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Mar 11

Vega-MT: The JD Explore Academy Translation System for WMT22

We describe the JD Explore Academy's submission of the WMT 2022 shared general translation task. We participated in all high-resource tracks and one medium-resource track, including Chinese-English, German-English, Czech-English, Russian-English, and Japanese-English. We push the limit of our previous work -- bidirectional training for translation by scaling up two main factors, i.e. language pairs and model sizes, namely the Vega-MT system. As for language pairs, we scale the "bidirectional" up to the "multidirectional" settings, covering all participating languages, to exploit the common knowledge across languages, and transfer them to the downstream bilingual tasks. As for model sizes, we scale the Transformer-Big up to the extremely large model that owns nearly 4.7 Billion parameters, to fully enhance the model capacity for our Vega-MT. Also, we adopt the data augmentation strategies, e.g. cycle translation for monolingual data, and bidirectional self-training for bilingual and monolingual data, to comprehensively exploit the bilingual and monolingual data. To adapt our Vega-MT to the general domain test set, generalization tuning is designed. Based on the official automatic scores of constrained systems, in terms of the sacreBLEU shown in Figure-1, we got the 1st place on {Zh-En (33.5), En-Zh (49.7), De-En (33.7), En-De (37.8), Cs-En (54.9), En-Cs (41.4) and En-Ru (32.7)}, 2nd place on {Ru-En (45.1) and Ja-En (25.6)}, and 3rd place on {En-Ja(41.5)}, respectively; W.R.T the COMET, we got the 1st place on {Zh-En (45.1), En-Zh (61.7), De-En (58.0), En-De (63.2), Cs-En (74.7), Ru-En (64.9), En-Ru (69.6) and En-Ja (65.1)}, 2nd place on {En-Cs (95.3) and Ja-En (40.6)}, respectively.

Domain Terminology Integration into Machine Translation: Leveraging Large Language Models

This paper discusses the methods that we used for our submissions to the WMT 2023 Terminology Shared Task for German-to-English (DE-EN), English-to-Czech (EN-CS), and Chinese-to-English (ZH-EN) language pairs. The task aims to advance machine translation (MT) by challenging participants to develop systems that accurately translate technical terms, ultimately enhancing communication and understanding in specialised domains. To this end, we conduct experiments that utilise large language models (LLMs) for two purposes: generating synthetic bilingual terminology-based data, and post-editing translations generated by an MT model through incorporating pre-approved terms. Our system employs a four-step process: (i) using an LLM to generate bilingual synthetic data based on the provided terminology, (ii) fine-tuning a generic encoder-decoder MT model, with a mix of the terminology-based synthetic data generated in the first step and a randomly sampled portion of the original generic training data, (iii) generating translations with the fine-tuned MT model, and (iv) finally, leveraging an LLM for terminology-constrained automatic post-editing of the translations that do not include the required terms. The results demonstrate the effectiveness of our proposed approach in improving the integration of pre-approved terms into translations. The number of terms incorporated into the translations of the blind dataset increases from an average of 36.67% with the generic model to an average of 72.88% by the end of the process. In other words, successful utilisation of terms nearly doubles across the three language pairs.

Google's Multilingual Neural Machine Translation System: Enabling Zero-Shot Translation

We propose a simple solution to use a single Neural Machine Translation (NMT) model to translate between multiple languages. Our solution requires no change in the model architecture from our base system but instead introduces an artificial token at the beginning of the input sentence to specify the required target language. The rest of the model, which includes encoder, decoder and attention, remains unchanged and is shared across all languages. Using a shared wordpiece vocabulary, our approach enables Multilingual NMT using a single model without any increase in parameters, which is significantly simpler than previous proposals for Multilingual NMT. Our method often improves the translation quality of all involved language pairs, even while keeping the total number of model parameters constant. On the WMT'14 benchmarks, a single multilingual model achieves comparable performance for EnglishrightarrowFrench and surpasses state-of-the-art results for EnglishrightarrowGerman. Similarly, a single multilingual model surpasses state-of-the-art results for FrenchrightarrowEnglish and GermanrightarrowEnglish on WMT'14 and WMT'15 benchmarks respectively. On production corpora, multilingual models of up to twelve language pairs allow for better translation of many individual pairs. In addition to improving the translation quality of language pairs that the model was trained with, our models can also learn to perform implicit bridging between language pairs never seen explicitly during training, showing that transfer learning and zero-shot translation is possible for neural translation. Finally, we show analyses that hints at a universal interlingua representation in our models and show some interesting examples when mixing languages.

