Daily Papers

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, which thrive on substantially larger scales. Furthermore, genome understanding involves numerous downstream genome annotation tasks with inherent data heterogeneity, thereby necessitating more efficient and robust fine-tuning methods tailored for genomics. Here, we present Lingo: Language prefix fIne-tuning for GenOmes. Unlike DNA foundation models, Lingo strategically leverages natural language foundation models' contextual cues, recalibrating their linguistic knowledge to genomic sequences. Lingo further accommodates numerous, heterogeneous downstream fine-tune tasks by an adaptive rank sampling method that prunes and stochastically reintroduces pruned singular vectors within small computational budgets. Adaptive rank sampling outperformed existing fine-tuning methods on all benchmarked 14 genome understanding tasks, while requiring fewer than 2\% of trainable parameters as genomic-specific adapters. Impressively, applying these adapters on natural language foundation models matched or even exceeded the performance of DNA foundation models. Lingo presents a new paradigm of efficient and scalable genome understanding via genomic-specific adapters on language models.

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

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

Unlocking deep, interpretable biological reasoning from complex genomic data is a major AI challenge hindering scientific discovery. Current DNA foundation models, despite strong sequence representation, struggle with multi-step reasoning and lack inherent transparent, biologically intuitive explanations. We introduce BioReason, a pioneering architecture that, for the first time, deeply integrates a DNA foundation model with a Large Language Model (LLM). This novel connection enables the LLM to directly process and reason with genomic information as a fundamental input, fostering a new form of multimodal biological understanding. BioReason's sophisticated multi-step reasoning is developed through supervised fine-tuning and targeted reinforcement learning, guiding the system to generate logical, biologically coherent deductions. On biological reasoning benchmarks including KEGG-based disease pathway prediction - where accuracy improves from 88% to 97% - and variant effect prediction, BioReason demonstrates an average 15% performance gain over strong single-modality baselines. BioReason reasons over unseen biological entities and articulates decision-making through interpretable, step-by-step biological traces, offering a transformative approach for AI in biology that enables deeper mechanistic insights and accelerates testable hypothesis generation from genomic data. Data, code, and checkpoints are publicly available at https://github.com/bowang-lab/BioReason

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

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.

This paper presents a systematic review of benchmarks and approaches for explainability in Machine Reading Comprehension (MRC). We present how the representation and inference challenges evolved and the steps which were taken to tackle these challenges. We also present the evaluation methodologies to assess the performance of explainable systems. In addition, we identify persisting open research questions and highlight critical directions for future work.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.

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

For natural language understanding (NLU) technology to be maximally useful, both practically and as a scientific object of study, it must be general: it must be able to process language in a way that is not exclusively tailored to any one specific task or dataset. In pursuit of this objective, we introduce the General Language Understanding Evaluation benchmark (GLUE), a tool for evaluating and analyzing the performance of models across a diverse range of existing NLU tasks. GLUE is model-agnostic, but it incentivizes sharing knowledge across tasks because certain tasks have very limited training data. We further provide a hand-crafted diagnostic test suite that enables detailed linguistic analysis of NLU models. We evaluate baselines based on current methods for multi-task and transfer learning and find that they do not immediately give substantial improvements over the aggregate performance of training a separate model per task, indicating room for improvement in developing general and robust NLU systems.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Scientific problem-solving involves synthesizing information while applying expert knowledge. We introduce CURIE, a scientific long-Context Understanding,Reasoning and Information Extraction benchmark to measure the potential of Large Language Models (LLMs) in scientific problem-solving and assisting scientists in realistic workflows. This benchmark introduces ten challenging tasks with a total of 580 problems and solution pairs curated by experts in six disciplines - materials science, condensed matter physics, quantum computing, geospatial analysis, biodiversity, and proteins - covering both experimental and theoretical work-flows in science. We evaluate a range of closed and open LLMs on tasks in CURIE which requires domain expertise, comprehension of long in-context information,and multi-step reasoning. While Gemini Flash 2.0 and Claude-3 show consistent high comprehension across domains, the popular GPT-4o and command-R+ fail dramatically on protein sequencing tasks. With the best performance at 32% there is much room for improvement for all models. We hope that insights gained from CURIE can guide the future development of LLMs in sciences. Evaluation code and data are in https://github.com/google/curie

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Large language models (LLMs) have demonstrated remarkable proficiency in generating detailed and coherent explanations of complex concepts. However, the extent to which these models truly comprehend the concepts they articulate remains unclear. To assess the level of comprehension of a model relative to the content it generates, we implemented a self-evaluation pipeline where models: (i) given a topic generate an excerpt with information about the topic, (ii) given an excerpt generate question-answer pairs, and finally (iii) given a question generate an answer. We refer to this self-evaluation approach as Explain-Query-Test (EQT). Interestingly, the accuracy on generated questions resulting from running the EQT pipeline correlates strongly with the model performance as verified by typical benchmarks such as MMLU-Pro. In other words, EQT's performance is predictive of MMLU-Pro's, and EQT can be used to rank models without the need for any external source of evaluation data other than lists of topics of interest. Moreover, our results reveal a disparity between the models' ability to produce detailed explanations and their performance on questions related to those explanations. This gap highlights fundamental limitations in the internal knowledge representation and reasoning abilities of current LLMs. We release the code at https://github.com/asgsaeid/EQT.

