models without fine-tuning in a proxy-tuning fashion. We will open-source training corpora, code, model weights and evaluation benchmark.

Since radiology reports needed for clinical practice and research are written and stored in free-text narrations, extraction of relative information for further analysis is difficult. In these circumstances, natural language processing (NLP) techniques can facilitate automatic information extraction and transformation of free-text formats to structured data. In recent years, deep learning (DL)-based models have been adapted for NLP experiments with promising results. Despite the significant potential of DL models based on artificial neural networks (ANN) and convolutional neural networks (CNN), the models face some limitations to implement in clinical practice. Transformers, another new DL architecture, have been increasingly applied to improve the process. Therefore, in this study, we propose a transformer-based fine-grained named entity recognition (NER) architecture for clinical information extraction. We collected 88 abdominopelvic sonography reports in free-text formats and annotated them based on our developed information schema. The text-to-text transfer transformer model (T5) and Scifive, a pre-trained domain-specific adaptation of the T5 model, were applied for fine-tuning to extract entities and relations and transform the input into a structured format. Our transformer-based model in this study outperformed previously applied approaches such as ANN and CNN models based on ROUGE-1, ROUGE-2, ROUGE-L, and BLEU scores of 0.816, 0.668, 0.528, and 0.743, respectively, while providing an interpretable structured report.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

Natural language inference (NLI) is formulated as a unified framework for solving various NLP problems such as relation extraction, question answering, summarization, etc. It has been studied intensively in the past few years thanks to the availability of large-scale labeled datasets. However, most existing studies focus on merely sentence-level inference, which limits the scope of NLI's application in downstream NLP problems. This work presents DocNLI -- a newly-constructed large-scale dataset for document-level NLI. DocNLI is transformed from a broad range of NLP problems and covers multiple genres of text. The premises always stay in the document granularity, whereas the hypotheses vary in length from single sentences to passages with hundreds of words. Additionally, DocNLI has pretty limited artifacts which unfortunately widely exist in some popular sentence-level NLI datasets. Our experiments demonstrate that, even without fine-tuning, a model pretrained on DocNLI shows promising performance on popular sentence-level benchmarks, and generalizes well to out-of-domain NLP tasks that rely on inference at document granularity. Task-specific fine-tuning can bring further improvements. Data, code, and pretrained models can be found at https://github.com/salesforce/DocNLI.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

Bangla -- ranked as the 6th most widely spoken language across the world (https://www.ethnologue.com/guides/ethnologue200), with 230 million native speakers -- is still considered as a low-resource language in the natural language processing (NLP) community. With three decades of research, Bangla NLP (BNLP) is still lagging behind mainly due to the scarcity of resources and the challenges that come with it. There is sparse work in different areas of BNLP; however, a thorough survey reporting previous work and recent advances is yet to be done. In this study, we first provide a review of Bangla NLP tasks, resources, and tools available to the research community; we benchmark datasets collected from various platforms for nine NLP tasks using current state-of-the-art algorithms (i.e., transformer-based models). We provide comparative results for the studied NLP tasks by comparing monolingual vs. multilingual models of varying sizes. We report our results using both individual and consolidated datasets and provide data splits for future research. We reviewed a total of 108 papers and conducted 175 sets of experiments. Our results show promising performance using transformer-based models while highlighting the trade-off with computational costs. We hope that such a comprehensive survey will motivate the community to build on and further advance the research on Bangla NLP.

Medical systematic reviews can be very costly and resource intensive. We explore how Large Language Models (LLMs) can support and be trained to perform literature screening when provided with a detailed set of selection criteria. Specifically, we instruction tune LLaMA and Guanaco models to perform abstract screening for medical systematic reviews. Our best model, Bio-SIEVE, outperforms both ChatGPT and trained traditional approaches, and generalises better across medical domains. However, there remains the challenge of adapting the model to safety-first scenarios. We also explore the impact of multi-task training with Bio-SIEVE-Multi, including tasks such as PICO extraction and exclusion reasoning, but find that it is unable to match single-task Bio-SIEVE's performance. We see Bio-SIEVE as an important step towards specialising LLMs for the biomedical systematic review process and explore its future developmental opportunities. We release our models, code and a list of DOIs to reconstruct our dataset for reproducibility.

