new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Jul 30

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.

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.

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.

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.

Unsupervised Translation of Programming Languages

A transcompiler, also known as source-to-source translator, is a system that converts source code from a high-level programming language (such as C++ or Python) to another. Transcompilers are primarily used for interoperability, and to port codebases written in an obsolete or deprecated language (e.g. COBOL, Python 2) to a modern one. They typically rely on handcrafted rewrite rules, applied to the source code abstract syntax tree. Unfortunately, the resulting translations often lack readability, fail to respect the target language conventions, and require manual modifications in order to work properly. The overall translation process is timeconsuming and requires expertise in both the source and target languages, making code-translation projects expensive. Although neural models significantly outperform their rule-based counterparts in the context of natural language translation, their applications to transcompilation have been limited due to the scarcity of parallel data in this domain. In this paper, we propose to leverage recent approaches in unsupervised machine translation to train a fully unsupervised neural transcompiler. We train our model on source code from open source GitHub projects, and show that it can translate functions between C++, Java, and Python with high accuracy. Our method relies exclusively on monolingual source code, requires no expertise in the source or target languages, and can easily be generalized to other programming languages. We also build and release a test set composed of 852 parallel functions, along with unit tests to check the correctness of translations. We show that our model outperforms rule-based commercial baselines by a significant margin.

Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Solving the unsolvable: Translating case law in Hong Kong

This paper addresses the challenges translating case law under Hong Kong's bilingual legal system. It highlights the initial success of translating all written statutes into Chinese before the 1997 handover, a task mandated by the Basic Law. The effort involved significant collaboration among legal, linguistic, and translation experts, resulting in a comprehensive and culturally appropriate bilingual legal system. However, translating case law remains a significant challenge due to the sheer volume and continuous growth of judicial decisions. The paper critiques the governments and judiciarys sporadic and uncoordinated efforts to translate case law, contrasting it with the thorough approach previously taken for statute translation. Although the government acknowledges the importance of legal bilingualism, it lacks a sustainable strategy for translating case law. The Judiciarys position that translating all judgments is unnecessary, unrealistic, and not cost-effectiveis analyzed and critiqued for its impact on legal transparency and public trust. A proposed solution involves leveraging machine translation technology through a human-machine interactive translation platform, which undergoes two major transitions. Initially based on a neural model, the platform transitions to using a large language model for improved translation accuracy. Furthermore, it evolves from a single-agent system to a multi-agent system, incorporating Translator, Annotator, and Proofreader agents. This multi-agent approach, supported by a grant, aims to facilitate efficient, high-quality translation of judicial judgments by integrating advanced artificial intelligence and continuous feedback mechanisms, thus better meeting the needs of a bilingual legal system.

TransBench: Benchmarking Machine Translation for Industrial-Scale Applications

Machine translation (MT) has become indispensable for cross-border communication in globalized industries like e-commerce, finance, and legal services, with recent advancements in large language models (LLMs) significantly enhancing translation quality. However, applying general-purpose MT models to industrial scenarios reveals critical limitations due to domain-specific terminology, cultural nuances, and stylistic conventions absent in generic benchmarks. Existing evaluation frameworks inadequately assess performance in specialized contexts, creating a gap between academic benchmarks and real-world efficacy. To address this, we propose a three-level translation capability framework: (1) Basic Linguistic Competence, (2) Domain-Specific Proficiency, and (3) Cultural Adaptation, emphasizing the need for holistic evaluation across these dimensions. We introduce TransBench, a benchmark tailored for industrial MT, initially targeting international e-commerce with 17,000 professionally translated sentences spanning 4 main scenarios and 33 language pairs. TransBench integrates traditional metrics (BLEU, TER) with Marco-MOS, a domain-specific evaluation model, and provides guidelines for reproducible benchmark construction. Our contributions include: (1) a structured framework for industrial MT evaluation, (2) the first publicly available benchmark for e-commerce translation, (3) novel metrics probing multi-level translation quality, and (4) open-sourced evaluation tools. This work bridges the evaluation gap, enabling researchers and practitioners to systematically assess and enhance MT systems for industry-specific needs.