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

Scientific literature is typically dense, requiring significant background knowledge and deep comprehension for effective engagement. We introduce SciDQA, a new dataset for reading comprehension that challenges LLMs for a deep understanding of scientific articles, consisting of 2,937 QA pairs. Unlike other scientific QA datasets, SciDQA sources questions from peer reviews by domain experts and answers by paper authors, ensuring a thorough examination of the literature. We enhance the dataset's quality through a process that carefully filters out lower quality questions, decontextualizes the content, tracks the source document across different versions, and incorporates a bibliography for multi-document question-answering. Questions in SciDQA necessitate reasoning across figures, tables, equations, appendices, and supplementary materials, and require multi-document reasoning. We evaluate several open-source and proprietary LLMs across various configurations to explore their capabilities in generating relevant and factual responses. Our comprehensive evaluation, based on metrics for surface-level similarity and LLM judgements, highlights notable performance discrepancies. SciDQA represents a rigorously curated, naturally derived scientific QA dataset, designed to facilitate research on complex scientific text understanding.

The automatic evaluation of instruction following typically involves using large language models (LLMs) to assess response quality. However, there is a lack of comprehensive evaluation of these LLM-based evaluators across two dimensions: the base LLMs and the evaluation protocols. Therefore, we present a thorough meta-evaluation of instruction following, including 25 base LLMs and 15 recently proposed evaluation protocols, on 4 human-annotated datasets, assessing the evaluation accuracy of the LLM-evaluators. Our evaluation allows us to identify the best-performing base LLMs and evaluation protocols with a high degree of robustness. Moreover, our large-scale evaluation reveals: (1) Base LLM performance ranking remains largely consistent across evaluation protocols, with less capable LLMs showing greater improvement from protocol enhancements; (2) Robust evaluation of evaluation protocols requires many base LLMs with varying capability levels, as protocol effectiveness can depend on the base LLM used; (3) Evaluation results on different datasets are not always consistent, so a rigorous evaluation requires multiple datasets with distinctive features. We release our meta-evaluation suite ReIFE, which provides the codebase and evaluation result collection for more than 500 LLM-evaluator configurations, to support future research in instruction-following evaluation.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

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

Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling. However, previous methods often relied on massive pre-training data or large-scale base models with huge parameters, imposing a significant computational burden. To address this, many works attempted to use more compact models to achieve similar outcomes but still fell short by a considerable margin. In this work, we propose a Hybrid Architecture Distillation (HAD) approach, leveraging both distillation and reconstruction tasks for more efficient and effective pre-training. Specifically, we employ the NTv2-500M as the teacher model and devise a grouping masking strategy to align the feature embeddings of visible tokens while concurrently reconstructing the invisible tokens during MLM pre-training. To validate the effectiveness of our proposed method, we conducted comprehensive experiments on the Nucleotide Transformer Benchmark and Genomic Benchmark. Compared to models with similar parameters, our model achieved excellent performance. More surprisingly, it even surpassed the distillation ceiling-teacher model on some sub-tasks, which is more than 500 times larger. Lastly, we utilize t-SNE for more intuitive visualization, which shows that our model can gain a sophisticated understanding of the intrinsic representation pattern in genomic sequences.

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

There is growing interest in systems that generate captions for scientific figures. However, assessing these systems output poses a significant challenge. Human evaluation requires academic expertise and is costly, while automatic evaluation depends on often low-quality author-written captions. This paper investigates using large language models (LLMs) as a cost-effective, reference-free method for evaluating figure captions. We first constructed SCICAP-EVAL, a human evaluation dataset that contains human judgments for 3,600 scientific figure captions, both original and machine-made, for 600 arXiv figures. We then prompted LLMs like GPT-4 and GPT-3 to score (1-6) each caption based on its potential to aid reader understanding, given relevant context such as figure-mentioning paragraphs. Results show that GPT-4, used as a zero-shot evaluator, outperformed all other models and even surpassed assessments made by Computer Science and Informatics undergraduates, achieving a Kendall correlation score of 0.401 with Ph.D. students rankings

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

As LLMs have become increasingly popular, they have been used in almost every field. But as the application for LLMs expands from generic fields to narrow, focused science domains, there exists an ever-increasing gap in ways to evaluate their efficacy in those fields. For the benchmarks that do exist, a lot of them focus on questions that don't require proper understanding of the subject in question. In this paper, we present NuclearQA, a human-made benchmark of 100 questions to evaluate language models in the nuclear domain, consisting of a varying collection of questions that have been specifically designed by experts to test the abilities of language models. We detail our approach and show how the mix of several types of questions makes our benchmark uniquely capable of evaluating models in the nuclear domain. We also present our own evaluation metric for assessing LLM's performances due to the limitations of existing ones. Our experiments on state-of-the-art models suggest that even the best LLMs perform less than satisfactorily on our benchmark, demonstrating the scientific knowledge gap of existing LLMs.

We present bgGLUE(Bulgarian General Language Understanding Evaluation), a benchmark for evaluating language models on Natural Language Understanding (NLU) tasks in Bulgarian. Our benchmark includes NLU tasks targeting a variety of NLP problems (e.g., natural language inference, fact-checking, named entity recognition, sentiment analysis, question answering, etc.) and machine learning tasks (sequence labeling, document-level classification, and regression). We run the first systematic evaluation of pre-trained language models for Bulgarian, comparing and contrasting results across the nine tasks in the benchmark. The evaluation results show strong performance on sequence labeling tasks, but there is a lot of room for improvement for tasks that require more complex reasoning. We make bgGLUE publicly available together with the fine-tuning and the evaluation code, as well as a public leaderboard at https://bgglue.github.io/, and we hope that it will enable further advancements in developing NLU models for Bulgarian.

