Daily Papers

We present a systematic study of healthcare-domain cross-lingual transfer to address the scarcity of biomedical NMT resources for Arabic-script languages. We use Arabic and Persian as higher-resource pivots to improve translation for four severely low-resource targets: Dari (Afghan Persian, a standardised variety of Persian), Pashto, Sorani Kurdish (Central Kurdish, a major standardized variety of Kurdish), and Urdu (closely related to Hindi). Using LoRA fine-tuning on small decoder-only LLMs, we train domain-specific pivot adapters and evaluate three transfer strategies: few-shot in-context learning, minimal supervised adaptation, and, to the best of our knowledge, for the first time in this setting, zero-data LoRA adapter merging. Supervised adaptation with just 500 sentences achieves near pivot-language quality for Dari (CHrF++ 41.01) and meaningful gains for Urdu (28.88), while adapter merging reaches within 3.5 CHrF++ of supervised adaptation for Dari at zero additional cost. Pashto and Sorani Kurdish remain insufficient for high-stakes clinical deployment exposing the limits of cross-lingual transfer when structural distance from the pivots is too great. LoRA adapter merging works surprisingly well for closely related languages, even without target-language biomedical data.

The basic concept in Neural Machine Translation (NMT) is to train a large Neural Network that maximizes the translation performance on a given parallel corpus. NMT is then using a simple left-to-right beam-search decoder to generate new translations that approximately maximize the trained conditional probability. The current beam search strategy generates the target sentence word by word from left-to- right while keeping a fixed amount of active candidates at each time step. First, this simple search is less adaptive as it also expands candidates whose scores are much worse than the current best. Secondly, it does not expand hypotheses if they are not within the best scoring candidates, even if their scores are close to the best one. The latter one can be avoided by increasing the beam size until no performance improvement can be observed. While you can reach better performance, this has the draw- back of a slower decoding speed. In this paper, we concentrate on speeding up the decoder by applying a more flexible beam search strategy whose candidate size may vary at each time step depending on the candidate scores. We speed up the original decoder by up to 43% for the two language pairs German-English and Chinese-English without losing any translation quality.

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.

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.

Neural Machine Translation (NMT) is an end-to-end learning approach for automated translation, with the potential to overcome many of the weaknesses of conventional phrase-based translation systems. Unfortunately, NMT systems are known to be computationally expensive both in training and in translation inference. Also, most NMT systems have difficulty with rare words. These issues have hindered NMT's use in practical deployments and services, where both accuracy and speed are essential. In this work, we present GNMT, Google's Neural Machine Translation system, which attempts to address many of these issues. Our model consists of a deep LSTM network with 8 encoder and 8 decoder layers using attention and residual connections. To improve parallelism and therefore decrease training time, our attention mechanism connects the bottom layer of the decoder to the top layer of the encoder. To accelerate the final translation speed, we employ low-precision arithmetic during inference computations. To improve handling of rare words, we divide words into a limited set of common sub-word units ("wordpieces") for both input and output. This method provides a good balance between the flexibility of "character"-delimited models and the efficiency of "word"-delimited models, naturally handles translation of rare words, and ultimately improves the overall accuracy of the system. Our beam search technique employs a length-normalization procedure and uses a coverage penalty, which encourages generation of an output sentence that is most likely to cover all the words in the source sentence. On the WMT'14 English-to-French and English-to-German benchmarks, GNMT achieves competitive results to state-of-the-art. Using a human side-by-side evaluation on a set of isolated simple sentences, it reduces translation errors by an average of 60% compared to Google's phrase-based production system.

In Africa, and the world at large, there is an increasing focus on developing Neural Machine Translation (NMT) systems to overcome language barriers. NMT for Low-resource language is particularly compelling as it involves learning with limited labelled data. However, obtaining a well-aligned parallel corpus for low-resource languages can be challenging. The disparity between the technological advancement of a few global languages and the lack of research on NMT for local languages in Chad is striking. End-to-end NMT trials on low-resource Chad languages have not been attempted. Additionally, there is a dearth of online and well-structured data gathering for research in Natural Language Processing, unlike some African languages. However, a guided approach for data gathering can produce bitext data for many Chadian language translation pairs with well-known languages that have ample data. In this project, we created the first sba-Fr Dataset, which is a corpus of Ngambay-to-French translations, and fine-tuned three pre-trained models using this dataset. Our experiments show that the M2M100 model outperforms other models with high BLEU scores on both original and original+synthetic data. The publicly available bitext dataset can be used for research purposes.

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.

Differently from the traditional statistical MT that decomposes the translation task into distinct separately learned components, neural machine translation uses a single neural network to model the entire translation process. Despite neural machine translation being de-facto standard, it is still not clear how NMT models acquire different competences over the course of training, and how this mirrors the different models in traditional SMT. In this work, we look at the competences related to three core SMT components and find that during training, NMT first focuses on learning target-side language modeling, then improves translation quality approaching word-by-word translation, and finally learns more complicated reordering patterns. We show that this behavior holds for several models and language pairs. Additionally, we explain how such an understanding of the training process can be useful in practice and, as an example, show how it can be used to improve vanilla non-autoregressive neural machine translation by guiding teacher model selection.

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.

Unsupervised Neural Machine Translation (UNMT) focuses on improving NMT results under the assumption there is no human translated parallel data, yet little work has been done so far in highlighting its advantages compared to supervised methods and analyzing its output in aspects other than translation accuracy. We focus on three very diverse languages, French, Gujarati, and Kazakh, and train bilingual NMT models, to and from English, with various levels of supervision, in high- and low- resource setups, measure quality of the NMT output and compare the generated sequences' word order and semantic similarity to source and reference sentences. We also use Layer-wise Relevance Propagation to evaluate the source and target sentences' contribution to the result, expanding the findings of previous works to the UNMT paradigm.

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.

Direct neural machine translation (direct NMT) is a type of NMT system that translates text between two non-English languages. Direct NMT systems often face limitations due to the scarcity of parallel data between non-English language pairs. Several approaches have been proposed to address this limitation, such as multilingual NMT and pivot NMT (translation between two languages via English). Task-level Mixture of expert models (Task-level MoE), an inference-efficient variation of Transformer-based models, has shown promising NMT performance for a large number of language pairs. In Task-level MoE, different language groups can use different routing strategies to optimize cross-lingual learning and inference speed. In this work, we examine Task-level MoE's applicability in direct NMT and propose a series of high-performing training and evaluation configurations, through which Task-level MoE-based direct NMT systems outperform bilingual and pivot-based models for a large number of low and high-resource direct pairs, and translation directions. Our Task-level MoE with 16 experts outperforms bilingual NMT, Pivot NMT models for 7 language pairs, while pivot-based models still performed better in 9 pairs and directions.

Neural Machine Translation (NMT) models are typically trained on datasets with limited exposure to Scientific, Technical and Educational domains. Translation models thus, in general, struggle with tasks that involve scientific understanding or technical jargon. Their performance is found to be even worse for low-resource Indian languages. Finding a translation dataset that tends to these domains in particular, poses a difficult challenge. In this paper, we address this by creating a multilingual parallel corpus containing more than 2.8 million rows of English-to-Indic and Indic-to-Indic high-quality translation pairs across 8 Indian languages. We achieve this by bitext mining human-translated transcriptions of NPTEL video lectures. We also finetune and evaluate NMT models using this corpus and surpass all other publicly available models at in-domain tasks. We also demonstrate the potential for generalizing to out-of-domain translation tasks by improving the baseline by over 2 BLEU on average for these Indian languages on the Flores+ benchmark. We are pleased to release our model and dataset via this link: https://huggingface.co/SPRINGLab.