MT-Ladder: A Model-Agnostic Framework Boosting LLM-based Machine Translation to the Next Level

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

Tower+: Bridging Generality and Translation Specialization in Multilingual LLMs

Fine-tuning pretrained LLMs has been shown to be an effective strategy for reaching state-of-the-art performance on specific tasks like machine translation. However, this process of adaptation often implies sacrificing general-purpose capabilities, such as conversational reasoning and instruction-following, hampering the utility of the system in real-world applications that require a mixture of skills. In this paper, we introduce Tower+, a suite of models designed to deliver strong performance across both translation and multilingual general-purpose text capabilities. We achieve a Pareto frontier between translation specialization and multilingual general-purpose capabilities by introducing a novel training recipe that builds on Tower (Alves et al., 2024), comprising continued pretraining, supervised fine-tuning, preference optimization, and reinforcement learning with verifiable rewards. At each stage of training, we carefully generate and curate data to strengthen performance on translation as well as general-purpose tasks involving code generation, mathematics problem solving, and general instruction-following. We develop models at multiple scales: 2B, 9B, and 72B. Our smaller models often outperform larger general-purpose open-weight and proprietary LLMs (e.g., Llama 3.3 70B, GPT-4o). Our largest model delivers best-in-class translation performance for high-resource languages and top results in multilingual Arena Hard evaluations and in IF-MT, a benchmark we introduce for evaluating both translation and instruction-following. Our findings highlight that it is possible to rival frontier models in general capabilities, while optimizing for specific business domains, such as translation and localization.

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

A Novel Paradigm Boosting Translation Capabilities of Large Language Models

This paper presents a study on strategies to enhance the translation capabilities of large language models (LLMs) in the context of machine translation (MT) tasks. The paper proposes a novel paradigm consisting of three stages: Secondary Pre-training using Extensive Monolingual Data, Continual Pre-training with Interlinear Text Format Documents, and Leveraging Source-Language Consistent Instruction for Supervised Fine-Tuning. Previous research on LLMs focused on various strategies for supervised fine-tuning (SFT), but their effectiveness has been limited. While traditional machine translation approaches rely on vast amounts of parallel bilingual data, our paradigm highlights the importance of using smaller sets of high-quality bilingual data. We argue that the focus should be on augmenting LLMs' cross-lingual alignment abilities during pre-training rather than solely relying on extensive bilingual data during SFT. Experimental results conducted using the Llama2 model, particularly on Chinese-Llama2 after monolingual augmentation, demonstrate the improved translation capabilities of LLMs. A significant contribution of our approach lies in Stage2: Continual Pre-training with Interlinear Text Format Documents, which requires less than 1B training data, making our method highly efficient. Additionally, in Stage3, we observed that setting instructions consistent with the source language benefits the supervised fine-tuning process. Experimental results demonstrate that our approach surpasses previous work and achieves superior performance compared to models such as NLLB-54B and GPT3.5-text-davinci-003, despite having a significantly smaller parameter count of only 7B or 13B. This achievement establishes our method as a pioneering strategy in the field of machine translation.

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.

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.

A Paradigm Shift in Machine Translation: Boosting Translation Performance of Large Language Models

Generative Large Language Models (LLMs) have achieved remarkable advancements in various NLP tasks. However, these advances have not been reflected in the translation task, especially those with moderate model sizes (i.e., 7B or 13B parameters), which still lag behind conventional supervised encoder-decoder translation models. Previous studies have attempted to improve the translation capabilities of these moderate LLMs, but their gains have been limited. In this study, we propose a novel fine-tuning approach for LLMs that is specifically designed for the translation task, eliminating the need for the abundant parallel data that traditional translation models usually depend on. Our approach consists of two fine-tuning stages: initial fine-tuning on monolingual data followed by subsequent fine-tuning on a small set of high-quality parallel data. We introduce the LLM developed through this strategy as Advanced Language Model-based trAnslator (ALMA). Based on LLaMA-2 as our underlying model, our results show that the model can achieve an average improvement of more than 12 BLEU and 12 COMET over its zero-shot performance across 10 translation directions from the WMT'21 (2 directions) and WMT'22 (8 directions) test datasets. The performance is significantly better than all prior work and even superior to the NLLB-54B model and GPT-3.5-text-davinci-003, with only 7B or 13B parameters. This method establishes the foundation for a novel training paradigm in machine translation.