LLMs-in-the-loop Part-1: Expert Small AI Models for Bio-Medical Text Translation

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.

Cross-Lingual Transfer for Low-Resource Natural Language Processing

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.

Machine Translation Advancements of Low-Resource Indian Languages by Transfer Learning

This paper introduces the submission by Huawei Translation Center (HW-TSC) to the WMT24 Indian Languages Machine Translation (MT) Shared Task. To develop a reliable machine translation system for low-resource Indian languages, we employed two distinct knowledge transfer strategies, taking into account the characteristics of the language scripts and the support available from existing open-source models for Indian languages. For Assamese(as) and Manipuri(mn), we fine-tuned the existing IndicTrans2 open-source model to enable bidirectional translation between English and these languages. For Khasi (kh) and Mizo (mz), We trained a multilingual model as a baseline using bilingual data from these four language pairs, along with an additional about 8kw English-Bengali bilingual data, all of which share certain linguistic features. This was followed by fine-tuning to achieve bidirectional translation between English and Khasi, as well as English and Mizo. Our transfer learning experiments produced impressive results: 23.5 BLEU for en-as, 31.8 BLEU for en-mn, 36.2 BLEU for as-en, and 47.9 BLEU for mn-en on their respective test sets. Similarly, the multilingual model transfer learning experiments yielded impressive outcomes, achieving 19.7 BLEU for en-kh, 32.8 BLEU for en-mz, 16.1 BLEU for kh-en, and 33.9 BLEU for mz-en on their respective test sets. These results not only highlight the effectiveness of transfer learning techniques for low-resource languages but also contribute to advancing machine translation capabilities for low-resource Indian languages.

In-BoXBART: Get Instructions into Biomedical Multi-Task Learning

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.

Large Language Models and Control Mechanisms Improve Text Readability of Biomedical Abstracts

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

Discourse Centric Evaluation of Machine Translation with a Densely Annotated Parallel Corpus

Several recent papers claim human parity at sentence-level Machine Translation (MT), especially in high-resource languages. Thus, in response, the MT community has, in part, shifted its focus to document-level translation. Translating documents requires a deeper understanding of the structure and meaning of text, which is often captured by various kinds of discourse phenomena such as consistency, coherence, and cohesion. However, this renders conventional sentence-level MT evaluation benchmarks inadequate for evaluating the performance of context-aware MT systems. This paper presents a new dataset with rich discourse annotations, built upon the large-scale parallel corpus BWB introduced in Jiang et al. (2022). The new BWB annotation introduces four extra evaluation aspects, i.e., entity, terminology, coreference, and quotation, covering 15,095 entity mentions in both languages. Using these annotations, we systematically investigate the similarities and differences between the discourse structures of source and target languages, and the challenges they pose to MT. We discover that MT outputs differ fundamentally from human translations in terms of their latent discourse structures. This gives us a new perspective on the challenges and opportunities in document-level MT. We make our resource publicly available to spur future research in document-level MT and the generalization to other language translation tasks.

Fine-tuning Large Language Models for Adaptive Machine Translation

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

BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

Medical mT5: An Open-Source Multilingual Text-to-Text LLM for The Medical Domain

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.

Tx-LLM: A Large Language Model for Therapeutics

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

Localising In-Domain Adaptation of Transformer-Based Biomedical Language Models

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.