Machine translation (MT) in the medical domain plays a pivotal role in enhancing healthcare quality and disseminating medical knowledge. Despite advancements in English-Thai MT technology, common MT approaches often underperform in the medical field due to their inability to precisely translate medical terminologies. Our research prioritizes not merely improving translation accuracy but also maintaining medical terminology in English within the translated text through code-switched (CS) translation. We developed a method to produce CS medical translation data, fine-tuned a CS translation model with this data, and evaluated its performance against strong baselines, such as Google Neural Machine Translation (NMT) and GPT-3.5/GPT-4. Our model demonstrated competitive performance in automatic metrics and was highly favored in human preference evaluations. Our evaluation result also shows that medical professionals significantly prefer CS translations that maintain critical English terms accurately, even if it slightly compromises fluency. Our code and test set are publicly available https://github.com/preceptorai-org/NLLB_CS_EM_NLP2024.

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

The quality of machine translation is rapidly evolving. Today one can find several machine translation systems on the web that provide reasonable translations, although the systems are not perfect. In some specific domains, the quality may decrease. A recently proposed approach to this domain is neural machine translation. It aims at building a jointly-tuned single neural network that maximizes translation performance, a very different approach from traditional statistical machine translation. Recently proposed neural machine translation models often belong to the encoder-decoder family in which a source sentence is encoded into a fixed length vector that is, in turn, decoded to generate a translation. The present research examines the effects of different training methods on a Polish-English Machine Translation system used for medical data. The European Medicines Agency parallel text corpus was used as the basis for training of neural and statistical network-based translation systems. The main machine translation evaluation metrics have also been used in analysis of the systems. A comparison and implementation of a real-time medical translator is the main focus of our experiments.

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.

In recent years, Neural Machine Translation (NMT) has been shown to be more effective than phrase-based statistical methods, thus quickly becoming the state of the art in machine translation (MT). However, NMT systems are limited in translating low-resourced languages, due to the significant amount of parallel data that is required to learn useful mappings between languages. In this work, we show how the so-called multilingual NMT can help to tackle the challenges associated with low-resourced language translation. The underlying principle of multilingual NMT is to force the creation of hidden representations of words in a shared semantic space across multiple languages, thus enabling a positive parameter transfer across languages. Along this direction, we present multilingual translation experiments with three languages (English, Italian, Romanian) covering six translation directions, utilizing both recurrent neural networks and transformer (or self-attentive) neural networks. We then focus on the zero-shot translation problem, that is how to leverage multi-lingual data in order to learn translation directions that are not covered by the available training material. To this aim, we introduce our recently proposed iterative self-training method, which incrementally improves a multilingual NMT on a zero-shot direction by just relying on monolingual data. Our results on TED talks data show that multilingual NMT outperforms conventional bilingual NMT, that the transformer NMT outperforms recurrent NMT, and that zero-shot NMT outperforms conventional pivoting methods and even matches the performance of a fully-trained bilingual system.

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the biomedical domain by exploring strategies to enhance their performance for the NER task. Our study reveals the importance of meticulously designed prompts in the biomedical. Strategic selection of in-context examples yields a marked improvement, offering ~15-20\% increase in F1 score across all benchmark datasets for biomedical few-shot NER. Additionally, our results indicate that integrating external biomedical knowledge via prompting strategies can enhance the proficiency of general-purpose LLMs to meet the specialized needs of biomedical NER. Leveraging a medical knowledge base, our proposed method, DiRAG, inspired by Retrieval-Augmented Generation (RAG), can boost the zero-shot F1 score of LLMs for biomedical NER. Code is released at https://github.com/masoud-monajati/LLM_Bio_NER

With the advent of the Transformer architecture, Neural Machine Translation (NMT) results have shown great improvement lately. However, results in low-resource conditions still lag behind in both bilingual and multilingual setups, due to the limited amount of available monolingual and/or parallel data; hence, the need for methods addressing data scarcity in an efficient, and explainable way, is eminent. We propose an explainability-based training approach for NMT, applied in Unsupervised and Supervised model training, for translation of three languages of varying resources, French, Gujarati, Kazakh, to and from English. Our results show our method can be promising, particularly when training in low-resource conditions, outperforming simple training baselines; though the improvement is marginal, it sets the ground for further exploration of the approach and the parameters, and its extension to other languages.

In this paper, we have shown the improvement of English to Bharti Braille machine translation system. We have shown how we can improve a baseline NMT model by adding some linguistic knowledge to it. This was done for five language pairs where English sentences were translated into five Indian languages and then subsequently to corresponding Bharti Braille. This has been demonstrated by adding a sub-module for translating multi-word expressions. The approach shows promising results as across language pairs, we could see improvement in the quality of NMT outputs. The least improvement was observed in English-Nepali language pair with 22.08% and the most improvement was observed in the English-Hindi language pair with 23.30%.

Processing of multi-word expressions (MWEs) is a known problem for any natural language processing task. Even neural machine translation (NMT) struggles to overcome it. This paper presents results of experiments on investigating NMT attention allocation to the MWEs and improving automated translation of sentences that contain MWEs in English->Latvian and English->Czech NMT systems. Two improvement strategies were explored -(1) bilingual pairs of automatically extracted MWE candidates were added to the parallel corpus used to train the NMT system, and (2) full sentences containing the automatically extracted MWE candidates were added to the parallel corpus. Both approaches allowed to increase automated evaluation results. The best result - 0.99 BLEU point increase - has been reached with the first approach, while with the second approach minimal improvements achieved. We also provide open-source software and tools used for MWE extraction and alignment inspection.

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.

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.

Does multilingual Neural Machine Translation (NMT) lead to The Curse of the Multlinguality or provides the Cross-lingual Knowledge Transfer within a language family? In this study, we explore multiple approaches for extending the available data-regime in NMT and we prove cross-lingual benefits even in 0-shot translation regime for low-resource languages. With this paper, we provide state-of-the-art open-source NMT models for translating between selected Slavic languages. We released our models on the HuggingFace Hub (https://hf.co/collections/allegro/multislav-6793d6b6419e5963e759a683) under the CC BY 4.0 license. Slavic language family comprises morphologically rich Central and Eastern European languages. Although counting hundreds of millions of native speakers, Slavic Neural Machine Translation is under-studied in our opinion. Recently, most NMT research focuses either on: high-resource languages like English, Spanish, and German - in WMT23 General Translation Task 7 out of 8 task directions are from or to English; massively multilingual models covering multiple language groups; or evaluation techniques.

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.

Despite impressive progress in high-resource settings, Neural Machine Translation (NMT) still struggles in low-resource and out-of-domain scenarios, often failing to match the quality of phrase-based translation. We propose a novel technique that combines back-translation and multilingual NMT to improve performance in these difficult cases. Our technique trains a single model for both directions of a language pair, allowing us to back-translate source or target monolingual data without requiring an auxiliary model. We then continue training on the augmented parallel data, enabling a cycle of improvement for a single model that can incorporate any source, target, or parallel data to improve both translation directions. As a byproduct, these models can reduce training and deployment costs significantly compared to uni-directional models. Extensive experiments show that our technique outperforms standard back-translation in low-resource scenarios, improves quality on cross-domain tasks, and effectively reduces costs across the board.