Advances in unsupervised probes such as Contrast-Consistent Search (CCS), which reveal latent beliefs without relying on token outputs, raise the question of whether these methods can reliably assess model alignment. We investigate this by examining the sensitivity of CCS to harmful vs. safe statements and by introducing Polarity-Aware CCS (PA-CCS), a method for evaluating whether a model's internal representations remain consistent under polarity inversion. We propose two alignment-oriented metrics, Polar-Consistency and the Contradiction Index, to quantify the semantic robustness of a model's latent knowledge. To validate PA-CCS, we curate two main datasets and one control dataset containing matched harmful-safe sentence pairs constructed using different methodologies (concurrent and antagonistic statements). We apply PA-CCS to 16 language models. Our results show that PA-CCS identifies both architectural and layer-specific differences in the encoding of latent harmful knowledge. Notably, replacing the negation token with a meaningless marker degrades PA-CCS scores for models with well-aligned internal representations, while models lacking robust internal calibration do not exhibit this degradation. Our findings highlight the potential of unsupervised probing for alignment evaluation and emphasize the need to incorporate structural robustness checks into interpretability benchmarks. Code and datasets are available at: https://github.com/SadSabrina/polarity-probing. WARNING: This paper contains potentially sensitive, harmful, and offensive content.

In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden of labor for genetic diagnostics and research from the gathering of data to its interpretation. Helix presents a state of the art platform for the prediction of pathogenicity in human missense variants. In addition to offering best-in-class predictive performance, Helix offers a platform that allows researchers to analyze and interpret variants in depth that can be accessed at helixlabs.ai.

Posing reading comprehension as a generation problem provides a great deal of flexibility, allowing for open-ended questions with few restrictions on possible answers. However, progress is impeded by existing generation metrics, which rely on token overlap and are agnostic to the nuances of reading comprehension. To address this, we introduce a benchmark for training and evaluating generative reading comprehension metrics: MOdeling Correctness with Human Annotations. MOCHA contains 40K human judgement scores on model outputs from 6 diverse question answering datasets and an additional set of minimal pairs for evaluation. Using MOCHA, we train a Learned Evaluation metric for Reading Comprehension, LERC, to mimic human judgement scores. LERC outperforms baseline metrics by 10 to 36 absolute Pearson points on held-out annotations. When we evaluate robustness on minimal pairs, LERC achieves 80% accuracy, outperforming baselines by 14 to 26 absolute percentage points while leaving significant room for improvement. MOCHA presents a challenging problem for developing accurate and robust generative reading comprehension metrics.

This paper introduces MedExQA, a novel benchmark in medical question-answering, to evaluate large language models' (LLMs) understanding of medical knowledge through explanations. By constructing datasets across five distinct medical specialties that are underrepresented in current datasets and further incorporating multiple explanations for each question-answer pair, we address a major gap in current medical QA benchmarks which is the absence of comprehensive assessments of LLMs' ability to generate nuanced medical explanations. Our work highlights the importance of explainability in medical LLMs, proposes an effective methodology for evaluating models beyond classification accuracy, and sheds light on one specific domain, speech language pathology, where current LLMs including GPT4 lack good understanding. Our results show generation evaluation with multiple explanations aligns better with human assessment, highlighting an opportunity for a more robust automated comprehension assessment for LLMs. To diversify open-source medical LLMs (currently mostly based on Llama2), this work also proposes a new medical model, MedPhi-2, based on Phi-2 (2.7B). The model outperformed medical LLMs based on Llama2-70B in generating explanations, showing its effectiveness in the resource-constrained medical domain. We will share our benchmark datasets and the trained model.

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

The issue of shortcut learning is widely known in NLP and has been an important research focus in recent years. Unintended correlations in the data enable models to easily solve tasks that were meant to exhibit advanced language understanding and reasoning capabilities. In this survey paper, we focus on the field of machine reading comprehension (MRC), an important task for showcasing high-level language understanding that also suffers from a range of shortcuts. We summarize the available techniques for measuring and mitigating shortcuts and conclude with suggestions for further progress in shortcut research. Importantly, we highlight two concerns for shortcut mitigation in MRC: (1) the lack of public challenge sets, a necessary component for effective and reusable evaluation, and (2) the lack of certain mitigation techniques that are prominent in other areas.

Human evaluation is the foundation upon which the evaluation of both summarization systems and automatic metrics rests. However, existing human evaluation studies for summarization either exhibit a low inter-annotator agreement or have insufficient scale, and an in-depth analysis of human evaluation is lacking. Therefore, we address the shortcomings of existing summarization evaluation along the following axes: (1) We propose a modified summarization salience protocol, Atomic Content Units (ACUs), which is based on fine-grained semantic units and allows for a high inter-annotator agreement. (2) We curate the Robust Summarization Evaluation (RoSE) benchmark, a large human evaluation dataset consisting of 22,000 summary-level annotations over 28 top-performing systems on three datasets. (3) We conduct a comparative study of four human evaluation protocols, underscoring potential confounding factors in evaluation setups. (4) We evaluate 50 automatic metrics and their variants using the collected human annotations across evaluation protocols and demonstrate how our benchmark leads to more statistically stable and significant results. The metrics we benchmarked include recent methods based on large language models (LLMs), GPTScore and G-Eval. Furthermore, our findings have important implications for evaluating LLMs, as we show that LLMs adjusted by human feedback (e.g., GPT-3.5) may overfit unconstrained human evaluation, which is affected by the annotators' prior, input-agnostic preferences, calling for more robust, targeted evaluation methods.

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

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

Offering a promising solution to the scalability challenges associated with human evaluation, the LLM-as-a-judge paradigm is rapidly gaining traction as an approach to evaluating large language models (LLMs). However, there are still many open questions about the strengths and weaknesses of this paradigm, and what potential biases it may hold. In this paper, we present a comprehensive study of the performance of various LLMs acting as judges. We leverage TriviaQA as a benchmark for assessing objective knowledge reasoning of LLMs and evaluate them alongside human annotations which we found to have a high inter-annotator agreement. Our study includes 9 judge models and 9 exam taker models -- both base and instruction-tuned. We assess the judge model's alignment across different model sizes, families, and judge prompts. Among other results, our research rediscovers the importance of using Cohen's kappa as a metric of alignment as opposed to simple percent agreement, showing that judges with high percent agreement can still assign vastly different scores. We find that both Llama-3 70B and GPT-4 Turbo have an excellent alignment with humans, but in terms of ranking exam taker models, they are outperformed by both JudgeLM-7B and the lexical judge Contains, which have up to 34 points lower human alignment. Through error analysis and various other studies, including the effects of instruction length and leniency bias, we hope to provide valuable lessons for using LLMs as judges in the future.