Crosslingual Generalization through Multitask Finetuning

Multitask prompted finetuning (MTF) has been shown to help large language models generalize to new tasks in a zero-shot setting, but so far explorations of MTF have focused on English data and models. We apply MTF to the pretrained multilingual BLOOM and mT5 model families to produce finetuned variants called BLOOMZ and mT0. We find finetuning large multilingual language models on English tasks with English prompts allows for task generalization to non-English languages that appear only in the pretraining corpus. Finetuning on multilingual tasks with English prompts further improves performance on English and non-English tasks leading to various state-of-the-art zero-shot results. We also investigate finetuning on multilingual tasks with prompts that have been machine-translated from English to match the language of each dataset. We find training on these machine-translated prompts leads to better performance on human-written prompts in the respective languages. Surprisingly, we find models are capable of zero-shot generalization to tasks in languages they have never intentionally seen. We conjecture that the models are learning higher-level capabilities that are both task- and language-agnostic. In addition, we introduce xP3, a composite of supervised datasets in 46 languages with English and machine-translated prompts. Our code, datasets and models are publicly available at https://github.com/bigscience-workshop/xmtf.

CLIPTrans: Transferring Visual Knowledge with Pre-trained Models for Multimodal Machine Translation

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

Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation

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.

No Language Left Behind: Scaling Human-Centered Machine Translation

Driven by the goal of eradicating language barriers on a global scale, machine translation has solidified itself as a key focus of artificial intelligence research today. However, such efforts have coalesced around a small subset of languages, leaving behind the vast majority of mostly low-resource languages. What does it take to break the 200 language barrier while ensuring safe, high quality results, all while keeping ethical considerations in mind? In No Language Left Behind, we took on this challenge by first contextualizing the need for low-resource language translation support through exploratory interviews with native speakers. Then, we created datasets and models aimed at narrowing the performance gap between low and high-resource languages. More specifically, we developed a conditional compute model based on Sparsely Gated Mixture of Experts that is trained on data obtained with novel and effective data mining techniques tailored for low-resource languages. We propose multiple architectural and training improvements to counteract overfitting while training on thousands of tasks. Critically, we evaluated the performance of over 40,000 different translation directions using a human-translated benchmark, Flores-200, and combined human evaluation with a novel toxicity benchmark covering all languages in Flores-200 to assess translation safety. Our model achieves an improvement of 44% BLEU relative to the previous state-of-the-art, laying important groundwork towards realizing a universal translation system. Finally, we open source all contributions described in this work, accessible at https://github.com/facebookresearch/fairseq/tree/nllb.

Text2MDT: Extracting Medical Decision Trees from Medical Texts

Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method Wei2022ChainOT can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at https://tianchi.aliyun.com/dataset/95414, and the source codes are open-sourced at https://github.com/michael-wzhu/text2dt.

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

MEDEC: A Benchmark for Medical Error Detection and Correction in Clinical Notes

Several studies showed that Large Language Models (LLMs) can answer medical questions correctly, even outperforming the average human score in some medical exams. However, to our knowledge, no study has been conducted to assess the ability of language models to validate existing or generated medical text for correctness and consistency. In this paper, we introduce MEDEC (https://github.com/abachaa/MEDEC), the first publicly available benchmark for medical error detection and correction in clinical notes, covering five types of errors (Diagnosis, Management, Treatment, Pharmacotherapy, and Causal Organism). MEDEC consists of 3,848 clinical texts, including 488 clinical notes from three US hospital systems that were not previously seen by any LLM. The dataset has been used for the MEDIQA-CORR shared task to evaluate seventeen participating systems [Ben Abacha et al., 2024]. In this paper, we describe the data creation methods and we evaluate recent LLMs (e.g., o1-preview, GPT-4, Claude 3.5 Sonnet, and Gemini 2.0 Flash) for the tasks of detecting and correcting medical errors requiring both medical knowledge and reasoning capabilities. We also conducted a comparative study where two medical doctors performed the same task on the MEDEC test set. The results showed that MEDEC is a sufficiently challenging benchmark to assess the ability of models to validate existing or generated notes and to correct medical errors. We also found that although recent LLMs have a good performance in error detection and correction, they are still outperformed by medical doctors in these tasks. We discuss the potential factors behind this gap, the insights from our experiments, the limitations of current evaluation metrics, and share potential pointers for future research.