Several medical Multimodal Large Languange Models (MLLMs) have been developed to address tasks involving visual images with textual instructions across various medical modalities, achieving impressive results. Most current medical generalist models are region-agnostic, treating the entire image as a holistic representation. However, they struggle to identify which specific regions they are focusing on when generating a sentence. To mimic the behavior of doctors, who typically begin by reviewing the entire image before concentrating on specific regions for a thorough evaluation, we aim to enhance the capability of medical MLLMs in understanding anatomical regions within entire medical scans. To achieve it, we first formulate Region-Centric tasks and construct a large-scale dataset, MedRegInstruct, to incorporate regional information into training. Combining our collected dataset with other medical multimodal corpora for training, we propose a Region-Aware medical MLLM, MedRegA, which is the first bilingual generalist medical AI system to simultaneously handle image-level and region-level medical vision-language tasks across a broad range of modalities. Our MedRegA not only enables three region-centric tasks, but also achieves the best performance for visual question answering, report generation and medical image classification over 8 modalities, showcasing significant versatility. Experiments demonstrate that our model can not only accomplish powerful performance across various medical vision-language tasks in bilingual settings, but also recognize and detect structures in multimodal medical scans, boosting the interpretability and user interactivity of medical MLLMs. Our project page is https://medrega.github.io.

Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such models do not take into consideration expert domain knowledge. In this work, we introduced UmlsBERT, a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. More specifically, the augmentation on UmlsBERT with the Unified Medical Language System (UMLS) Metathesaurus was performed in two ways: i) connecting words that have the same underlying `concept' in UMLS, and ii) leveraging semantic group knowledge in UMLS to create clinically meaningful input embeddings. By applying these two strategies, UmlsBERT can encode clinical domain knowledge into word embeddings and outperform existing domain-specific models on common named-entity recognition (NER) and clinical natural language inference clinical NLP tasks.

Large Language Models (LLMs) have shown the potential to significantly contribute to patient care, diagnostics, and administrative processes. Emerging biomedical LLMs address healthcare-specific challenges, including privacy demands and computational constraints. However, evaluation of these models has primarily been limited to non-clinical tasks, which do not reflect the complexity of practical clinical applications. Additionally, there has been no thorough comparison between biomedical and general-domain LLMs for clinical tasks. To fill this gap, we present the Clinical Language Understanding Evaluation (CLUE), a benchmark tailored to evaluate LLMs on real-world clinical tasks. CLUE includes two novel datasets derived from MIMIC IV discharge letters and four existing tasks designed to test the practical applicability of LLMs in healthcare settings. Our evaluation covers several biomedical and general domain LLMs, providing insights into their clinical performance and applicability. CLUE represents a step towards a standardized approach to evaluating and developing LLMs in healthcare to align future model development with the real-world needs of clinical application. We publish our evaluation and data generation scripts: https://github.com/dadaamin/CLUE

Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n = 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

A long-running goal of the clinical NLP community is the extraction of important variables trapped in clinical notes. However, roadblocks have included dataset shift from the general domain and a lack of public clinical corpora and annotations. In this work, we show that large language models, such as InstructGPT, perform well at zero- and few-shot information extraction from clinical text despite not being trained specifically for the clinical domain. Whereas text classification and generation performance have already been studied extensively in such models, here we additionally demonstrate how to leverage them to tackle a diverse set of NLP tasks which require more structured outputs, including span identification, token-level sequence classification, and relation extraction. Further, due to the dearth of available data to evaluate these systems, we introduce new datasets for benchmarking few-shot clinical information extraction based on a manual re-annotation of the CASI dataset for new tasks. On the clinical extraction tasks we studied, the GPT-3 systems significantly outperform existing zero- and few-shot baselines.