Effective evaluation of language models remains an open challenge in NLP. Researchers and engineers face methodological issues such as the sensitivity of models to evaluation setup, difficulty of proper comparisons across methods, and the lack of reproducibility and transparency. In this paper we draw on three years of experience in evaluating large language models to provide guidance and lessons for researchers. First, we provide an overview of common challenges faced in language model evaluation. Second, we delineate best practices for addressing or lessening the impact of these challenges on research. Third, we present the Language Model Evaluation Harness (lm-eval): an open source library for independent, reproducible, and extensible evaluation of language models that seeks to address these issues. We describe the features of the library as well as case studies in which the library has been used to alleviate these methodological concerns.

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Instruction-tuned Large Language Models (LLMs) have recently showcased remarkable advancements in their ability to generate fitting responses to natural language instructions. However, many current works rely on manual evaluation to judge the quality of generated responses. Since such manual evaluation is time-consuming, it does not easily scale to the evaluation of multiple models and model variants. In this short paper, we propose a straightforward but remarkably effective evaluation metric called SemScore, in which we directly compare model outputs to gold target responses using semantic textual similarity (STS). We conduct a comparative evaluation of the model outputs of 12 prominent instruction-tuned LLMs using 8 widely-used evaluation metrics for text generation. We find that our proposed SemScore metric outperforms all other, in many cases more complex, evaluation metrics in terms of correlation to human evaluation. These findings indicate the utility of our proposed metric for the evaluation of instruction-tuned LLMs.

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

Recently, reading comprehension models achieved near-human performance on large-scale datasets such as SQuAD, CoQA, MS Macro, RACE, etc. This is largely due to the release of pre-trained contextualized representations such as BERT and ELMo, which can be fine-tuned for the target task. Despite those advances and the creation of more challenging datasets, most of the work is still done for English. Here, we study the effectiveness of multilingual BERT fine-tuned on large-scale English datasets for reading comprehension (e.g., for RACE), and we apply it to Bulgarian multiple-choice reading comprehension. We propose a new dataset containing 2,221 questions from matriculation exams for twelfth grade in various subjects -history, biology, geography and philosophy-, and 412 additional questions from online quizzes in history. While the quiz authors gave no relevant context, we incorporate knowledge from Wikipedia, retrieving documents matching the combination of question + each answer option. Moreover, we experiment with different indexing and pre-training strategies. The evaluation results show accuracy of 42.23%, which is well above the baseline of 24.89%.

Retrieval-Augmented Generation (RAG) has advanced significantly in recent years. The complexity of RAG systems, which involve multiple components-such as indexing, retrieval, and generation-along with numerous other parameters, poses substantial challenges for systematic evaluation and quality enhancement. Previous research highlights that evaluating RAG systems is essential for documenting advancements, comparing configurations, and identifying effective approaches for domain-specific applications. This study systematically reviews 63 academic articles to provide a comprehensive overview of state-of-the-art RAG evaluation methodologies, focusing on four key areas: datasets, retrievers, indexing and databases, and the generator component. We observe the feasibility of an automated evaluation approach for each component of a RAG system, leveraging an LLM capable of both generating evaluation datasets and conducting evaluations. In addition, we found that further practical research is essential to provide companies with clear guidance on the do's and don'ts of implementing and evaluating RAG systems. By synthesizing evaluation approaches for key RAG components and emphasizing the creation and adaptation of domain-specific datasets for benchmarking, we contribute to the advancement of systematic evaluation methods and the improvement of evaluation rigor for RAG systems. Furthermore, by examining the interplay between automated approaches leveraging LLMs and human judgment, we contribute to the ongoing discourse on balancing automation and human input, clarifying their respective contributions, limitations, and challenges in achieving robust and reliable evaluations.

Recent advances have been improving the context windows of Large Language Models (LLMs). To quantify the real long-context capabilities of LLMs, evaluators such as the popular Needle in a Haystack have been developed to test LLMs over a large chunk of raw texts. While effective, current evaluations overlook the insight of how LLMs work with long-context code, i.e., repositories. To this end, we initiate the RepoQA benchmark to evaluate LLMs on long-context code understanding. Traditional needle testers ask LLMs to directly retrieve the answer from the context without necessary deep understanding. In RepoQA, we built our initial task, namely Searching Needle Function (SNF), which exercises LLMs to search functions given their natural-language description, i.e., LLMs cannot find the desired function if they cannot understand the description and code. RepoQA is multilingual and comprehensive: it includes 500 code search tasks gathered from 50 popular repositories across 5 modern programming languages. By evaluating 26 general and code-specific LLMs on RepoQA, we show (i) there is still a small gap between the best open and proprietary models; (ii) different models are good at different languages; and (iii) models may understand code better without comments.

We present STARC (Structured Annotations for Reading Comprehension), a new annotation framework for assessing reading comprehension with multiple choice questions. Our framework introduces a principled structure for the answer choices and ties them to textual span annotations. The framework is implemented in OneStopQA, a new high-quality dataset for evaluation and analysis of reading comprehension in English. We use this dataset to demonstrate that STARC can be leveraged for a key new application for the development of SAT-like reading comprehension materials: automatic annotation quality probing via span ablation experiments. We further show that it enables in-depth analyses and comparisons between machine and human reading comprehension behavior, including error distributions and guessing ability. Our experiments also reveal that the standard multiple choice dataset in NLP, RACE, is limited in its ability to measure reading comprehension. 47% of its questions can be guessed by machines without accessing the passage, and 18% are unanimously judged by humans as not having a unique correct answer. OneStopQA provides an alternative test set for reading comprehension which alleviates these shortcomings and has a substantially higher human ceiling performance.