Trans-Tokenization and Cross-lingual Vocabulary Transfers: Language Adaptation of LLMs for Low-Resource NLP

The development of monolingual language models for low and mid-resource languages continues to be hindered by the difficulty in sourcing high-quality training data. In this study, we present a novel cross-lingual vocabulary transfer strategy, trans-tokenization, designed to tackle this challenge and enable more efficient language adaptation. Our approach focuses on adapting a high-resource monolingual LLM to an unseen target language by initializing the token embeddings of the target language using a weighted average of semantically similar token embeddings from the source language. For this, we leverage a translation resource covering both the source and target languages. We validate our method with the Tweeties, a series of trans-tokenized LLMs, and demonstrate their competitive performance on various downstream tasks across a small but diverse set of languages. Additionally, we introduce Hydra LLMs, models with multiple swappable language modeling heads and embedding tables, which further extend the capabilities of our trans-tokenization strategy. By designing a Hydra LLM based on the multilingual model TowerInstruct, we developed a state-of-the-art machine translation model for Tatar, in a zero-shot manner, completely bypassing the need for high-quality parallel data. This breakthrough is particularly significant for low-resource languages like Tatar, where high-quality parallel data is hard to come by. By lowering the data and time requirements for training high-quality models, our trans-tokenization strategy allows for the development of LLMs for a wider range of languages, especially those with limited resources. We hope that our work will inspire further research and collaboration in the field of cross-lingual vocabulary transfer and contribute to the empowerment of languages on a global scale.

Can LLMs Really Learn to Translate a Low-Resource Language from One Grammar Book?

Extremely low-resource (XLR) languages lack substantial corpora for training NLP models, motivating the use of all available resources such as dictionaries and grammar books. Machine Translation from One Book (Tanzer et al., 2024) suggests that prompting long-context LLMs with one grammar book enables English-Kalamang translation, an XLR language unseen by LLMs - a noteworthy case of linguistics helping an NLP task. We investigate the source of this translation ability, finding almost all improvements stem from the book's parallel examples rather than its grammatical explanations. We find similar results for Nepali and Guarani, seen low-resource languages, and we achieve performance comparable to an LLM with a grammar book by simply fine-tuning an encoder-decoder translation model. We then investigate where grammar books help by testing two linguistic tasks, grammaticality judgment and gloss prediction, and we explore what kind of grammatical knowledge helps by introducing a typological feature prompt that achieves leading results on these more relevant tasks. We thus emphasise the importance of task-appropriate data for XLR languages: parallel examples for translation, and grammatical data for linguistic tasks. As we find no evidence that long-context LLMs can make effective use of grammatical explanations for XLR translation, we conclude data collection for multilingual XLR tasks such as translation is best focused on parallel data over linguistic description.

SciLitLLM: How to Adapt LLMs for Scientific Literature Understanding

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

LAB-Bench: Measuring Capabilities of Language Models for Biology Research

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

Language Modelling Approaches to Adaptive Machine Translation

Consistency is a key requirement of high-quality translation. It is especially important to adhere to pre-approved terminology and adapt to corrected translations in domain-specific projects. Machine translation (MT) has achieved significant progress in the area of domain adaptation. However, in-domain data scarcity is common in translation settings, due to the lack of specialised datasets and terminology, or inconsistency and inaccuracy of available in-domain translations. In such scenarios where there is insufficient in-domain data to fine-tune MT models, producing translations that are consistent with the relevant context is challenging. While real-time adaptation can make use of smaller amounts of in-domain data to improve the translation on the fly, it remains challenging due to supported context limitations and efficiency constraints. Large language models (LLMs) have recently shown interesting capabilities of in-context learning, where they learn to replicate certain input-output text generation patterns, without further fine-tuning. Such capabilities have opened new horizons for domain-specific data augmentation and real-time adaptive MT. This work attempts to address two main relevant questions: 1) in scenarios involving human interaction and continuous feedback, can we employ language models to improve the quality of adaptive MT at inference time? and 2) in the absence of sufficient in-domain data, can we use pre-trained large-scale language models to improve the process of MT domain adaptation?