Two key obstacles in biomedical relation extraction (RE) are the scarcity of annotations and the prevalence of instances without explicitly pre-defined labels due to low annotation coverage. Existing approaches, which treat biomedical RE as a multi-class classification task, often result in poor generalization in low-resource settings and do not have the ability to make selective prediction on unknown cases but give a guess from seen relations, hindering the applicability of those approaches. We present NBR, which converts biomedical RE as natural language inference formulation through indirect supervision. By converting relations to natural language hypotheses, NBR is capable of exploiting semantic cues to alleviate annotation scarcity. By incorporating a ranking-based loss that implicitly calibrates abstinent instances, NBR learns a clearer decision boundary and is instructed to abstain on uncertain instances. Extensive experiments on three widely-used biomedical RE benchmarks, namely ChemProt, DDI and GAD, verify the effectiveness of NBR in both full-set and low-resource regimes. Our analysis demonstrates that indirect supervision benefits biomedical RE even when a domain gap exists, and combining NLI knowledge with biomedical knowledge leads to the best performance gains.

The increasing number of benchmarks for Natural Language Processing (NLP) tasks in the computational job market domain highlights the demand for methods that can handle job-related tasks such as skill extraction, skill classification, job title classification, and de-identification. While some approaches have been developed that are specific to the job market domain, there is a lack of generalized, multilingual models and benchmarks for these tasks. In this study, we introduce a language model called ESCOXLM-R, based on XLM-R, which uses domain-adaptive pre-training on the European Skills, Competences, Qualifications and Occupations (ESCO) taxonomy, covering 27 languages. The pre-training objectives for ESCOXLM-R include dynamic masked language modeling and a novel additional objective for inducing multilingual taxonomical ESCO relations. We comprehensively evaluate the performance of ESCOXLM-R on 6 sequence labeling and 3 classification tasks in 4 languages and find that it achieves state-of-the-art results on 6 out of 9 datasets. Our analysis reveals that ESCOXLM-R performs better on short spans and outperforms XLM-R on entity-level and surface-level span-F1, likely due to ESCO containing short skill and occupation titles, and encoding information on the entity-level.

Although recent advances in scaling large language models (LLMs) have resulted in improvements on many NLP tasks, it remains unclear whether these models trained primarily with general web text are the right tool in highly specialized, safety critical domains such as clinical text. Recent results have suggested that LLMs encode a surprising amount of medical knowledge. This raises an important question regarding the utility of smaller domain-specific language models. With the success of general-domain LLMs, is there still a need for specialized clinical models? To investigate this question, we conduct an extensive empirical analysis of 12 language models, ranging from 220M to 175B parameters, measuring their performance on 3 different clinical tasks that test their ability to parse and reason over electronic health records. As part of our experiments, we train T5-Base and T5-Large models from scratch on clinical notes from MIMIC III and IV to directly investigate the efficiency of clinical tokens. We show that relatively small specialized clinical models substantially outperform all in-context learning approaches, even when finetuned on limited annotated data. Further, we find that pretraining on clinical tokens allows for smaller, more parameter-efficient models that either match or outperform much larger language models trained on general text. We release the code and the models used under the PhysioNet Credentialed Health Data license and data use agreement.

This paper presents RISC, an open-source Python package data generator (https://github.com/GRAAL-Research/risc). RISC generates look-alike automobile insurance contracts based on the Quebec regulatory insurance form in French and English. Insurance contracts are 90 to 100 pages long and use complex legal and insurance-specific vocabulary for a layperson. Hence, they are a much more complex class of documents than those in traditional NLP corpora. Therefore, we introduce RISCBAC, a Realistic Insurance Synthetic Bilingual Automobile Contract dataset based on the mandatory Quebec car insurance contract. The dataset comprises 10,000 French and English unannotated insurance contracts. RISCBAC enables NLP research for unsupervised automatic summarisation, question answering, text simplification, machine translation and more. Moreover, it can be further automatically annotated as a dataset for supervised tasks such as NER