Given the dominance of dense retrievers that do not generalize well beyond their training dataset distributions, domain-specific test sets are essential in evaluating retrieval. There are few test datasets for retrieval systems intended for use by healthcare providers in a point-of-care setting. To fill this gap we have collaborated with medical professionals to create CURE, an ad-hoc retrieval test dataset for passage ranking with 2000 queries spanning 10 medical domains with a monolingual (English) and two cross-lingual (French/Spanish -> English) conditions. In this paper, we describe how CURE was constructed and provide baseline results to showcase its effectiveness as an evaluation tool. CURE is published with a Creative Commons Attribution Non Commercial 4.0 license and can be accessed on Hugging Face.

This technical report briefly describes our JDExplore d-team's submission Vega v1 on the General Language Understanding Evaluation (GLUE) leaderboard, where GLUE is a collection of nine natural language understanding tasks, including question answering, linguistic acceptability, sentiment analysis, text similarity, paraphrase detection, and natural language inference. [Method] We investigate several effective strategies and choose their best combination setting as the training recipes. As for model structure, we employ the vanilla Transformer with disentangled attention as the basic block encoder. For self-supervised training, we employ the representative denoising objective (i.e., replaced token detection) in phase 1 and combine the contrastive objective (i.e., sentence embedding contrastive learning) with it in phase 2. During fine-tuning, several advanced techniques such as transductive fine-tuning, self-calibrated fine-tuning, and adversarial fine-tuning are adopted. [Results] According to our submission record (Jan. 2022), with our optimized pretraining and fine-tuning strategies, our 1.3 billion model sets new state-of-the-art on 4/9 tasks, achieving the best average score of 91.3. Encouragingly, our Vega v1 is the first to exceed powerful human performance on the two challenging tasks, i.e., SST-2 and WNLI. We believe our empirically successful recipe with a bag of tricks could shed new light on developing efficient discriminative large language models.

We introduce AbGen, the first benchmark designed to evaluate the capabilities of LLMs in designing ablation studies for scientific research. AbGen consists of 1,500 expert-annotated examples derived from 807 NLP papers. In this benchmark, LLMs are tasked with generating detailed ablation study designs for a specified module or process based on the given research context. Our evaluation of leading LLMs, such as DeepSeek-R1-0528 and o4-mini, highlights a significant performance gap between these models and human experts in terms of the importance, faithfulness, and soundness of the ablation study designs. Moreover, we demonstrate that current automated evaluation methods are not reliable for our task, as they show a significant discrepancy when compared to human assessment. To better investigate this, we develop AbGen-Eval, a meta-evaluation benchmark designed to assess the reliability of commonly used automated evaluation systems in measuring LLM performance on our task. We investigate various LLM-as-Judge systems on AbGen-Eval, providing insights for future research on developing more effective and reliable LLM-based evaluation systems for complex scientific tasks.

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

In the automatic evaluation of generative question answering (GenQA) systems, it is difficult to assess the correctness of generated answers due to the free-form of the answer. Especially, widely used n-gram similarity metrics often fail to discriminate the incorrect answers since they equally consider all of the tokens. To alleviate this problem, we propose KPQA-metric, a new metric for evaluating the correctness of GenQA. Specifically, our new metric assigns different weights to each token via keyphrase prediction, thereby judging whether a generated answer sentence captures the key meaning of the reference answer. To evaluate our metric, we create high-quality human judgments of correctness on two GenQA datasets. Using our human-evaluation datasets, we show that our proposed metric has a significantly higher correlation with human judgments than existing metrics. The code is available at https://github.com/hwanheelee1993/KPQA.

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

The Needle-in-a-Haystack (NIAH) benchmark is widely used to evaluate Large Language Models' (LLMs) ability to understand long contexts (LC). It evaluates the capability to identify query-relevant context within extensive query-irrelevant passages. Although this method serves as a widely accepted standard for evaluating long-context understanding, our findings suggest it may overestimate the true LC capability of LLMs. We demonstrate that even state-of-the-art models such as GPT-4o struggle to intactly incorporate given contexts made up of solely query-relevant ten sentences. In response, we introduce a novel benchmark, NeedleChain, where the context consists entirely of query-relevant information, requiring the LLM to fully grasp the input to answer correctly. Our benchmark allows for flexible context length and reasoning order, offering a more comprehensive analysis of LLM performance. Additionally, we propose an extremely simple yet compelling strategy to improve LC understanding capability of LLM: ROPE Contraction. Our experiments with various advanced LLMs reveal a notable disparity between their ability to process large contexts and their capacity to fully understand them. Source code and datasets are available at https://github.com/hyeonseokk/NeedleChain

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

The advent of natural language understanding (NLU) benchmarks for English, such as GLUE and SuperGLUE allows new NLU models to be evaluated across a diverse set of tasks. These comprehensive benchmarks have facilitated a broad range of research and applications in natural language processing (NLP). The problem, however, is that most such benchmarks are limited to English, which has made it difficult to replicate many of the successes in English NLU for other languages. To help remedy this issue, we introduce the first large-scale Chinese Language Understanding Evaluation (CLUE) benchmark. CLUE is an open-ended, community-driven project that brings together 9 tasks spanning several well-established single-sentence/sentence-pair classification tasks, as well as machine reading comprehension, all on original Chinese text. To establish results on these tasks, we report scores using an exhaustive set of current state-of-the-art pre-trained Chinese models (9 in total). We also introduce a number of supplementary datasets and additional tools to help facilitate further progress on Chinese NLU. Our benchmark is released at https://www.CLUEbenchmarks.com