Recent research in neural machine translation (NMT) has shown that training on high-quality machine-generated data can outperform training on human-generated data. This work accompanies the first-ever release of a LLM-generated, MBR-decoded and QE-reranked dataset with both sentence-level and multi-sentence examples. We perform extensive experiments to demonstrate the quality of our dataset in terms of its downstream impact on NMT model performance. We find that training from scratch on our (machine-generated) dataset outperforms training on the (web-crawled) WMT'23 training dataset (which is 300 times larger), and also outperforms training on the top-quality subset of the WMT'23 training dataset. We also find that performing self-distillation by finetuning the LLM which generated this dataset outperforms the LLM's strong few-shot baseline. These findings corroborate the quality of our dataset, and demonstrate the value of high-quality machine-generated data in improving performance of NMT models.

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.

Neural machine translation (NMT) offers a novel alternative formulation of translation that is potentially simpler than statistical approaches. However to reach competitive performance, NMT models need to be exceedingly large. In this paper we consider applying knowledge distillation approaches (Bucila et al., 2006; Hinton et al., 2015) that have proven successful for reducing the size of neural models in other domains to the problem of NMT. We demonstrate that standard knowledge distillation applied to word-level prediction can be effective for NMT, and also introduce two novel sequence-level versions of knowledge distillation that further improve performance, and somewhat surprisingly, seem to eliminate the need for beam search (even when applied on the original teacher model). Our best student model runs 10 times faster than its state-of-the-art teacher with little loss in performance. It is also significantly better than a baseline model trained without knowledge distillation: by 4.2/1.7 BLEU with greedy decoding/beam search. Applying weight pruning on top of knowledge distillation results in a student model that has 13 times fewer parameters than the original teacher model, with a decrease of 0.4 BLEU.

Interest in neural machine translation has grown rapidly as its effectiveness has been demonstrated across language and data scenarios. New research regularly introduces architectural and algorithmic improvements that lead to significant gains over "vanilla" NMT implementations. However, these new techniques are rarely evaluated in the context of previously published techniques, specifically those that are widely used in state-of-theart production and shared-task systems. As a result, it is often difficult to determine whether improvements from research will carry over to systems deployed for real-world use. In this work, we recommend three specific methods that are relatively easy to implement and result in much stronger experimental systems. Beyond reporting significantly higher BLEU scores, we conduct an in-depth analysis of where improvements originate and what inherent weaknesses of basic NMT models are being addressed. We then compare the relative gains afforded by several other techniques proposed in the literature when starting with vanilla systems versus our stronger baselines, showing that experimental conclusions may change depending on the baseline chosen. This indicates that choosing a strong baseline is crucial for reporting reliable experimental results.

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.

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

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.

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.

It has been shown that the performance of neural machine translation (NMT) drops starkly in low-resource conditions, underperforming phrase-based statistical machine translation (PBSMT) and requiring large amounts of auxiliary data to achieve competitive results. In this paper, we re-assess the validity of these results, arguing that they are the result of lack of system adaptation to low-resource settings. We discuss some pitfalls to be aware of when training low-resource NMT systems, and recent techniques that have shown to be especially helpful in low-resource settings, resulting in a set of best practices for low-resource NMT. In our experiments on German--English with different amounts of IWSLT14 training data, we show that, without the use of any auxiliary monolingual or multilingual data, an optimized NMT system can outperform PBSMT with far less data than previously claimed. We also apply these techniques to a low-resource Korean-English dataset, surpassing previously reported results by 4 BLEU.

An attentional mechanism has lately been used to improve neural machine translation (NMT) by selectively focusing on parts of the source sentence during translation. However, there has been little work exploring useful architectures for attention-based NMT. This paper examines two simple and effective classes of attentional mechanism: a global approach which always attends to all source words and a local one that only looks at a subset of source words at a time. We demonstrate the effectiveness of both approaches over the WMT translation tasks between English and German in both directions. With local attention, we achieve a significant gain of 5.0 BLEU points over non-attentional systems which already incorporate known techniques such as dropout. Our ensemble model using different attention architectures has established a new state-of-the-art result in the WMT'15 English to German translation task with 25.9 BLEU points, an improvement of 1.0 BLEU points over the existing best system backed by NMT and an n-gram reranker.

The field of neural machine translation (NMT) has changed with the advent of large language models (LLMs). Much of the recent emphasis in natural language processing (NLP) has been on modeling machine translation and many other problems using a single pre-trained Transformer decoder, while encoder-decoder architectures, which were the standard in earlier NMT models, have received relatively less attention. In this paper, we explore translation models that are universal, efficient, and easy to optimize, by marrying the world of LLMs with the world of NMT. We apply LLMs to NMT encoding and leave the NMT decoder unchanged. We also develop methods for adapting LLMs to work better with the NMT decoder. Furthermore, we construct a new dataset involving multiple tasks to assess how well the machine translation system generalizes across various tasks. Evaluations on the WMT and our datasets show that results using our method match or surpass a range of baselines in terms of translation quality, but achieve 2.4 sim 6.5 times inference speedups and a 75% reduction in the memory footprint of the KV cache. It also demonstrates strong generalization across a variety of translation-related tasks.

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text through discriminative tasks. However, encoders have seen slower development compared to decoder models, leading to limited domain adaptation in biomedical and clinical settings. We introduce BioClinical ModernBERT, a domain-adapted encoder that builds on the recent ModernBERT release, incorporating long-context processing and substantial improvements in speed and performance for biomedical and clinical NLP. BioClinical ModernBERT is developed through continued pretraining on the largest biomedical and clinical corpus to date, with over 53.5 billion tokens, and addresses a key limitation of prior clinical encoders by leveraging 20 datasets from diverse institutions, domains, and geographic regions, rather than relying on data from a single source. It outperforms existing biomedical and clinical encoders on four downstream tasks spanning a broad range of use cases. We release both base (150M parameters) and large (396M parameters) versions of BioClinical ModernBERT, along with training checkpoints to support further research.

Single-task models have proven pivotal in solving specific tasks; however, they have limitations in real-world applications where multi-tasking is necessary and domain shifts are exhibited. Recently, instructional prompts have shown significant improvement towards multi-task generalization; however, the effect of instructional prompts and Multi-Task Learning (MTL) has not been systematically studied in the biomedical domain. Motivated by this, this paper explores the impact of instructional prompts for biomedical MTL. We introduce the BoX, a collection of 32 instruction tasks for Biomedical NLP across (X) various categories. Using this meta-dataset, we propose a unified model termed In-BoXBART, that can jointly learn all tasks of the BoX without any task-specific modules. To the best of our knowledge, this is the first attempt to propose a unified model in the biomedical domain and use instructions to achieve generalization across several biomedical tasks. Experimental results indicate that the proposed model: 1) outperforms the single-task baseline by ~3% and multi-task (without instruction) baseline by ~18% on an average, and 2) shows ~23% improvement compared to the single-task baseline in few-shot learning (i.e., 32 instances per task) on an average. Our analysis indicates that there is significant room for improvement across tasks in the BoX, implying the scope for future research direction.

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.