In Brazil, the governmental body responsible for overseeing and coordinating post-graduate programs, CAPES, keeps records of all theses and dissertations presented in the country. Information regarding such documents can be accessed online in the Theses and Dissertations Catalog (TDC), which contains abstracts in Portuguese and English, and additional metadata. Thus, this database can be a potential source of parallel corpora for the Portuguese and English languages. In this article, we present the development of a parallel corpus from TDC, which is made available by CAPES under the open data initiative. Approximately 240,000 documents were collected and aligned using the Hunalign tool. We demonstrate the capability of our developed corpus by training Statistical Machine Translation (SMT) and Neural Machine Translation (NMT) models for both language directions, followed by a comparison with Google Translate (GT). Both translation models presented better BLEU scores than GT, with NMT system being the most accurate one. Sentence alignment was also manually evaluated, presenting an average of 82.30% correctly aligned sentences. Our parallel corpus is freely available in TMX format, with complementary information regarding document metadata

Large language models (LLM) have demonstrated remarkable capabilities in various biomedical natural language processing (NLP) tasks, leveraging the demonstration within the input context to adapt to new tasks. However, LLM is sensitive to the selection of demonstrations. To address the hallucination issue inherent in LLM, retrieval-augmented LLM (RAL) offers a solution by retrieving pertinent information from an established database. Nonetheless, existing research work lacks rigorous evaluation of the impact of retrieval-augmented large language models on different biomedical NLP tasks. This deficiency makes it challenging to ascertain the capabilities of RAL within the biomedical domain. Moreover, the outputs from RAL are affected by retrieving the unlabeled, counterfactual, or diverse knowledge that is not well studied in the biomedical domain. However, such knowledge is common in the real world. Finally, exploring the self-awareness ability is also crucial for the RAL system. So, in this paper, we systematically investigate the impact of RALs on 5 different biomedical tasks (triple extraction, link prediction, classification, question answering, and natural language inference). We analyze the performance of RALs in four fundamental abilities, including unlabeled robustness, counterfactual robustness, diverse robustness, and negative awareness. To this end, we proposed an evaluation framework to assess the RALs' performance on different biomedical NLP tasks and establish four different testbeds based on the aforementioned fundamental abilities. Then, we evaluate 3 representative LLMs with 3 different retrievers on 5 tasks over 9 datasets.

The Scielo database is an important source of scientific information in Latin America, containing articles from several research domains. A striking characteristic of Scielo is that many of its full-text contents are presented in more than one language, thus being a potential source of parallel corpora. In this article, we present the development of a parallel corpus from Scielo in three languages: English, Portuguese, and Spanish. Sentences were automatically aligned using the Hunalign algorithm for all language pairs, and for a subset of trilingual articles also. We demonstrate the capabilities of our corpus by training a Statistical Machine Translation system (Moses) for each language pair, which outperformed related works on scientific articles. Sentence alignment was also manually evaluated, presenting an average of 98.8% correctly aligned sentences across all languages. Our parallel corpus is freely available in the TMX format, with complementary information regarding article metadata.

The advancement of natural language processing (NLP) systems in healthcare hinges on language model ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient's medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba, with 130 million and 2.8 billion parameters, demonstrates a superior performance in modeling clinical language across extended text lengths compared to Mamba and clinical Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and accuracy, outperforming existing clinical language models and general domain large models like GPT-4 in longitudinal clinical notes information extraction tasks.

Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical domain. Despite the effectiveness, these models have hundreds of millions of parameters and are computationally expensive when applied to large-scale NLP applications. We hypothesized that the number of parameters of the original BERT can be dramatically reduced with minor impact on performance. In this study, we present Bioformer, a compact BERT model for biomedical text mining. We pretrained two Bioformer models (named Bioformer8L and Bioformer16L) which reduced the model size by 60% compared to BERTBase. Bioformer uses a biomedical vocabulary and was pre-trained from scratch on PubMed abstracts and PubMed Central full-text articles. We thoroughly evaluated the performance of Bioformer as well as existing biomedical BERT models including BioBERT and PubMedBERT on 15 benchmark datasets of four different biomedical NLP tasks: named entity recognition, relation extraction, question answering and document classification. The results show that with 60% fewer parameters, Bioformer16L is only 0.1% less accurate than PubMedBERT while Bioformer8L is 0.9% less accurate than PubMedBERT. Both Bioformer16L and Bioformer8L outperformed BioBERTBase-v1.1. In addition, Bioformer16L and Bioformer8L are 2-3 fold as fast as PubMedBERT/BioBERTBase-v1.1. Bioformer has been successfully deployed to PubTator Central providing gene annotations over 35 million PubMed abstracts and 5 million PubMed Central full-text articles. We make Bioformer publicly available via https://github.com/WGLab/bioformer, including pre-trained models, datasets, and instructions for downstream use.