If you had an AI Whale-to-English translator, how could you validate whether or not it is working? Does one need to interact with the animals or rely on grounded observations such as temperature? We provide theoretical and proof-of-concept experimental evidence suggesting that interaction and even observations may not be necessary for sufficiently complex languages. One may be able to evaluate translators solely by their English outputs, offering potential advantages in terms of safety, ethics, and cost. This is an instance of machine translation quality evaluation (MTQE) without any reference translations available. A key challenge is identifying ``hallucinations,'' false translations which may appear fluent and plausible. We propose using segment-by-segment translation together with the classic NLP shuffle test to evaluate translators. The idea is to translate animal communication, turn by turn, and evaluate how often the resulting translations make more sense in order than permuted. Proof-of-concept experiments on data-scarce human languages and constructed languages demonstrate the potential utility of this evaluation methodology. These human-language experiments serve solely to validate our reference-free metric under data scarcity. It is found to correlate highly with a standard evaluation based on reference translations, which are available in our experiments. We also perform a theoretical analysis suggesting that interaction may not be necessary nor efficient in the early stages of learning to translate.

Achieving human-level performance on some of Machine Reading Comprehension (MRC) datasets is no longer challenging with the help of powerful Pre-trained Language Models (PLMs). However, it is necessary to provide both answer prediction and its explanation to further improve the MRC system's reliability, especially for real-life applications. In this paper, we propose a new benchmark called ExpMRC for evaluating the explainability of the MRC systems. ExpMRC contains four subsets, including SQuAD, CMRC 2018, RACE^+, and C^3 with additional annotations of the answer's evidence. The MRC systems are required to give not only the correct answer but also its explanation. We use state-of-the-art pre-trained language models to build baseline systems and adopt various unsupervised approaches to extract evidence without a human-annotated training set. The experimental results show that these models are still far from human performance, suggesting that the ExpMRC is challenging. Resources will be available through https://github.com/ymcui/expmrc

Recent advancements in large language models (LLM) capable of processing extremely long texts highlight the need for a dedicated evaluation benchmark to assess their long-context capabilities. However, existing methods, like the needle-in-a-haystack test, do not effectively assess whether these models fully utilize contextual information, raising concerns about the reliability of current evaluation techniques. To thoroughly examine the effectiveness of existing benchmarks, we introduce a new metric called information coverage (IC), which quantifies the proportion of the input context necessary for answering queries. Our findings indicate that current benchmarks exhibit low IC; although the input context may be extensive, the actual usable context is often limited. To address this, we present ETHIC, a novel benchmark designed to assess LLMs' ability to leverage the entire context. Our benchmark comprises 2,648 test instances spanning four long-context tasks with high IC scores in the domains of books, debates, medicine, and law. Our evaluations reveal significant performance drops in contemporary LLMs, highlighting a critical challenge in managing long contexts. Our benchmark is available at https://github.com/dmis-lab/ETHIC.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

Machine Translation (MT) evaluation metrics assess translation quality automatically. Recently, researchers have employed MT metrics for various new use cases, such as data filtering and translation re-ranking. However, most MT metrics return assessments as scalar scores that are difficult to interpret, posing a challenge to making informed design choices. Moreover, MT metrics' capabilities have historically been evaluated using correlation with human judgment, which, despite its efficacy, falls short of providing intuitive insights into metric performance, especially in terms of new metric use cases. To address these issues, we introduce an interpretable evaluation framework for MT metrics. Within this framework, we evaluate metrics in two scenarios that serve as proxies for the data filtering and translation re-ranking use cases. Furthermore, by measuring the performance of MT metrics using Precision, Recall, and F-score, we offer clearer insights into their capabilities than correlation with human judgments. Finally, we raise concerns regarding the reliability of manually curated data following the Direct Assessments+Scalar Quality Metrics (DA+SQM) guidelines, reporting a notably low agreement with Multidimensional Quality Metrics (MQM) annotations.

Evaluating the performance of various model architectures, such as transformers, large language models (LLMs), and other NLP systems, requires comprehensive benchmarks that measure performance across multiple dimensions. Among these, the evaluation of natural language understanding (NLU) is particularly critical as it serves as a fundamental criterion for assessing model capabilities. Thus, it is essential to establish benchmarks that enable thorough evaluation and analysis of NLU abilities from diverse perspectives. While the GLUE benchmark has set a standard for evaluating English NLU, similar benchmarks have been developed for other languages, such as CLUE for Chinese, FLUE for French, and JGLUE for Japanese. However, no comparable benchmark currently exists for the Turkish language. To address this gap, we introduce TrGLUE, a comprehensive benchmark encompassing a variety of NLU tasks for Turkish. In addition, we present SentiTurca, a specialized benchmark for sentiment analysis. To support researchers, we also provide fine-tuning and evaluation code for transformer-based models, facilitating the effective use of these benchmarks. TrGLUE comprises Turkish-native corpora curated to mirror the domains and task formulations of GLUE-style evaluations, with labels obtained through a semi-automated pipeline that combines strong LLM-based annotation, cross-model agreement checks, and subsequent human validation. This design prioritizes linguistic naturalness, minimizes direct translation artifacts, and yields a scalable, reproducible workflow. With TrGLUE, our goal is to establish a robust evaluation framework for Turkish NLU, empower researchers with valuable resources, and provide insights into generating high-quality semi-automated datasets.