The unreasonable effectiveness of few-shot learning for machine translation

We demonstrate the potential of few-shot translation systems, trained with unpaired language data, for both high and low-resource language pairs. We show that with only 5 examples of high-quality translation data shown at inference, a transformer decoder-only model trained solely with self-supervised learning, is able to match specialized supervised state-of-the-art models as well as more general commercial translation systems. In particular, we outperform the best performing system on the WMT'21 English - Chinese news translation task by only using five examples of English - Chinese parallel data at inference. Moreover, our approach in building these models does not necessitate joint multilingual training or back-translation, is conceptually simple and shows the potential to extend to the multilingual setting. Furthermore, the resulting models are two orders of magnitude smaller than state-of-the-art language models. We then analyze the factors which impact the performance of few-shot translation systems, and highlight that the quality of the few-shot demonstrations heavily determines the quality of the translations generated by our models. Finally, we show that the few-shot paradigm also provides a way to control certain attributes of the translation -- we show that we are able to control for regional varieties and formality using only a five examples at inference, paving the way towards controllable machine translation systems.

Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing

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.

MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

A Benchmark for Learning to Translate a New Language from One Grammar Book

Large language models (LLMs) can perform impressive feats with in-context learning or lightweight finetuning. It is natural to wonder how well these models adapt to genuinely new tasks, but how does one find tasks that are unseen in internet-scale training sets? We turn to a field that is explicitly motivated and bottlenecked by a scarcity of web data: low-resource languages. In this paper, we introduce MTOB (Machine Translation from One Book), a benchmark for learning to translate between English and Kalamang -- a language with less than 200 speakers and therefore virtually no presence on the web -- using several hundred pages of field linguistics reference materials. This task framing is novel in that it asks a model to learn a language from a single human-readable book of grammar explanations, rather than a large mined corpus of in-domain data, more akin to L2 learning than L1 acquisition. We demonstrate that baselines using current LLMs are promising but fall short of human performance, achieving 44.7 chrF on Kalamang to English translation and 45.8 chrF on English to Kalamang translation, compared to 51.6 and 57.0 chrF by a human who learned Kalamang from the same reference materials. We hope that MTOB will help measure LLM capabilities along a new dimension, and that the methods developed to solve it could help expand access to language technology for underserved communities by leveraging qualitatively different kinds of data than traditional machine translation.

SeamlessM4T-Massively Multilingual & Multimodal Machine Translation

What does it take to create the Babel Fish, a tool that can help individuals translate speech between any two languages? While recent breakthroughs in text-based models have pushed machine translation coverage beyond 200 languages, unified speech-to-speech translation models have yet to achieve similar strides. More specifically, conventional speech-to-speech translation systems rely on cascaded systems that perform translation progressively, putting high-performing unified systems out of reach. To address these gaps, we introduce SeamlessM4T, a single model that supports speech-to-speech translation, speech-to-text translation, text-to-speech translation, text-to-text translation, and automatic speech recognition for up to 100 languages. To build this, we used 1 million hours of open speech audio data to learn self-supervised speech representations with w2v-BERT 2.0. Subsequently, we created a multimodal corpus of automatically aligned speech translations. Filtered and combined with human-labeled and pseudo-labeled data, we developed the first multilingual system capable of translating from and into English for both speech and text. On FLEURS, SeamlessM4T sets a new standard for translations into multiple target languages, achieving an improvement of 20% BLEU over the previous SOTA in direct speech-to-text translation. Compared to strong cascaded models, SeamlessM4T improves the quality of into-English translation by 1.3 BLEU points in speech-to-text and by 2.6 ASR-BLEU points in speech-to-speech. Tested for robustness, our system performs better against background noises and speaker variations in speech-to-text tasks compared to the current SOTA model. Critically, we evaluated SeamlessM4T on gender bias and added toxicity to assess translation safety. Finally, all contributions in this work are open-sourced and accessible at https://github.com/facebookresearch/seamless_communication

BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine

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.