The principal task in supervised neural machine translation (NMT) is to learn to generate target sentences conditioned on the source inputs from a set of parallel sentence pairs, and thus produce a model capable of generalizing to unseen instances. However, it is commonly observed that the generalization performance of the model is highly influenced by the amount of parallel data used in training. Although data augmentation is widely used to enrich the training data, conventional methods with discrete manipulations fail to generate diverse and faithful training samples. In this paper, we present a novel data augmentation paradigm termed Continuous Semantic Augmentation (CsaNMT), which augments each training instance with an adjacency semantic region that could cover adequate variants of literal expression under the same meaning. We conduct extensive experiments on both rich-resource and low-resource settings involving various language pairs, including WMT14 English-{German,French}, NIST Chinese-English and multiple low-resource IWSLT translation tasks. The provided empirical evidences show that CsaNMT sets a new level of performance among existing augmentation techniques, improving on the state-of-the-art by a large margin. The core codes are contained in Appendix E.

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.

The end-to-end nature of neural machine translation (NMT) removes many ways of manually guiding the translation process that were available in older paradigms. Recent work, however, has introduced a new capability: lexically constrained or guided decoding, a modification to beam search that forces the inclusion of pre-specified words and phrases in the output. However, while theoretically sound, existing approaches have computational complexities that are either linear (Hokamp and Liu, 2017) or exponential (Anderson et al., 2017) in the number of constraints. We present a algorithm for lexically constrained decoding with a complexity of O(1) in the number of constraints. We demonstrate the algorithms remarkable ability to properly place these constraints, and use it to explore the shaky relationship between model and BLEU scores. Our implementation is available as part of Sockeye.

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.

Neural machine translation (NMT) has achieved great successes with large datasets, so NMT is more premised on high-resource languages. This continuously underpins the low resource languages such as Luganda due to the lack of high-quality parallel corpora, so even 'Google translate' does not serve Luganda at the time of this writing. In this paper, we build a parallel corpus with 41,070 pairwise sentences for Luganda and English which is based on three different open-sourced corpora. Then, we train NMT models with hyper-parameter search on the dataset. Experiments gave us a BLEU score of 21.28 from Luganda to English and 17.47 from English to Luganda. Some translation examples show high quality of the translation. We believe that our model is the first Luganda-English NMT model. The bilingual dataset we built will be available to the public.

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.

Recent studies have revealed a number of pathologies of neural machine translation (NMT) systems. Hypotheses explaining these mostly suggest there is something fundamentally wrong with NMT as a model or its training algorithm, maximum likelihood estimation (MLE). Most of this evidence was gathered using maximum a posteriori (MAP) decoding, a decision rule aimed at identifying the highest-scoring translation, i.e. the mode. We argue that the evidence corroborates the inadequacy of MAP decoding more than casts doubt on the model and its training algorithm. In this work, we show that translation distributions do reproduce various statistics of the data well, but that beam search strays from such statistics. We show that some of the known pathologies and biases of NMT are due to MAP decoding and not to NMT's statistical assumptions nor MLE. In particular, we show that the most likely translations under the model accumulate so little probability mass that the mode can be considered essentially arbitrary. We therefore advocate for the use of decision rules that take into account the translation distribution holistically. We show that an approximation to minimum Bayes risk decoding gives competitive results confirming that NMT models do capture important aspects of translation well in expectation.

Recent advances in neural machine translation (NMT) have pushed the quality of machine translation systems to the point where they are becoming widely adopted to build competitive systems. However, there is still a large number of languages that are yet to reap the benefits of NMT. In this paper, we provide the first large-scale case study of the practical application of MT in the Turkic language family in order to realize the gains of NMT for Turkic languages under high-resource to extremely low-resource scenarios. In addition to presenting an extensive analysis that identifies the bottlenecks towards building competitive systems to ameliorate data scarcity, our study has several key contributions, including, i) a large parallel corpus covering 22 Turkic languages consisting of common public datasets in combination with new datasets of approximately 2 million parallel sentences, ii) bilingual baselines for 26 language pairs, iii) novel high-quality test sets in three different translation domains and iv) human evaluation scores. All models, scripts, and data will be released to the public.

Most translation tasks among languages belong to the zero-resource translation problem where parallel corpora are unavailable. Multilingual neural machine translation (MNMT) enables one-pass translation using shared semantic space for all languages compared to the two-pass pivot translation but often underperforms the pivot-based method. In this paper, we propose a novel method, named as Unified Multilingual Multiple teacher-student Model for NMT (UM4). Our method unifies source-teacher, target-teacher, and pivot-teacher models to guide the student model for the zero-resource translation. The source teacher and target teacher force the student to learn the direct source to target translation by the distilled knowledge on both source and target sides. The monolingual corpus is further leveraged by the pivot-teacher model to enhance the student model. Experimental results demonstrate that our model of 72 directions significantly outperforms previous methods on the WMT benchmark.

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

Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult to estimate their performance on datasets containing biomedical texts as the word distributions of general and biomedical corpora are quite different. Moreover, the medical domain has long-tail concepts and terminologies that are difficult to be learned via language models. For the Chinese biomedical text, it is more difficult due to its complex structure and the variety of phrase combinations. In this paper, we investigate how the recently introduced pre-trained language model BERT can be adapted for Chinese biomedical corpora and propose a novel conceptualized representation learning approach. We also release a new Chinese Biomedical Language Understanding Evaluation benchmark (ChineseBLUE). We examine the effectiveness of Chinese pre-trained models: BERT, BERT-wwm, RoBERTa, and our approach. Experimental results on the benchmark show that our approach could bring significant gain. We release the pre-trained model on GitHub: https://github.com/alibaba-research/ChineseBLUE.

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.

The evolution of Neural Machine Translation (NMT) has been significantly influenced by six core challenges (Koehn and Knowles, 2017), which have acted as benchmarks for progress in this field. This study revisits these challenges, offering insights into their ongoing relevance in the context of advanced Large Language Models (LLMs): domain mismatch, amount of parallel data, rare word prediction, translation of long sentences, attention model as word alignment, and sub-optimal beam search. Our empirical findings indicate that LLMs effectively lessen the reliance on parallel data for major languages in the pretraining phase. Additionally, the LLM-based translation system significantly enhances the translation of long sentences that contain approximately 80 words and shows the capability to translate documents of up to 512 words. However, despite these significant improvements, the challenges of domain mismatch and prediction of rare words persist. While the challenges of word alignment and beam search, specifically associated with NMT, may not apply to LLMs, we identify three new challenges for LLMs in translation tasks: inference efficiency, translation of low-resource languages in the pretraining phase, and human-aligned evaluation. The datasets and models are released at https://github.com/pangjh3/LLM4MT.

Neural machine translation (NMT) has progressed rapidly over the past several years, and modern models are able to achieve relatively high quality using only monolingual text data, an approach dubbed Unsupervised Machine Translation (UNMT). However, these models still struggle in a variety of ways, including aspects of translation that for a human are the easiest - for instance, correctly translating common nouns. This work explores a cheap and abundant resource to combat this problem: bilingual lexica. We test the efficacy of bilingual lexica in a real-world set-up, on 200-language translation models trained on web-crawled text. We present several findings: (1) using lexical data augmentation, we demonstrate sizable performance gains for unsupervised translation; (2) we compare several families of data augmentation, demonstrating that they yield similar improvements, and can be combined for even greater improvements; (3) we demonstrate the importance of carefully curated lexica over larger, noisier ones, especially with larger models; and (4) we compare the efficacy of multilingual lexicon data versus human-translated parallel data. Finally, we open-source GATITOS (available at https://github.com/google-research/url-nlp/tree/main/gatitos), a new multilingual lexicon for 26 low-resource languages, which had the highest performance among lexica in our experiments.