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

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

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

In recent times, substantial advancements have been witnessed in large language models (LLMs), exemplified by ChatGPT, showcasing remarkable proficiency across a range of complex tasks. However, many mainstream LLMs (e.g. LLaMA) are pretrained on English-dominant corpus, which limits their performance in other non-English languages. In this paper, we focus on how to effectively transfer the capabilities of language generation and following instructions to a non-English language. To answer this question, we conduct an extensive empirical investigation based on LLaMA, accumulating over 1440 GPU hours. We analyze the impact of key factors such as vocabulary extension, further pretraining, and instruction tuning on transfer. To accurately assess the model's level of knowledge, we employ four widely used standardized testing benchmarks: C-Eval, MMLU, AGI-Eval, and GAOKAO-Bench. Furthermore, a comprehensive evaluation of the model's response quality is conducted, considering aspects such as accuracy, fluency, informativeness, logical coherence, and harmlessness, based on LLM-Eval, a benchmarks consisting instruction tasks from 17 diverse categories. Our evaluation results demonstrate that comparable performance to state-of-the-art transfer models can be achieved with less than 1% of the pretraining data, both in terms of knowledge alignment and response quality. Furthermore, the experimental outcomes across the thirteen low-resource languages also exhibit similar trends. We anticipate that the conclusions revealed by the experiments will aid the community in developing non-English LLMs.

Recent advancements in machine learning have significantly improved the identification of disease-associated genes from gene expression datasets. However, these processes often require extensive expertise and manual effort, limiting their scalability. Large Language Model (LLM)-based agents have shown promise in automating these tasks due to their increasing problem-solving abilities. To support the evaluation and development of such methods, we introduce GenoTEX, a benchmark dataset for the automated analysis of gene expression data. GenoTEX provides annotated code and results for solving a wide range of gene identification problems, encompassing dataset selection, preprocessing, and statistical analysis, in a pipeline that follows computational genomics standards. The benchmark includes expert-curated annotations from bioinformaticians to ensure accuracy and reliability. To provide baselines for these tasks, we present GenoAgent, a team of LLM-based agents that adopt a multi-step programming workflow with flexible self-correction, to collaboratively analyze gene expression datasets. Our experiments demonstrate the potential of LLM-based methods in analyzing genomic data, while error analysis highlights the challenges and areas for future improvement. We propose GenoTEX as a promising resource for benchmarking and enhancing automated methods for gene expression data analysis. The benchmark is available at https://github.com/Liu-Hy/GenoTex.

Recently, the evaluation of Large Language Models has emerged as a popular area of research. The three crucial questions for LLM evaluation are ``what, where, and how to evaluate''. However, the existing research mainly focuses on the first two questions, which are basically what tasks to give the LLM during testing and what kind of knowledge it should deal with. As for the third question, which is about what standards to use, the types of evaluators, how to score, and how to rank, there hasn't been much discussion. In this paper, we analyze evaluation methods by comparing various criteria with both manual and automatic evaluation, utilizing onsite, crowd-sourcing, public annotators and GPT-4, with different scoring methods and ranking systems. We propose a new dataset, LLMEval and conduct evaluations on 20 LLMs. A total of 2,186 individuals participated, leading to the generation of 243,337 manual annotations and 57,511 automatic evaluation results. We perform comparisons and analyses of different settings and conduct 10 conclusions that can provide some insights for evaluating LLM in the future. The dataset and the results are publicly available at https://github.com/llmeval .

Despite the significant advancements in keyphrase extraction and keyphrase generation methods, the predominant approach for evaluation only relies on exact matching with human references and disregards reference-free attributes. This scheme fails to recognize systems that generate keyphrases that are semantically equivalent to the references or keyphrases that have practical utility. To better understand the strengths and weaknesses of different keyphrase systems, we propose a comprehensive evaluation framework consisting of six critical dimensions: naturalness, faithfulness, saliency, coverage, diversity, and utility. For each dimension, we discuss the desiderata and design semantic-based metrics that align with the evaluation objectives. Rigorous meta-evaluation studies demonstrate that our evaluation strategy correlates better with human preferences compared to a range of previously used metrics. Using this framework, we re-evaluate 18 keyphrase systems and further discover that (1) the best model differs in different dimensions, with pre-trained language models achieving the best in most dimensions; (2) the utility in downstream tasks does not always correlate well with reference-based metrics; and (3) large language models exhibit a strong performance in reference-free evaluation.

Given the widespread adoption and usage of Large Language Models (LLMs), it is crucial to have flexible and interpretable evaluations of their instruction-following ability. Preference judgments between model outputs have become the de facto evaluation standard, despite distilling complex, multi-faceted preferences into a single ranking. Furthermore, as human annotation is slow and costly, LLMs are increasingly used to make these judgments, at the expense of reliability and interpretability. In this work, we propose TICK (Targeted Instruct-evaluation with ChecKlists), a fully automated, interpretable evaluation protocol that structures evaluations with LLM-generated, instruction-specific checklists. We first show that, given an instruction, LLMs can reliably produce high-quality, tailored evaluation checklists that decompose the instruction into a series of YES/NO questions. Each question asks whether a candidate response meets a specific requirement of the instruction. We demonstrate that using TICK leads to a significant increase (46.4% to 52.2%) in the frequency of exact agreements between LLM judgements and human preferences, as compared to having an LLM directly score an output. We then show that STICK (Self-TICK) can be used to improve generation quality across multiple benchmarks via self-refinement and Best-of-N selection. STICK self-refinement on LiveBench reasoning tasks leads to an absolute gain of +7.8%, whilst Best-of-N selection with STICK attains +6.3% absolute improvement on the real-world instruction dataset, WildBench. In light of this, structured, multi-faceted self-improvement is shown to be a promising way to further advance LLM capabilities. Finally, by providing LLM-generated checklists to human evaluators tasked with directly scoring LLM responses to WildBench instructions, we notably increase inter-annotator agreement (0.194 to 0.256).