As large language models (LLMs) gain popularity among speakers of diverse languages, we believe that it is crucial to benchmark them to better understand model behaviors, failures, and limitations in languages beyond English. In this work, we evaluate LLM APIs (ChatGPT, GPT-3, and GPT-4) on the Japanese national medical licensing examinations from the past five years, including the current year. Our team comprises native Japanese-speaking NLP researchers and a practicing cardiologist based in Japan. Our experiments show that GPT-4 outperforms ChatGPT and GPT-3 and passes all six years of the exams, highlighting LLMs' potential in a language that is typologically distant from English. However, our evaluation also exposes critical limitations of the current LLM APIs. First, LLMs sometimes select prohibited choices that should be strictly avoided in medical practice in Japan, such as suggesting euthanasia. Further, our analysis shows that the API costs are generally higher and the maximum context size is smaller for Japanese because of the way non-Latin scripts are currently tokenized in the pipeline. We release our benchmark as Igaku QA as well as all model outputs and exam metadata. We hope that our results and benchmark will spur progress on more diverse applications of LLMs. Our benchmark is available at https://github.com/jungokasai/IgakuQA.

Despite Greece's pivotal role in the global economy, large language models (LLMs) remain underexplored for Greek financial context due to the linguistic complexity of Greek and the scarcity of domain-specific datasets. Previous efforts in multilingual financial natural language processing (NLP) have exposed considerable performance disparities, yet no dedicated Greek financial benchmarks or Greek-specific financial LLMs have been developed until now. To bridge this gap, we introduce Plutus-ben, the first Greek Financial Evaluation Benchmark, and Plutus-8B, the pioneering Greek Financial LLM, fine-tuned with Greek domain-specific data. Plutus-ben addresses five core financial NLP tasks in Greek: numeric and textual named entity recognition, question answering, abstractive summarization, and topic classification, thereby facilitating systematic and reproducible LLM assessments. To underpin these tasks, we present three novel, high-quality Greek financial datasets, thoroughly annotated by expert native Greek speakers, augmented by two existing resources. Our comprehensive evaluation of 22 LLMs on Plutus-ben reveals that Greek financial NLP remains challenging due to linguistic complexity, domain-specific terminology, and financial reasoning gaps. These findings underscore the limitations of cross-lingual transfer, the necessity for financial expertise in Greek-trained models, and the challenges of adapting financial LLMs to Greek text. We release Plutus-ben, Plutus-8B, and all associated datasets publicly to promote reproducible research and advance Greek financial NLP, fostering broader multilingual inclusivity in finance.

Recently, it has been found that monolingual English language models can be used as knowledge bases. Instead of structural knowledge base queries, masked sentences such as "Paris is the capital of [MASK]" are used as probes. We translate the established benchmarks TREx and GoogleRE into 53 languages. Working with mBERT, we investigate three questions. (i) Can mBERT be used as a multilingual knowledge base? Most prior work only considers English. Extending research to multiple languages is important for diversity and accessibility. (ii) Is mBERT's performance as knowledge base language-independent or does it vary from language to language? (iii) A multilingual model is trained on more text, e.g., mBERT is trained on 104 Wikipedias. Can mBERT leverage this for better performance? We find that using mBERT as a knowledge base yields varying performance across languages and pooling predictions across languages improves performance. Conversely, mBERT exhibits a language bias; e.g., when queried in Italian, it tends to predict Italy as the country of origin.