Biomedical text mining and question-answering are essential yet highly demanding tasks, particularly in the face of the exponential growth of biomedical literature. In this work, we present our participation in the 13th edition of the BioASQ challenge, which involves biomedical semantic question-answering for Task 13b and biomedical question-answering for developing topics for the Synergy task. We deploy a selection of open-source large language models (LLMs) as retrieval-augmented generators to answer biomedical questions. Various models are used to process the questions. A majority voting system combines their output to determine the final answer for Yes/No questions, while for list and factoid type questions, the union of their answers in used. We evaluated 13 state-of-the-art open source LLMs, exploring all possible model combinations to contribute to the final answer, resulting in tailored LLM pipelines for each question type. Our findings provide valuable insight into which combinations of LLMs consistently produce superior results for specific question types. In the four rounds of the 2025 BioASQ challenge, our system achieved notable results: in the Synergy task, we secured 1st place for ideal answers and 2nd place for exact answers in round 2, as well as two shared 1st places for exact answers in round 3 and 4.

Large Language Models (LLMs) have demonstrated impressive capabilities across natural language processing tasks. However, their application to specialized domains such as medicine and biology requires further optimization to ensure factual accuracy, reliability, and contextual depth. We introduce MedBioLM, a domain-adapted biomedical question-answering model designed to enhance both short-form and long-form queries. By integrating fine-tuning and retrieval-augmented generation (RAG), MedBioLM dynamically incorporates domain-specific knowledge, improving reasoning abilities and factual accuracy. To evaluate its effectiveness, we fine-tuned the model on diverse biomedical QA datasets, covering structured multiple-choice assessments and complex clinical reasoning tasks. Fine-tuning significantly improves accuracy on benchmark datasets, while RAG enhances factual consistency. These results highlight the potential of domain-optimized LLMs in advancing biomedical research, medical education, and clinical decision support.

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

Neural machine translation (NMT) methods developed for natural language processing have been shown to be highly successful in automating translation from one natural language to another. Recently, these NMT methods have been adapted to the generation of program code. In NMT for code generation, the task is to generate output source code that satisfies constraints expressed in the input. In the literature, a variety of different input scenarios have been explored, including generating code based on natural language description, lower-level representations such as binary or assembly (neural decompilation), partial representations of source code (code completion and repair), and source code in another language (code translation). In this paper we survey the NMT for code generation literature, cataloging the variety of methods that have been explored according to input and output representations, model architectures, optimization techniques used, data sets, and evaluation methods. We discuss the limitations of existing methods and future research directions

Large Language Models (LLMs) are at the forefront of NLP achievements but fall short in dealing with shortcut learning, factual inconsistency, and vulnerability to adversarial inputs.These shortcomings are especially critical in medical contexts, where they can misrepresent actual model capabilities. Addressing this, we present SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for ClinicalTrials. Our contributions include the refined NLI4CT-P dataset (i.e., Natural Language Inference for Clinical Trials - Perturbed), designed to challenge LLMs with interventional and causal reasoning tasks, along with a comprehensive evaluation of methods and results for participant submissions. A total of 106 participants registered for the task contributing to over 1200 individual submissions and 25 system overview papers. This initiative aims to advance the robustness and applicability of NLI models in healthcare, ensuring safer and more dependable AI assistance in clinical decision-making. We anticipate that the dataset, models, and outcomes of this task can support future research in the field of biomedical NLI. The dataset, competition leaderboard, and website are publicly available.

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.

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.

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model, nach0, capable of solving various chemical and biological tasks: biomedical question answering, named entity recognition, molecular generation, molecular synthesis, attributes prediction, and others. nach0 is a multi-domain and multi-task encoder-decoder LLM pre-trained on unlabeled text from scientific literature, patents, and molecule strings to incorporate a range of chemical and linguistic knowledge. We employed instruction tuning, where specific task-related instructions are utilized to fine-tune nach0 for the final set of tasks. To train nach0 effectively, we leverage the NeMo framework, enabling efficient parallel optimization of both base and large model versions. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on single-domain and cross-domain tasks. Furthermore, it can generate high-quality outputs in molecular and textual formats, showcasing its effectiveness in multi-domain setups.

Neural machine translation (NMT) for low-resource local languages in Indonesia faces significant challenges, including the need for a representative benchmark and limited data availability. This work addresses these challenges by comprehensively analyzing training NMT systems for four low-resource local languages in Indonesia: Javanese, Sundanese, Minangkabau, and Balinese. Our study encompasses various training approaches, paradigms, data sizes, and a preliminary study into using large language models for synthetic low-resource languages parallel data generation. We reveal specific trends and insights into practical strategies for low-resource language translation. Our research demonstrates that despite limited computational resources and textual data, several of our NMT systems achieve competitive performances, rivaling the translation quality of zero-shot gpt-3.5-turbo. These findings significantly advance NMT for low-resource languages, offering valuable guidance for researchers in similar contexts.

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.

Natural language inference (NLI) is critical for complex decision-making in biomedical domain. One key question, for example, is whether a given biomedical mechanism is supported by experimental evidence. This can be seen as an NLI problem but there are no directly usable datasets to address this. The main challenge is that manually creating informative negative examples for this task is difficult and expensive. We introduce a novel semi-supervised procedure that bootstraps an NLI dataset from existing biomedical dataset that pairs mechanisms with experimental evidence in abstracts. We generate a range of negative examples using nine strategies that manipulate the structure of the underlying mechanisms both with rules, e.g., flip the roles of the entities in the interaction, and, more importantly, as perturbations via logical constraints in a neuro-logical decoding system. We use this procedure to create a novel dataset for NLI in the biomedical domain, called BioNLI and benchmark two state-of-the-art biomedical classifiers. The best result we obtain is around mid 70s in F1, suggesting the difficulty of the task. Critically, the performance on the different classes of negative examples varies widely, from 97% F1 on the simple role change negative examples, to barely better than chance on the negative examples generated using neuro-logic decoding.

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.

Machine Translation (MT) is one of the most prominent tasks in Natural Language Processing (NLP) which involves the automatic conversion of texts from one natural language to another while preserving its meaning and fluency. Although the research in machine translation has been going on since multiple decades, the newer approach of integrating deep learning techniques in natural language processing has led to significant improvements in the translation quality. In this paper, we have developed a Neural Machine Translation (NMT) system by training the Transformer model to translate texts from Indian Language Hindi to English. Hindi being a low resource language has made it difficult for neural networks to understand the language thereby leading to a slow growth in the development of neural machine translators. Thus, to address this gap, we implemented back-translation to augment the training data and for creating the vocabulary, we experimented with both word and subword level tokenization using Byte Pair Encoding (BPE) thereby ending up training the Transformer in 10 different configurations. This led us to achieve a state-of-the-art BLEU score of 24.53 on the test set of IIT Bombay English-Hindi Corpus in one of the configurations.

Neural machine translation (NMT) systems have recently obtained state-of-the art in many machine translation systems between popular language pairs because of the availability of data. For low-resourced language pairs, there are few researches in this field due to the lack of bilingual data. In this paper, we attempt to build the first NMT systems for a low-resourced language pairs:Japanese-Vietnamese. We have also shown significant improvements when combining advanced methods to reduce the adverse impacts of data sparsity and improve the quality of NMT systems. In addition, we proposed a variant of Byte-Pair Encoding algorithm to perform effective word segmentation for Vietnamese texts and alleviate the rare-word problem that persists in NMT systems.