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.

Indonesian Text-to-Image Synthesis with Sentence-BERT and FastGAN

Currently, text-to-image synthesis uses text encoder and image generator architecture. Research on this topic is challenging. This is because of the domain gap between natural language and vision. Nowadays, most research on this topic only focuses on producing a photo-realistic image, but the other domain, in this case, is the language, which is less concentrated. A lot of the current research uses English as the input text. Besides, there are many languages around the world. Bahasa Indonesia, as the official language of Indonesia, is quite popular. This language has been taught in Philipines, Australia, and Japan. Translating or recreating a new dataset into another language with good quality will cost a lot. Research on this domain is necessary because we need to examine how the image generator performs in other languages besides generating photo-realistic images. To achieve this, we translate the CUB dataset into Bahasa using google translate and manually by humans. We use Sentence BERT as the text encoder and FastGAN as the image generator. FastGAN uses lots of skip excitation modules and auto-encoder to generate an image with resolution 512x512x3, which is twice as bigger as the current state-of-the-art model (Zhang, Xu, Li, Zhang, Wang, Huang and Metaxas, 2019). We also get 4.76 +- 0.43 and 46.401 on Inception Score and Fr\'echet inception distance, respectively, and comparable with the current English text-to-image generation models. The mean opinion score also gives as 3.22 out of 5, which means the generated image is acceptable by humans. Link to source code: https://github.com/share424/Indonesian-Text-to-Image-synthesis-with-Sentence-BERT-and-FastGAN

The Impact of Large Language Models on Scientific Discovery: a Preliminary Study using GPT-4

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

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

Automatically Extracting Numerical Results from Randomized Controlled Trials with Large Language Models

Meta-analyses statistically aggregate the findings of different randomized controlled trials (RCTs) to assess treatment effectiveness. Because this yields robust estimates of treatment effectiveness, results from meta-analyses are considered the strongest form of evidence. However, rigorous evidence syntheses are time-consuming and labor-intensive, requiring manual extraction of data from individual trials to be synthesized. Ideally, language technologies would permit fully automatic meta-analysis, on demand. This requires accurately extracting numerical results from individual trials, which has been beyond the capabilities of natural language processing (NLP) models to date. In this work, we evaluate whether modern large language models (LLMs) can reliably perform this task. We annotate (and release) a modest but granular evaluation dataset of clinical trial reports with numerical findings attached to interventions, comparators, and outcomes. Using this dataset, we evaluate the performance of seven LLMs applied zero-shot for the task of conditionally extracting numerical findings from trial reports. We find that massive LLMs that can accommodate lengthy inputs are tantalizingly close to realizing fully automatic meta-analysis, especially for dichotomous (binary) outcomes (e.g., mortality). However, LLMs -- including ones trained on biomedical texts -- perform poorly when the outcome measures are complex and tallying the results requires inference. This work charts a path toward fully automatic meta-analysis of RCTs via LLMs, while also highlighting the limitations of existing models for this aim.