SCALE: Synergized Collaboration of Asymmetric Language Translation Engines

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

DRT-o1: Optimized Deep Reasoning Translation via Long Chain-of-Thought

Recently, O1-like models have emerged as representative examples, illustrating the effectiveness of long chain-of-thought (CoT) in reasoning tasks such as math and coding tasks. In this paper, we introduce DRT-o1, an attempt to bring the success of long CoT to neural machine translation (MT). Specifically, in view of the literature books that might involve similes and metaphors, translating these texts to a target language is very difficult in practice due to cultural differences. In such cases, literal translation often fails to convey the intended meaning effectively. Even for professional human translators, considerable thought must be given to preserving semantics throughout the translation process. To simulate LLMs' long thought ability in MT, we first mine sentences containing similes or metaphors from existing literature books, and then develop a multi-agent framework to translate these sentences via long thought. In the multi-agent framework, a translator is used to iteratively translate the source sentence under the suggestions provided by an advisor. To ensure the effectiveness of the long thoughts, an evaluator is also employed to judge whether the translation in the current round is better than the previous one or not. In this manner, we collect tens of thousands of long-thought MT data, which is used to train our DRT-o1. The experimental results on literature translation demonstrate the effectiveness of the DRT-o1. Using Qwen2.5-7B and Qwen2.5-14B as the backbones, the improvement brought by DRT-o1 achieves 7.33~8.26 BLEU and 1.66~3.36 CometScore. Besides, DRT-o1-7B can outperform QwQ-32B-Preview by 7.82 BLEU and 1.46 CometScore, showing its effectiveness. The project is available at https://github.com/krystalan/DRT-o1

Bridging the Gap: Enhancing LLM Performance for Low-Resource African Languages with New Benchmarks, Fine-Tuning, and Cultural Adjustments

Large Language Models (LLMs) have shown remarkable performance across various tasks, yet significant disparities remain for non-English languages, and especially native African languages. This paper addresses these disparities by creating approximately 1 million human-translated words of new benchmark data in 8 low-resource African languages, covering a population of over 160 million speakers of: Amharic, Bambara, Igbo, Sepedi (Northern Sotho), Shona, Sesotho (Southern Sotho), Setswana, and Tsonga. Our benchmarks are translations of Winogrande and three sections of MMLU: college medicine, clinical knowledge, and virology. Using the translated benchmarks, we report previously unknown performance gaps between state-of-the-art (SOTA) LLMs in English and African languages. Finally, using results from over 400 fine-tuned models, we explore several methods to reduce the LLM performance gap, including high-quality dataset fine-tuning (using an LLM-as-an-Annotator), cross-lingual transfer, and cultural appropriateness adjustments. Key findings include average mono-lingual improvements of 5.6% with fine-tuning (with 5.4% average mono-lingual improvements when using high-quality data over low-quality data), 2.9% average gains from cross-lingual transfer, and a 3.0% out-of-the-box performance boost on culturally appropriate questions. The publicly available benchmarks, translations, and code from this study support further research and development aimed at creating more inclusive and effective language technologies.

Visualizing Uncertainty in Translation Tasks: An Evaluation of LLM Performance and Confidence Metrics

Large language models (LLMs) are increasingly utilized for machine translation, yet their predictions often exhibit uncertainties that hinder interpretability and user trust. Effectively visualizing these uncertainties can enhance the usability of LLM outputs, particularly in contexts where translation accuracy is critical. This paper addresses two primary objectives: (1) providing users with token-level insights into model confidence and (2) developing a web-based visualization tool to quantify and represent translation uncertainties. To achieve these goals, we utilized the T5 model with the WMT19 dataset for translation tasks and evaluated translation quality using established metrics such as BLEU, METEOR, and ROUGE. We introduced three novel uncertainty quantification (UQ) metrics: (1) the geometric mean of token probabilities, (2) the arithmetic mean of token probabilities, and (3) the arithmetic mean of the kurtosis of token distributions. These metrics provide a simple yet effective framework for evaluating translation performance. Our analysis revealed a linear relationship between the traditional evaluation metrics and our UQ metrics, demonstrating the validity of our approach. Additionally, we developed an interactive web-based visualization that uses a color gradient to represent token confidence. This tool offers users a clear and intuitive understanding of translation quality while providing valuable insights into model performance. Overall, we show that our UQ metrics and visualization are both robust and interpretable, offering practical tools for evaluating and accessing machine translation systems.