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.

Many works proposed methods to improve the performance of Neural Machine Translation (NMT) models in a domain/multi-domain adaptation scenario. However, an understanding of how NMT baselines represent text domain information internally is still lacking. Here we analyze the sentence representations learned by NMT Transformers and show that these explicitly include the information on text domains, even after only seeing the input sentences without domains labels. Furthermore, we show that this internal information is enough to cluster sentences by their underlying domains without supervision. We show that NMT models produce clusters better aligned to the actual domains compared to pre-trained language models (LMs). Notably, when computed on document-level, NMT cluster-to-domain correspondence nears 100%. We use these findings together with an approach to NMT domain adaptation using automatically extracted domains. Whereas previous work relied on external LMs for text clustering, we propose re-using the NMT model as a source of unsupervised clusters. We perform an extensive experimental study comparing two approaches across two data scenarios, three language pairs, and both sentence-level and document-level clustering, showing equal or significantly superior performance compared to LMs.

Neural Machine Translation (NMT) has improved translation by using Transformer-based models, but it still struggles with word ambiguity and context. This problem is especially important in domain-specific applications, which often have problems with unclear sentences or poor data quality. Our research explores how adding information to models can improve translations in the context of e-commerce data. To this end we create ConECT -- a new Czech-to-Polish e-commerce product translation dataset coupled with images and product metadata consisting of 11,400 sentence pairs. We then investigate and compare different methods that are applicable to context-aware translation. We test a vision-language model (VLM), finding that visual context aids translation quality. Additionally, we explore the incorporation of contextual information into text-to-text models, such as the product's category path or image descriptions. The results of our study demonstrate that the incorporation of contextual information leads to an improvement in the quality of machine translation. We make the new dataset publicly available.

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.

In this paper, we present Neural Phrase-based Machine Translation (NPMT). Our method explicitly models the phrase structures in output sequences using Sleep-WAke Networks (SWAN), a recently proposed segmentation-based sequence modeling method. To mitigate the monotonic alignment requirement of SWAN, we introduce a new layer to perform (soft) local reordering of input sequences. Different from existing neural machine translation (NMT) approaches, NPMT does not use attention-based decoding mechanisms. Instead, it directly outputs phrases in a sequential order and can decode in linear time. Our experiments show that NPMT achieves superior performances on IWSLT 2014 German-English/English-German and IWSLT 2015 English-Vietnamese machine translation tasks compared with strong NMT baselines. We also observe that our method produces meaningful phrases in output languages.

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

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 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.

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.

Although the problem of hallucinations in neural machine translation (NMT) has received some attention, research on this highly pathological phenomenon lacks solid ground. Previous work has been limited in several ways: it often resorts to artificial settings where the problem is amplified, it disregards some (common) types of hallucinations, and it does not validate adequacy of detection heuristics. In this paper, we set foundations for the study of NMT hallucinations. First, we work in a natural setting, i.e., in-domain data without artificial noise neither in training nor in inference. Next, we annotate a dataset of over 3.4k sentences indicating different kinds of critical errors and hallucinations. Then, we turn to detection methods and both revisit methods used previously and propose using glass-box uncertainty-based detectors. Overall, we show that for preventive settings, (i) previously used methods are largely inadequate, (ii) sequence log-probability works best and performs on par with reference-based methods. Finally, we propose DeHallucinator, a simple method for alleviating hallucinations at test time that significantly reduces the hallucinatory rate. To ease future research, we release our annotated dataset for WMT18 German-English data, along with the model, training data, and code.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

Medical reasoning in large language models (LLMs) aims to emulate clinicians' diagnostic thinking, but current benchmarks such as MedQA-USMLE, MedMCQA, and PubMedQA often mix reasoning with factual recall. We address this by separating 11 biomedical QA benchmarks into reasoning- and knowledge-focused subsets using a PubMedBERT classifier that reaches 81 percent accuracy, comparable to human performance. Our analysis shows that only 32.8 percent of questions require complex reasoning. We evaluate biomedical models (HuatuoGPT-o1, MedReason, m1) and general-domain models (DeepSeek-R1, o4-mini, Qwen3), finding consistent gaps between knowledge and reasoning performance. For example, m1 scores 60.5 on knowledge but only 47.1 on reasoning. In adversarial tests where models are misled with incorrect initial reasoning, biomedical models degrade sharply, while larger or RL-trained general models show more robustness. To address this, we train BioMed-R1 using fine-tuning and reinforcement learning on reasoning-heavy examples. It achieves the strongest performance among similarly sized models. Further gains may come from incorporating clinical case reports and training with adversarial and backtracking scenarios.

Neural machine translation (NMT) has progressed rapidly in the past few years, promising improvements and quality translations for different languages. Evaluation of this task is crucial to determine the quality of the translation. Overall, insufficient emphasis is placed on the actual sense of the translation in traditional methods. We propose a bidirectional semantic-based evaluation method designed to assess the sense distance of the translation from the source text. This approach employs the comprehensive multilingual encyclopedic dictionary BabelNet. Through the calculation of the semantic distance between the source and its back translation of the output, our method introduces a quantifiable approach that empowers sentence comparison on the same linguistic level. Factual analysis shows a strong correlation between the average evaluation scores generated by our method and the human assessments across various machine translation systems for English-German language pair. Finally, our method proposes a new multilingual approach to rank MT systems without the need for parallel corpora.

Conversational generative AI has demonstrated remarkable promise for empowering biomedical practitioners, but current investigations focus on unimodal text. Multimodal conversational AI has seen rapid progress by leveraging billions of image-text pairs from the public web, but such general-domain vision-language models still lack sophistication in understanding and conversing about biomedical images. In this paper, we propose a cost-efficient approach for training a vision-language conversational assistant that can answer open-ended research questions of biomedical images. The key idea is to leverage a large-scale, broad-coverage biomedical figure-caption dataset extracted from PubMed Central, use GPT-4 to self-instruct open-ended instruction-following data from the captions, and then fine-tune a large general-domain vision-language model using a novel curriculum learning method. Specifically, the model first learns to align biomedical vocabulary using the figure-caption pairs as is, then learns to master open-ended conversational semantics using GPT-4 generated instruction-following data, broadly mimicking how a layperson gradually acquires biomedical knowledge. This enables us to train a Large Language and Vision Assistant for BioMedicine (LLaVA-Med) in less than 15 hours (with eight A100s). LLaVA-Med exhibits excellent multimodal conversational capability and can follow open-ended instruction to assist with inquiries about a biomedical image. On three standard biomedical visual question answering datasets, LLaVA-Med outperforms previous supervised state-of-the-art on certain metrics. To facilitate biomedical multimodal research, we will release our instruction-following data and the LLaVA-Med model.

OpenNMT is an open-source toolkit for neural machine translation (NMT). The system prioritizes efficiency, modularity, and extensibility with the goal of supporting NMT research into model architectures, feature representations, and source modalities, while maintaining competitive performance and reasonable training requirements. The toolkit consists of modeling and translation support, as well as detailed pedagogical documentation about the underlying techniques. OpenNMT has been used in several production MT systems, modified for numerous research papers, and is implemented across several deep learning frameworks.