Adaptive Machine Translation with Large Language Models

Consistency is a key requirement of high-quality translation. It is especially important to adhere to pre-approved terminology and adapt to corrected translations in domain-specific projects. Machine translation (MT) has achieved significant progress in the area of domain adaptation. However, real-time adaptation remains challenging. Large-scale language models (LLMs) have recently shown interesting capabilities of in-context learning, where they learn to replicate certain input-output text generation patterns, without further fine-tuning. By feeding an LLM at inference time with a prompt that consists of a list of translation pairs, it can then simulate the domain and style characteristics. This work aims to investigate how we can utilize in-context learning to improve real-time adaptive MT. Our extensive experiments show promising results at translation time. For example, LLMs can adapt to a set of in-domain sentence pairs and/or terminology while translating a new sentence. We observe that the translation quality with few-shot in-context learning can surpass that of strong encoder-decoder MT systems, especially for high-resource languages. Moreover, we investigate whether we can combine MT from strong encoder-decoder models with fuzzy matches, which can further improve translation quality, especially for less supported languages. We conduct our experiments across five diverse language pairs, namely English-to-Arabic (EN-AR), English-to-Chinese (EN-ZH), English-to-French (EN-FR), English-to-Kinyarwanda (EN-RW), and English-to-Spanish (EN-ES).

ClimateGPT: Towards AI Synthesizing Interdisciplinary Research on Climate Change

This paper introduces ClimateGPT, a model family of domain-specific large language models that synthesize interdisciplinary research on climate change. We trained two 7B models from scratch on a science-oriented dataset of 300B tokens. For the first model, the 4.2B domain-specific tokens were included during pre-training and the second was adapted to the climate domain after pre-training. Additionally, ClimateGPT-7B, 13B and 70B are continuously pre-trained from Llama~2 on a domain-specific dataset of 4.2B tokens. Each model is instruction fine-tuned on a high-quality and human-generated domain-specific dataset that has been created in close cooperation with climate scientists. To reduce the number of hallucinations, we optimize the model for retrieval augmentation and propose a hierarchical retrieval strategy. To increase the accessibility of our model to non-English speakers, we propose to make use of cascaded machine translation and show that this approach can perform comparably to natively multilingual models while being easier to scale to a large number of languages. Further, to address the intrinsic interdisciplinary aspect of climate change we consider different research perspectives. Therefore, the model can produce in-depth answers focusing on different perspectives in addition to an overall answer. We propose a suite of automatic climate-specific benchmarks to evaluate LLMs. On these benchmarks, ClimateGPT-7B performs on par with the ten times larger Llama-2-70B Chat model while not degrading results on general domain benchmarks. Our human evaluation confirms the trends we saw in our benchmarks. All models were trained and evaluated using renewable energy and are released publicly.

Assessing Translation capabilities of Large Language Models involving English and Indian Languages

Generative Large Language Models (LLMs) have achieved remarkable advancements in various NLP tasks. In this work, our aim is to explore the multilingual capabilities of large language models by using machine translation as a task involving English and 22 Indian languages. We first investigate the translation capabilities of raw large language models, followed by exploring the in-context learning capabilities of the same raw models. We fine-tune these large language models using parameter efficient fine-tuning methods such as LoRA and additionally with full fine-tuning. Through our study, we have identified the best performing large language model for the translation task involving LLMs, which is based on LLaMA. Our results demonstrate significant progress, with average BLEU scores of 13.42, 15.93, 12.13, 12.30, and 12.07, as well as CHRF scores of 43.98, 46.99, 42.55, 42.42, and 45.39, respectively, using 2-stage fine-tuned LLaMA-13b for English to Indian languages on IN22 (conversational), IN22 (general), flores200-dev, flores200-devtest, and newstest2019 testsets. Similarly, for Indian languages to English, we achieved average BLEU scores of 14.03, 16.65, 16.17, 15.35 and 12.55 along with chrF scores of 36.71, 40.44, 40.26, 39.51, and 36.20, respectively, using fine-tuned LLaMA-13b on IN22 (conversational), IN22 (general), flores200-dev, flores200-devtest, and newstest2019 testsets. Overall, our findings highlight the potential and strength of large language models for machine translation capabilities, including for languages that are currently underrepresented in LLMs.

DICTDIS: Dictionary Constrained Disambiguation for Improved NMT

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.

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

Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processing

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.