Multilingual Translation with Extensible Multilingual Pretraining and Finetuning

Recent work demonstrates the potential of multilingual pretraining of creating one model that can be used for various tasks in different languages. Previous work in multilingual pretraining has demonstrated that machine translation systems can be created by finetuning on bitext. In this work, we show that multilingual translation models can be created through multilingual finetuning. Instead of finetuning on one direction, a pretrained model is finetuned on many directions at the same time. Compared to multilingual models trained from scratch, starting from pretrained models incorporates the benefits of large quantities of unlabeled monolingual data, which is particularly important for low resource languages where bitext is not available. We demonstrate that pretrained models can be extended to incorporate additional languages without loss of performance. We double the number of languages in mBART to support multilingual machine translation models of 50 languages. Finally, we create the ML50 benchmark, covering low, mid, and high resource languages, to facilitate reproducible research by standardizing training and evaluation data. On ML50, we demonstrate that multilingual finetuning improves on average 1 BLEU over the strongest baselines (being either multilingual from scratch or bilingual finetuning) while improving 9.3 BLEU on average over bilingual baselines from scratch.

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

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

Bidirectional Language Models Are Also Few-shot Learners

Large language models such as GPT-3 (Brown et al., 2020) can perform arbitrary tasks without undergoing fine-tuning after being prompted with only a few labeled examples. An arbitrary task can be reformulated as a natural language prompt, and a language model can be asked to generate the completion, indirectly performing the task in a paradigm known as prompt-based learning. To date, emergent prompt-based learning capabilities have mainly been demonstrated for unidirectional language models. However, bidirectional language models pre-trained on denoising objectives such as masked language modeling produce stronger learned representations for transfer learning. This motivates the possibility of prompting bidirectional models, but their pre-training objectives have made them largely incompatible with the existing prompting paradigm. We present SAP (Sequential Autoregressive Prompting), a technique that enables the prompting of bidirectional models. Utilizing the machine translation task as a case study, we prompt the bidirectional mT5 model (Xue et al., 2021) with SAP and demonstrate its few-shot and zero-shot translations outperform the few-shot translations of unidirectional models like GPT-3 and XGLM (Lin et al., 2021), despite mT5's approximately 50% fewer parameters. We further show SAP is effective on question answering and summarization. For the first time, our results demonstrate prompt-based learning is an emergent property of a broader class of language models, rather than only unidirectional models.

Languages You Know Influence Those You Learn: Impact of Language Characteristics on Multi-Lingual Text-to-Text Transfer

Multi-lingual language models (LM), such as mBERT, XLM-R, mT5, mBART, have been remarkably successful in enabling natural language tasks in low-resource languages through cross-lingual transfer from high-resource ones. In this work, we try to better understand how such models, specifically mT5, transfer *any* linguistic and semantic knowledge across languages, even though no explicit cross-lingual signals are provided during pre-training. Rather, only unannotated texts from each language are presented to the model separately and independently of one another, and the model appears to implicitly learn cross-lingual connections. This raises several questions that motivate our study, such as: Are the cross-lingual connections between every language pair equally strong? What properties of source and target language impact the strength of cross-lingual transfer? Can we quantify the impact of those properties on the cross-lingual transfer? In our investigation, we analyze a pre-trained mT5 to discover the attributes of cross-lingual connections learned by the model. Through a statistical interpretation framework over 90 language pairs across three tasks, we show that transfer performance can be modeled by a few linguistic and data-derived features. These observations enable us to interpret cross-lingual understanding of the mT5 model. Through these observations, one can favorably choose the best source language for a task, and can anticipate its training data demands. A key finding of this work is that similarity of syntax, morphology and phonology are good predictors of cross-lingual transfer, significantly more than just the lexical similarity of languages. For a given language, we are able to predict zero-shot performance, that increases on a logarithmic scale with the number of few-shot target language data points.