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.

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

In this paper, we introduce a unified and generalist Biomedical Generative Pre-trained Transformer (BiomedGPT) model, which leverages self-supervision on large and diverse datasets to accept multi-modal inputs and perform a range of downstream tasks. Our experiments demonstrate that BiomedGPT delivers expansive and inclusive representations of biomedical data, outperforming the majority of preceding state-of-the-art models across five distinct tasks with 20 public datasets spanning over 15 unique biomedical modalities. Through the ablation study, we also showcase the efficacy of our multi-modal and multi-task pretraining approach in transferring knowledge to previously unseen data. Overall, our work presents a significant step forward in developing unified and generalist models for biomedicine, with far-reaching implications for improving healthcare outcomes.

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.

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.

We present KokborokMT, a high-quality neural machine translation (NMT) system for Kokborok (ISO 639-3), a Tibeto-Burman language spoken primarily in Tripura, India with approximately 1.5 million speakers. Despite its status as an official language of Tripura, Kokborok has remained severely under-resourced in the NLP community, with prior machine translation attempts limited to systems trained on small Bible-derived corpora achieving BLEU scores below 7. We fine-tune the NLLB-200-distilled-600M model on a multi-source parallel corpus comprising 36,052 sentence pairs: 9,284 professionally translated sentences from the SMOL dataset, 1,769 Bible-domain sentences from WMT shared task data, and 24,999 synthetic back-translated pairs generated via Gemini Flash from Tatoeba English source sentences. We introduce as a new language token for Kokborok in the NLLB framework. Our best system achieves BLEU scores of 17.30 and 38.56 on held-out test sets, representing substantial improvements over prior published results. Human evaluation by three annotators yields mean adequacy of 3.74/5 and fluency of 3.70/5, with substantial agreement between trained evaluators.

Self-supervised learning in vision-language processing exploits semantic alignment between imaging and text modalities. Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images. This does not only introduce poor alignment between the modalities but also a missed opportunity to exploit rich self-supervision through existing temporal content in the data. In this work, we explicitly account for prior images and reports when available during both training and fine-tuning. Our approach, named BioViL-T, uses a CNN-Transformer hybrid multi-image encoder trained jointly with a text model. It is designed to be versatile to arising challenges such as pose variations and missing input images across time. The resulting model excels on downstream tasks both in single- and multi-image setups, achieving state-of-the-art performance on (I) progression classification, (II) phrase grounding, and (III) report generation, whilst offering consistent improvements on disease classification and sentence-similarity tasks. We release a novel multi-modal temporal benchmark dataset, MS-CXR-T, to quantify the quality of vision-language representations in terms of temporal semantics. Our experimental results show the advantages of incorporating prior images and reports to make most use of the data.

Simultaneous neural machine translation(SNMT) models start emitting the target sequence before they have processed the source sequence. The recent adaptive policies for SNMT use monotonic attention to perform read/write decisions based on the partial source and target sequences. The lack of sufficient information might cause the monotonic attention to take poor read/write decisions, which in turn negatively affects the performance of the SNMT model. On the other hand, human translators make better read/write decisions since they can anticipate the immediate future words using linguistic information and domain knowledge.Motivated by human translators, in this work, we propose a framework to aid monotonic attention with an external language model to improve its decisions.We conduct experiments on the MuST-C English-German and English-French speech-to-text translation tasks to show the effectiveness of the proposed framework.The proposed SNMT method improves the quality-latency trade-off over the state-of-the-art monotonic multihead attention.

When adapting an encoder to a new domain, the standard approach is to continue training with Masked Language Modeling (MLM). We show that temporarily switching to Causal Language Modeling (CLM) followed by a short MLM decay improves downstream performance. On biomedical texts with ModernBERT, this CLM detour outperforms MLM baselines trained on identical data and compute across 8 French and 11 English biomedical tasks, by +1.2-2.8pp and +0.3-0.8pp respectively, depending on model size. We investigate the reasons for these gains. We find that CLM's dense supervision impacts low transformer layers (0-7) far more than MLM does. Freezing low layers during CLM eliminates the downstream benefit; freezing mid layers preserves it. The representational changes persist through the MLM decay phase, even when it matches the CLM phase in length, and they scale with model capacity. We release ModernCamemBERT-bio and ModernBERT-bio as state-of-the-art biomedical encoders in Base and Large sizes.

Adding linguistic information (syntax or semantics) to neural machine translation (NMT) has mostly focused on using point estimates from pre-trained models. Directly using the capacity of massive pre-trained contextual word embedding models such as BERT (Devlin et al., 2019) has been marginally useful in NMT because effective fine-tuning is difficult to obtain for NMT without making training brittle and unreliable. We augment NMT by extracting dense fine-tuned vector-based linguistic information from BERT instead of using point estimates. Experimental results show that our method of incorporating linguistic information helps NMT to generalize better in a variety of training contexts and is no more difficult to train than conventional Transformer-based NMT.

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.

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.

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

Domain-specific neural machine translation (NMT) systems (e.g., in educational applications) are socially significant with the potential to help make information accessible to a diverse set of users in multilingual societies. It is desirable that such NMT systems be lexically constrained and draw from domain-specific dictionaries. Dictionaries could present multiple candidate translations for a source word/phrase due to the polysemous nature of words. The onus is then on the NMT model to choose the contextually most appropriate candidate. Prior work has largely ignored this problem and focused on the single candidate constraint setting wherein the target word or phrase is replaced by a single constraint. In this work we present DictDis, a lexically constrained NMT system that disambiguates between multiple candidate translations derived from dictionaries. We achieve this by augmenting training data with multiple dictionary candidates to actively encourage disambiguation during training by implicitly aligning multiple candidate constraints. We demonstrate the utility of DictDis via extensive experiments on English-Hindi and English-German sentences in a variety of domains including regulatory, finance, engineering. We also present comparisons on standard benchmark test datasets. In comparison with existing approaches for lexically constrained and unconstrained NMT, we demonstrate superior performance with respect to constraint copy and disambiguation related measures on all domains while also obtaining improved fluency of up to 2-3 BLEU points on some domains.

Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it is natural to explore how a general-purpose language model can be efficiently adapted for molecular science applications. In this work, we introduce BioMedGPT-Mol, a molecular language model designed to support molecular understanding and generation tasks. By curating and unifying existing public instruction datasets, we have assembled a large-scale, comprehensive, and high-quality training dataset. The model is then fine-tuned through a meticulously designed multi-task learning framework. On a consolidated benchmark derived from LlaSMol, TOMG-Bench, and MuMOInstruct, BioMedGPT-Mol achieves remarkable performance. Our experimental results demonstrate that a general-purpose reasoning model can be effectively and efficiently post-trained into a professional molecular language model through a well-structured multi-task curriculum. Leveraging these capabilities, we further apply the model to multi-step retrosynthetic planning, achieving state-of-the-art performance on RetroBench and demonstrating its superior efficacy as an end-to-end retrosynthetic planner. We anticipate that our approach can be extended to other biomedical scientific domains.

In this paper, we address the task of improving pair-wise machine translation for specific low resource Indian languages. Multilingual NMT models have demonstrated a reasonable amount of effectiveness on resource-poor languages. In this work, we show that the performance of these models can be significantly improved upon by using back-translation through a filtered back-translation process and subsequent fine-tuning on the limited pair-wise language corpora. The analysis in this paper suggests that this method can significantly improve a multilingual model's performance over its baseline, yielding state-of-the-art results for various Indian languages.