Regression Transformer: Concurrent sequence regression and generation for molecular language modeling

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

Agent AI with LangGraph: A Modular Framework for Enhancing Machine Translation Using Large Language Models

This paper explores the transformative role of Agent AI and LangGraph in advancing the automation and effectiveness of machine translation (MT). Agents are modular components designed to perform specific tasks, such as translating between particular languages, with specializations like TranslateEnAgent, TranslateFrenchAgent, and TranslateJpAgent for English, French, and Japanese translations, respectively. These agents leverage the powerful semantic capabilities of large language models (LLMs), such as GPT-4o, to ensure accurate, contextually relevant translations while maintaining modularity, scalability, and context retention. LangGraph, a graph-based framework built on LangChain, simplifies the creation and management of these agents and their workflows. It supports dynamic state management, enabling agents to maintain dialogue context and automates complex workflows by linking agents and facilitating their collaboration. With flexibility, open-source community support, and seamless integration with LLMs, LangGraph empowers agents to deliver high-quality translations. Together, Agent AI and LangGraph create a cohesive system where LangGraph orchestrates agent interactions, ensuring that user inputs are analyzed, routed, and processed efficiently. Experimental results demonstrate the potential of this system to enhance multilingual translation accuracy and scalability. By highlighting modular design and automated workflows, this paper sets the stage for further innovations in intelligent machine translation services.

Fine-tuning Large Language Models for Domain-specific Machine Translation

Large language models (LLMs) have made significant progress in machine translation (MT). However, their potential in domain-specific MT remains under-explored. Current LLM-based MT systems still face several challenges. First, for LLMs with in-context learning, their effectiveness is highly sensitive to input translation examples, and processing them can increase inference costs. They often require extra post-processing due to over-generation. Second, LLMs with fine-tuning on domain-specific data often require high training costs for domain adaptation, and may weaken the zero-shot MT capabilities of LLMs due to over-specialization. The aforementioned methods can struggle to translate rare words in domain transfer scenarios. To address these challenges, this paper proposes a prompt-oriented fine-tuning method, denoted as LlamaIT, to effectively and efficiently fine-tune a general-purpose LLM for domain-specific MT tasks. First, we construct a task-specific mix-domain dataset, which is then used to fine-tune the LLM with LoRA. This can eliminate the need for input translation examples, post-processing, or over-specialization. By zero-shot prompting with instructions, we adapt the MT tasks to the target domain at inference time. To further elicit the MT capability for rare words, we construct new prompts by incorporating domain-specific bilingual vocabulary. We also conduct extensive experiments on both publicly available and self-constructed datasets. The results show that our LlamaIT can significantly enhance the domain-specific MT capabilities of the LLM, meanwhile preserving its zero-shot MT capabilities.

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.

Self-Distillation for Model Stacking Unlocks Cross-Lingual NLU in 200+ Languages

LLMs have become a go-to solution not just for text generation, but also for natural language understanding (NLU) tasks. Acquiring extensive knowledge through language modeling on web-scale corpora, they excel on English NLU, yet struggle to extend their NLU capabilities to underrepresented languages. In contrast, machine translation models (MT) produce excellent multilingual representations, resulting in strong translation performance even for low-resource languages. MT encoders, however, lack the knowledge necessary for comprehensive NLU that LLMs obtain through language modeling training on immense corpora. In this work, we get the best both worlds by integrating MT encoders directly into LLM backbones via sample-efficient self-distillation. The resulting MT-LLMs preserve the inherent multilingual representational alignment from the MT encoder, allowing lower-resource languages to tap into the rich knowledge embedded in English-centric LLMs. Merging the MT encoder and LLM in a single model, we mitigate the propagation of translation errors and inference overhead of MT decoding inherent to discrete translation-based cross-lingual transfer (e.g., translate-test). Evaluation spanning three prominent NLU tasks and 127 predominantly low-resource languages renders MT-LLMs highly effective in cross-lingual transfer. MT-LLMs substantially and consistently outperform translate-test based on the same MT model, showing that we truly unlock multilingual language understanding for LLMs.