Generative Large Language Models Are All-purpose Text Analytics Engines: Text-to-text Learning Is All Your Need

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

Unifying Molecular and Textual Representations via Multi-task Language Modelling

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

Panacea: A foundation model for clinical trial search, summarization, design, and recruitment

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

FILTER: An Enhanced Fusion Method for Cross-lingual Language Understanding

Large-scale cross-lingual language models (LM), such as mBERT, Unicoder and XLM, have achieved great success in cross-lingual representation learning. However, when applied to zero-shot cross-lingual transfer tasks, most existing methods use only single-language input for LM finetuning, without leveraging the intrinsic cross-lingual alignment between different languages that proves essential for multilingual tasks. In this paper, we propose FILTER, an enhanced fusion method that takes cross-lingual data as input for XLM finetuning. Specifically, FILTER first encodes text input in the source language and its translation in the target language independently in the shallow layers, then performs cross-language fusion to extract multilingual knowledge in the intermediate layers, and finally performs further language-specific encoding. During inference, the model makes predictions based on the text input in the target language and its translation in the source language. For simple tasks such as classification, translated text in the target language shares the same label as the source language. However, this shared label becomes less accurate or even unavailable for more complex tasks such as question answering, NER and POS tagging. To tackle this issue, we further propose an additional KL-divergence self-teaching loss for model training, based on auto-generated soft pseudo-labels for translated text in the target language. Extensive experiments demonstrate that FILTER achieves new state of the art on two challenging multilingual multi-task benchmarks, XTREME and XGLUE.

Machine Translation Meta Evaluation through Translation Accuracy Challenge Sets

Recent machine translation (MT) metrics calibrate their effectiveness by correlating with human judgement but without any insights about their behaviour across different error types. Challenge sets are used to probe specific dimensions of metric behaviour but there are very few such datasets and they either focus on a limited number of phenomena or a limited number of language pairs. We introduce ACES, a contrastive challenge set spanning 146 language pairs, aimed at discovering whether metrics can identify 68 translation accuracy errors. These phenomena range from simple alterations at the word/character level to more complex errors based on discourse and real-world knowledge. We conduct a large-scale study by benchmarking ACES on 50 metrics submitted to the WMT 2022 and 2023 metrics shared tasks. We benchmark metric performance, assess their incremental performance over successive campaigns, and measure their sensitivity to a range of linguistic phenomena. We also investigate claims that Large Language Models (LLMs) are effective as MT evaluators by evaluating on ACES. Our results demonstrate that different metric families struggle with different phenomena and that LLM-based methods fail to demonstrate reliable performance. Our analyses indicate that most metrics ignore the source sentence, tend to prefer surface-level overlap and end up incorporating properties of base models which are not always beneficial. We expand ACES to include error span annotations, denoted as SPAN-ACES and we use this dataset to evaluate span-based error metrics showing these metrics also need considerable improvement. Finally, we provide a set of recommendations for building better MT metrics, including focusing on error labels instead of scores, ensembling, designing strategies to explicitly focus on the source sentence, focusing on semantic content and choosing the right base model for representations.

A Survey for Large Language Models in Biomedicine

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

Exploring the Effectiveness of Instruction Tuning in Biomedical Language Processing

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.