This paper introduces AFRIDOC-MT, a document-level multi-parallel translation dataset covering English and five African languages: Amharic, Hausa, Swahili, Yor\`ub\'a, and Zulu. The dataset comprises 334 health and 271 information technology news documents, all human-translated from English to these languages. We conduct document-level translation benchmark experiments by evaluating neural machine translation (NMT) models and large language models (LLMs) for translations between English and these languages, at both the sentence and pseudo-document levels. These outputs are realigned to form complete documents for evaluation. Our results indicate that NLLB-200 achieved the best average performance among the standard NMT models, while GPT-4o outperformed general-purpose LLMs. Fine-tuning selected models led to substantial performance gains, but models trained on sentences struggled to generalize effectively to longer documents. Furthermore, our analysis reveals that some LLMs exhibit issues such as under-generation, repetition of words or phrases, and off-target translations, especially for African languages.

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.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

We introduce Clinical ModernBERT, a transformer based encoder pretrained on large scale biomedical literature, clinical notes, and medical ontologies, incorporating PubMed abstracts, MIMIC IV clinical data, and medical codes with their textual descriptions. Building on ModernBERT the current state of the art natural language text encoder featuring architectural upgrades such as rotary positional embeddings (RoPE), Flash Attention, and extended context length up to 8,192 tokens our model adapts these innovations specifically for biomedical and clinical domains. Clinical ModernBERT excels at producing semantically rich representations tailored for long context tasks. We validate this both by analyzing its pretrained weights and through empirical evaluation on a comprehensive suite of clinical NLP benchmarks.

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs.

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

Neural machine translation (NMT) models typically operate with a fixed vocabulary, but translation is an open-vocabulary problem. Previous work addresses the translation of out-of-vocabulary words by backing off to a dictionary. In this paper, we introduce a simpler and more effective approach, making the NMT model capable of open-vocabulary translation by encoding rare and unknown words as sequences of subword units. This is based on the intuition that various word classes are translatable via smaller units than words, for instance names (via character copying or transliteration), compounds (via compositional translation), and cognates and loanwords (via phonological and morphological transformations). We discuss the suitability of different word segmentation techniques, including simple character n-gram models and a segmentation based on the byte pair encoding compression algorithm, and empirically show that subword models improve over a back-off dictionary baseline for the WMT 15 translation tasks English-German and English-Russian by 1.1 and 1.3 BLEU, respectively.

Document-level Neural Machine Translation (DocNMT) has been proven crucial for handling discourse phenomena by introducing document-level context information. One of the most important directions is to input the whole document directly to the standard Transformer model. In this case, efficiency becomes a critical concern due to the quadratic complexity of the attention module. Existing studies either focus on the encoder part, which cannot be deployed on sequence-to-sequence generation tasks, e.g., Machine Translation (MT), or suffer from a significant performance drop. In this work, we keep the translation performance while gaining 20\% speed up by introducing extra selection layer based on lightweight attention that selects a small portion of tokens to be attended. It takes advantage of the original attention to ensure performance and dimension reduction to accelerate inference. Experimental results show that our method could achieve up to 95\% sparsity (only 5\% tokens attended) approximately, and save 93\% computation cost on the attention module compared with the original Transformer, while maintaining the performance.

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.

We conducted a detailed analysis on the quality of web-mined corpora for two low-resource languages (making three language pairs, English-Sinhala, English-Tamil and Sinhala-Tamil). We ranked each corpus according to a similarity measure and carried out an intrinsic and extrinsic evaluation on different portions of this ranked corpus. We show that there are significant quality differences between different portions of web-mined corpora and that the quality varies across languages and datasets. We also show that, for some web-mined datasets, Neural Machine Translation (NMT) models trained with their highest-ranked 25k portion can be on par with human-curated datasets.

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.

As a commercial provider of machine translation, we are constantly training engines for a variety of uses, languages, and content types. In each case, there can be many variables, such as the amount of training data available, and the quality requirements of the end user. These variables can have an impact on the robustness of Neural MT engines. On the whole, Neural MT cures many ills of other MT paradigms, but at the same time, it has introduced a new set of challenges to address. In this paper, we describe some of the specific issues with practical NMT and the approaches we take to improve model robustness in real-world scenarios.

In neural machine translation (NMT), the most common practice is to stack a number of recurrent or feed-forward layers in the encoder and the decoder. As a result, the addition of each new layer improves the translation quality significantly. However, this also leads to a significant increase in the number of parameters. In this paper, we propose to share parameters across all the layers thereby leading to a recurrently stacked NMT model. We empirically show that the translation quality of a model that recurrently stacks a single layer 6 times is comparable to the translation quality of a model that stacks 6 separate layers. We also show that using pseudo-parallel corpora by back-translation leads to further significant improvements in translation quality.

Neural Machine Translation (NMT) systems face significant challenges when working with low-resource languages, particularly in domain adaptation tasks. These difficulties arise due to limited training data and suboptimal model generalization, As a result, selecting an optimal model for translation is crucial for achieving strong performance on in-domain data, particularly in scenarios where fine-tuning is not feasible or practical. In this paper, we investigate strategies for selecting the most suitable NMT model for a given domain using bandit-based algorithms, including Upper Confidence Bound, Linear UCB, Neural Linear Bandit, and Thompson Sampling. Our method effectively addresses the resource constraints by facilitating optimal model selection with high confidence. We evaluate the approach across three African languages and domains, demonstrating its robustness and effectiveness in both scenarios where target data is available and where it is absent.

Data-to-text (D2T) generation in the biomedical domain is a promising - yet mostly unexplored - field of research. Here, we apply neural models for D2T generation to a real-world dataset consisting of package leaflets of European medicines. We show that fine-tuned transformers are able to generate realistic, multisentence text from data in the biomedical domain, yet have important limitations. We also release a new dataset (BioLeaflets) for benchmarking D2T generation models in the biomedical domain.

Models such as GPT-4 and Med-PaLM 2 have demonstrated impressive performance on a wide variety of biomedical NLP tasks. However, these models have hundreds of billions of parameters, are computationally expensive to run, require users to send their input data over the internet, and are trained on unknown data sources. Can smaller, more targeted models compete? To address this question, we build and release BioMedLM, a 2.7 billion parameter GPT-style autoregressive model trained exclusively on PubMed abstracts and full articles. When fine-tuned, BioMedLM can produce strong multiple-choice biomedical question-answering results competitive with much larger models, such as achieving a score of 57.3% on MedMCQA (dev) and 69.0% on the MMLU Medical Genetics exam. BioMedLM can also be fine-tuned to produce useful answers to patient questions on medical topics. This demonstrates that smaller models can potentially serve as transparent, privacy-preserving, economical and environmentally friendly foundations for particular NLP applications, such as in biomedicine. The model is available on the Hugging Face Hub: https://huggingface.co/stanford-crfm/BioMedLM.

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.

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.

In this paper, we describe a tool for debugging the output and attention weights of neural machine translation (NMT) systems and for improved estimations of confidence about the output based on the attention. The purpose of the tool is to help researchers and developers find weak and faulty example translations that their NMT systems produce without the need for reference translations. Our tool also includes an option to directly compare translation outputs from two different NMT engines or experiments. In addition, we present a demo website of our tool with examples of good and bad translations: http://attention.lielakeda.lv