Large language models (LLMs) are transforming the ways the general public accesses and consumes information. Their influence is particularly pronounced in pivotal sectors like healthcare, where lay individuals are increasingly appropriating LLMs as conversational agents for everyday queries. While LLMs demonstrate impressive language understanding and generation proficiencies, concerns regarding their safety remain paramount in these high-stake domains. Moreover, the development of LLMs is disproportionately focused on English. It remains unclear how these LLMs perform in the context of non-English languages, a gap that is critical for ensuring equity in the real-world use of these systems.This paper provides a framework to investigate the effectiveness of LLMs as multi-lingual dialogue systems for healthcare queries. Our empirically-derived framework XlingEval focuses on three fundamental criteria for evaluating LLM responses to naturalistic human-authored health-related questions: correctness, consistency, and verifiability. Through extensive experiments on four major global languages, including English, Spanish, Chinese, and Hindi, spanning three expert-annotated large health Q&A datasets, and through an amalgamation of algorithmic and human-evaluation strategies, we found a pronounced disparity in LLM responses across these languages, indicating a need for enhanced cross-lingual capabilities. We further propose XlingHealth, a cross-lingual benchmark for examining the multilingual capabilities of LLMs in the healthcare context. Our findings underscore the pressing need to bolster the cross-lingual capacities of these models, and to provide an equitable information ecosystem accessible to all.

In this work, we compare the domain-specific translation performance of open-source autoregressive decoder-only large language models (LLMs) with task-oriented machine translation (MT) models. Our experiments focus on the medical domain and cover four language pairs with varied resource availability: English-to-French, English-to-Portuguese, English-to-Swahili, and Swahili-to-English. Despite recent advancements, LLMs exhibit a clear gap in specialized translation quality compared to multilingual encoder-decoder MT models such as NLLB-200. In three out of four language directions in our study, NLLB-200 3.3B outperforms all LLMs in the size range of 8B parameters in medical translation. While fine-tuning LLMs such as Mistral and Llama improves their performance at medical translation, these models still fall short compared to fine-tuned NLLB-200 3.3B models. Our findings highlight the ongoing need for specialized MT models to achieve higher-quality domain-specific translation, especially in medium-resource and low-resource settings. As larger LLMs outperform their 8B variants, this also encourages pre-training domain-specific medium-sized LMs to improve quality and efficiency in specialized translation tasks.

Medical benchmark datasets significantly contribute to developing Large Language Models (LLMs) for medical knowledge extraction, diagnosis, summarization, and other uses. Yet, current benchmarks are mainly derived from exam questions given to medical students or cases described in the medical literature, lacking the complexity of real-world patient cases that deviate from classic textbook abstractions. These include rare diseases, uncommon presentations of common diseases, and unexpected treatment responses. Here, we construct Clinically Uncommon Patient Cases and Diagnosis Dataset (CUPCase) based on 3,562 real-world case reports from BMC, including diagnoses in open-ended textual format and as multiple-choice options with distractors. Using this dataset, we evaluate the ability of state-of-the-art LLMs, including both general-purpose and Clinical LLMs, to identify and correctly diagnose a patient case, and test models' performance when only partial information about cases is available. Our findings show that general-purpose GPT-4o attains the best performance in both the multiple-choice task (average accuracy of 87.9%) and the open-ended task (BERTScore F1 of 0.764), outperforming several LLMs with a focus on the medical domain such as Meditron-70B and MedLM-Large. Moreover, GPT-4o was able to maintain 87% and 88% of its performance with only the first 20% of tokens of the case presentation in multiple-choice and free text, respectively, highlighting the potential of LLMs to aid in early diagnosis in real-world cases. CUPCase expands our ability to evaluate LLMs for clinical decision support in an open and reproducible manner.

This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Biomedical Named Entity Recognition and Linking, data splits for training and testing are included in the release, and a baseline model and its metrics for entity linking are also described.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

Objective To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning. Methods We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (i.e., trainable vectors) with frozen LLM, where the LLM parameters were not updated (i.e., frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models. Results and Conclusion The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ~3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4~10% for clinical abbreviation disambiguation, and 5.5~9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the ``one model for all`` promise from training to deployment using a unified generative LLM.