Development of a Large-scale Dataset of Chest Computed Tomography Reports in Japanese and a High-performance Finding Classification Model

Background: Recent advances in large language models highlight the need for high-quality multilingual medical datasets. While Japan leads globally in CT scanner deployment and utilization, the lack of large-scale Japanese radiology datasets has hindered the development of specialized language models for medical imaging analysis. Objective: To develop a comprehensive Japanese CT report dataset through machine translation and establish a specialized language model for structured finding classification. Additionally, to create a rigorously validated evaluation dataset through expert radiologist review. Methods: We translated the CT-RATE dataset (24,283 CT reports from 21,304 patients) into Japanese using GPT-4o mini. The training dataset consisted of 22,778 machine-translated reports, while the validation dataset included 150 radiologist-revised reports. We developed CT-BERT-JPN based on "tohoku-nlp/bert-base-japanese-v3" architecture for extracting 18 structured findings from Japanese radiology reports. Results: Translation metrics showed strong performance with BLEU scores of 0.731 and 0.690, and ROUGE scores ranging from 0.770 to 0.876 for Findings and from 0.748 to 0.857 for Impression sections. CT-BERT-JPN demonstrated superior performance compared to GPT-4o in 11 out of 18 conditions, including lymphadenopathy (+14.2%), interlobular septal thickening (+10.9%), and atelectasis (+7.4%). The model maintained F1 scores exceeding 0.95 in 14 out of 18 conditions and achieved perfect scores in four conditions. Conclusions: Our study establishes a robust Japanese CT report dataset and demonstrates the effectiveness of a specialized language model for structured finding classification. The hybrid approach of machine translation and expert validation enables the creation of large-scale medical datasets while maintaining high quality.

Towards Evaluating and Building Versatile Large Language Models for Medicine

In this study, we present MedS-Bench, a comprehensive benchmark designed to evaluate the performance of large language models (LLMs) in clinical contexts. Unlike existing benchmarks that focus on multiple-choice question answering, MedS-Bench spans 11 high-level clinical tasks, including clinical report summarization, treatment recommendations, diagnosis, named entity recognition, and medical concept explanation, among others. We evaluated six leading LLMs, e.g., MEDITRON, Mistral, InternLM 2, Llama 3, GPT-4, and Claude-3.5 using few-shot prompting, and found that even the most sophisticated models struggle with these complex tasks. To address these limitations, we developed MedS-Ins, a large-scale instruction tuning dataset for medicine. MedS-Ins comprises 58 medically oriented language corpora, totaling 13.5 million samples across 122 tasks. To demonstrate the dataset's utility, we conducted a proof-of-concept experiment by performing instruction tuning on a lightweight, open-source medical language model. The resulting model, MMedIns-Llama 3, significantly outperformed existing models across nearly all clinical tasks. To promote further advancements in the application of LLMs to clinical challenges, we have made the MedS-Ins dataset fully accessible and invite the research community to contribute to its expansion.Additionally, we have launched a dynamic leaderboard for MedS-Bench, which we plan to regularly update the test set to track progress and enhance the adaptation of general LLMs to the medical domain. Leaderboard: https://henrychur.github.io/MedS-Bench/. Github: https://github.com/MAGIC-AI4Med/MedS-Ins.

Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events

Large language models (LLMs), such as GPT-4, have demonstrated remarkable capabilities across a wide range of tasks, including health applications. In this paper, we study how LLMs can be used to scale biomedical knowledge curation. We find that while LLMs already possess decent competency in structuring biomedical text, by distillation into a task-specific student model through self-supervised learning, substantial gains can be attained over out-of-box LLMs, with additional advantages such as cost, efficiency, and white-box model access. We conduct a case study on adverse drug event (ADE) extraction, which is an important area for improving care. On standard ADE extraction evaluation, a GPT-3.5 distilled PubMedBERT model attained comparable accuracy as supervised state-of-the-art models without using any labeled data. Despite being over 1,000 times smaller, the distilled model outperformed its teacher GPT-3.5 by over 6 absolute points in F1 and GPT-4 by over 5 absolute points. Ablation studies on distillation model choice (e.g., PubMedBERT vs BioGPT) and ADE extraction architecture shed light on best practice for biomedical knowledge extraction. Similar gains were attained by distillation for other standard biomedical knowledge extraction tasks such as gene-disease associations and protected health information, further illustrating the promise of this approach.