Objective: To improve performance of medical entity normalization across many languages, especially when fewer language resources are available compared to English. Materials and Methods: We introduce xMEN, a modular system for cross-lingual medical entity normalization, which performs well in both low- and high-resource scenarios. When synonyms in the target language are scarce for a given terminology, we leverage English aliases via cross-lingual candidate generation. For candidate ranking, we incorporate a trainable cross-encoder model if annotations for the target task are available. We also evaluate cross-encoders trained in a weakly supervised manner based on machine-translated datasets from a high resource domain. Our system is publicly available as an extensible Python toolkit. Results: xMEN improves the state-of-the-art performance across a wide range of multilingual benchmark datasets. Weakly supervised cross-encoders are effective when no training data is available for the target task. Through the compatibility of xMEN with the BigBIO framework, it can be easily used with existing and prospective datasets. Discussion: Our experiments show the importance of balancing the output of general-purpose candidate generators with subsequent trainable re-rankers, which we achieve through a rank regularization term in the loss function of the cross-encoder. However, error analysis reveals that multi-word expressions and other complex entities are still challenging. Conclusion: xMEN exhibits strong performance for medical entity normalization in multiple languages, even when no labeled data and few terminology aliases for the target language are available. Its configuration system and evaluation modules enable reproducible benchmarks. Models and code are available online at the following URL: https://github.com/hpi-dhc/xmen

Multilingual automatic speech recognition (ASR) in the medical domain serves as a foundational task for various downstream applications such as speech translation, spoken language understanding, and voice-activated assistants. This technology enhances patient care by enabling efficient communication across language barriers, alleviating specialized workforce shortages, and facilitating improved diagnosis and treatment, particularly during pandemics. In this work, we introduce MultiMed, a collection of small-to-large end-to-end ASR models for the medical domain, spanning five languages: Vietnamese, English, German, French, and Mandarin Chinese, together with the corresponding real-world ASR dataset. To our best knowledge, MultiMed stands as the largest and the first multilingual medical ASR dataset, in terms of total duration, number of speakers, diversity of diseases, recording conditions, speaker roles, unique medical terms, accents, and ICD-10 codes. Secondly, we establish the empirical baselines, present the first reproducible study of multilinguality in medical ASR, conduct a layer-wise ablation study for end-to-end ASR training, and provide the first linguistic analysis for multilingual medical ASR. All code, data, and models are available online https://github.com/leduckhai/MultiMed/tree/master/MultiMed

Information Extraction (IE) from text refers to the task of extracting structured knowledge from unstructured text. The task typically consists of a series of sub-tasks such as Named Entity Recognition and Relation Extraction. Sourcing entity and relation type specific training data is a major bottleneck in domains with limited resources such as biomedicine. In this work we present a slot filling approach to the task of biomedical IE, effectively replacing the need for entity and relation-specific training data, allowing us to deal with zero-shot settings. We follow the recently proposed paradigm of coupling a Tranformer-based bi-encoder, Dense Passage Retrieval, with a Transformer-based reading comprehension model to extract relations from biomedical text. We assemble a biomedical slot filling dataset for both retrieval and reading comprehension and conduct a series of experiments demonstrating that our approach outperforms a number of simpler baselines. We also evaluate our approach end-to-end for standard as well as zero-shot settings. Our work provides a fresh perspective on how to solve biomedical IE tasks, in the absence of relevant training data. Our code, models and datasets are available at https://github.com/ypapanik/biomedical-slot-filling.

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

This paper introduces EventNet-ITA, a large, multi-domain corpus annotated with event frames for Italian, and presents an efficient approach for multi-label Frame Parsing. The approach is then evaluated on the dataset. Covering a wide range of individual, social and historical phenomena, the main contribution of EventNet-ITA is to provide the research community with a resource for textual event mining and a novel and extensive tool for Frame Parsing in Italian.

Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language. Meanwhile, there is a growing need for applications that can understand the public's voice in the health domain. To address this we introduce a new corpus called COMETA, consisting of 20k English biomedical entity mentions from Reddit expert-annotated with links to SNOMED CT, a widely-used medical knowledge graph. Our corpus satisfies a combination of desirable properties, from scale and coverage to diversity and quality, that to the best of our knowledge has not been met by any of the existing resources in the field. Through benchmark experiments on 20 EL baselines from string- to neural-based models we shed light on the ability of these systems to perform complex inference on entities and concepts under 2 challenging evaluation scenarios. Our experimental results on COMETA illustrate that no golden bullet exists and even the best mainstream techniques still have a significant performance gap to fill, while the best solution relies on combining different views of data.

In Indonesia, local languages play an integral role in the culture. However, the available Indonesian language resources still fall into the category of limited data in the Natural Language Processing (NLP) field. This is become problematic when build NLP model for these languages. To address this gap, we introduce Bhinneka Korpus, a multilingual parallel corpus featuring five Indonesian local languages. Our goal is to enhance access and utilization of these resources, extending their reach within the country. We explained in a detail the dataset collection process and associated challenges. Additionally, we experimented with translation task using the IBM Model 1 due to data constraints. The result showed that the performance of each language already shows good indications for further development. Challenges such as lexical variation, smoothing effects, and cross-linguistic variability are discussed. We intend to evaluate the corpus using advanced NLP techniques for low-resource languages, paving the way for multilingual translation models.

Keyphrase generation is the task consisting in generating a set of words or phrases that highlight the main topics of a document. There are few datasets for keyphrase generation in the biomedical domain and they do not meet the expectations in terms of size for training generative models. In this paper, we introduce kp-biomed, the first large-scale biomedical keyphrase generation dataset with more than 5M documents collected from PubMed abstracts. We train and release several generative models and conduct a series of experiments showing that using large scale datasets improves significantly the performances for present and absent keyphrase generation. The dataset is available under CC-BY-NC v4.0 license at https://huggingface.co/ datasets/taln-ls2n/kpbiomed.

Word embeddings and pre-trained language models allow to build rich representations of text and have enabled improvements across most NLP tasks. Unfortunately they are very expensive to train, and many small companies and research groups tend to use models that have been pre-trained and made available by third parties, rather than building their own. This is suboptimal as, for many languages, the models have been trained on smaller (or lower quality) corpora. In addition, monolingual pre-trained models for non-English languages are not always available. At best, models for those languages are included in multilingual versions, where each language shares the quota of substrings and parameters with the rest of the languages. This is particularly true for smaller languages such as Basque. In this paper we show that a number of monolingual models (FastText word embeddings, FLAIR and BERT language models) trained with larger Basque corpora produce much better results than publicly available versions in downstream NLP tasks, including topic classification, sentiment classification, PoS tagging and NER. This work sets a new state-of-the-art in those tasks for Basque. All benchmarks and models used in this work are publicly available.

The rapid development of Large Language Models (LLMs) and the emergence of novel abilities with scale have necessitated the construction of holistic, diverse and challenging benchmarks such as HELM and BIG-bench. However, at the moment, most of these benchmarks focus only on performance in English and evaluations that include Southeast Asian (SEA) languages are few in number. We therefore propose BHASA, a holistic linguistic and cultural evaluation suite for LLMs in SEA languages. It comprises three components: (1) a NLP benchmark covering eight tasks across Natural Language Understanding (NLU), Generation (NLG) and Reasoning (NLR) tasks, (2) LINDSEA, a linguistic diagnostic toolkit that spans the gamut of linguistic phenomena including syntax, semantics and pragmatics, and (3) a cultural diagnostics dataset that probes for both cultural representation and sensitivity. For this preliminary effort, we implement the NLP benchmark only for Indonesian, Vietnamese, Thai and Tamil, and we only include Indonesian and Tamil for LINDSEA and the cultural diagnostics dataset. As GPT-4 is purportedly one of the best-performing multilingual LLMs at the moment, we use it as a yardstick to gauge the capabilities of LLMs in the context of SEA languages. Our initial experiments on GPT-4 with BHASA find it lacking in various aspects of linguistic capabilities, cultural representation and sensitivity in the targeted SEA languages. BHASA is a work in progress and will continue to be improved and expanded in the future. The repository for this paper can be found at: https://github.com/aisingapore/BHASA