Recent advancements in large language models (LLMs) have transformed the field of question answering (QA). However, evaluating LLMs in the medical field is challenging due to the lack of standardized and comprehensive datasets. To address this gap, we introduce CMExam, sourced from the Chinese National Medical Licensing Examination. CMExam consists of 60K+ multiple-choice questions for standardized and objective evaluations, as well as solution explanations for model reasoning evaluation in an open-ended manner. For in-depth analyses of LLMs, we invited medical professionals to label five additional question-wise annotations, including disease groups, clinical departments, medical disciplines, areas of competency, and question difficulty levels. Alongside the dataset, we further conducted thorough experiments with representative LLMs and QA algorithms on CMExam. The results show that GPT-4 had the best accuracy of 61.6% and a weighted F1 score of 0.617. These results highlight a great disparity when compared to human accuracy, which stood at 71.6%. For explanation tasks, while LLMs could generate relevant reasoning and demonstrate improved performance after finetuning, they fall short of a desired standard, indicating ample room for improvement. To the best of our knowledge, CMExam is the first Chinese medical exam dataset to provide comprehensive medical annotations. The experiments and findings of LLM evaluation also provide valuable insights into the challenges and potential solutions in developing Chinese medical QA systems and LLM evaluation pipelines. The dataset and relevant code are available at https://github.com/williamliujl/CMExam.

In this paper, we uncover a systematic bias in the evaluation paradigm of adopting large language models~(LLMs), e.g., GPT-4, as a referee to score and compare the quality of responses generated by candidate models. We find that the quality ranking of candidate responses can be easily hacked by simply altering their order of appearance in the context. This manipulation allows us to skew the evaluation result, making one model appear considerably superior to the other, e.g., Vicuna-13B could beat ChatGPT on 66 over 80 tested queries with ChatGPT as an evaluator. To address this issue, we propose a calibration framework with three simple yet effective strategies: 1) Multiple Evidence Calibration, which requires the evaluator model to generate multiple evaluation evidence before assigning ratings; 2) Balanced Position Calibration, which aggregates results across various orders to determine the final score; 3) Human-in-the-Loop Calibration, which introduces a balanced position diversity entropy to measure the difficulty of each example and seeks human assistance when needed. We also manually annotate the "win/tie/lose" outcomes of responses from ChatGPT and Vicuna-13B in the Vicuna Benchmark's question prompt, and extensive experiments demonstrate that our approach successfully mitigates evaluation bias, resulting in closer alignment with human judgments. We release our code and human annotation at https://github.com/i-Eval/FairEval to facilitate future research.

This paper introduces MISS-QA, the first benchmark specifically designed to evaluate the ability of models to interpret schematic diagrams within scientific literature. MISS-QA comprises 1,500 expert-annotated examples over 465 scientific papers. In this benchmark, models are tasked with interpreting schematic diagrams that illustrate research overviews and answering corresponding information-seeking questions based on the broader context of the paper. We assess the performance of 18 frontier multimodal foundation models, including o4-mini, Gemini-2.5-Flash, and Qwen2.5-VL. We reveal a significant performance gap between these models and human experts on MISS-QA. Our analysis of model performance on unanswerable questions and our detailed error analysis further highlight the strengths and limitations of current models, offering key insights to enhance models in comprehending multimodal scientific literature.

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.

Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.

Machine reading comprehension has been an interesting and challenging task in recent years, with the purpose of extracting useful information from texts. To attain the computer ability to understand the reading text and answer relevant information, we introduce ViMMRC 2.0 - an extension of the previous ViMMRC for the task of multiple-choice reading comprehension in Vietnamese Textbooks which contain the reading articles for students from Grade 1 to Grade 12. This dataset has 699 reading passages which are prose and poems, and 5,273 questions. The questions in the new dataset are not fixed with four options as in the previous version. Moreover, the difficulty of questions is increased, which challenges the models to find the correct choice. The computer must understand the whole context of the reading passage, the question, and the content of each choice to extract the right answers. Hence, we propose a multi-stage approach that combines the multi-step attention network (MAN) with the natural language inference (NLI) task to enhance the performance of the reading comprehension model. Then, we compare the proposed methodology with the baseline BERTology models on the new dataset and the ViMMRC 1.0. From the results of the error analysis, we found that the challenge of the reading comprehension models is understanding the implicit context in texts and linking them together in order to find the correct answers. Finally, we hope our new dataset will motivate further research to enhance the ability of computers to understand the Vietnamese language.

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

Large language models (LLMs) have emerged as powerful tools for analyzing complex datasets. Recent studies demonstrate their potential to generate useful, personalized responses when provided with patient-specific health information that encompasses lifestyle, biomarkers, and context. As LLM-driven health applications are increasingly adopted, rigorous and efficient one-sided evaluation methodologies are crucial to ensure response quality across multiple dimensions, including accuracy, personalization and safety. Current evaluation practices for open-ended text responses heavily rely on human experts. This approach introduces human factors and is often cost-prohibitive, labor-intensive, and hinders scalability, especially in complex domains like healthcare where response assessment necessitates domain expertise and considers multifaceted patient data. In this work, we introduce Adaptive Precise Boolean rubrics: an evaluation framework that streamlines human and automated evaluation of open-ended questions by identifying gaps in model responses using a minimal set of targeted rubrics questions. Our approach is based on recent work in more general evaluation settings that contrasts a smaller set of complex evaluation targets with a larger set of more precise, granular targets answerable with simple boolean responses. We validate this approach in metabolic health, a domain encompassing diabetes, cardiovascular disease, and obesity. Our results demonstrate that Adaptive Precise Boolean rubrics yield higher inter-rater agreement among expert and non-expert human evaluators, and in automated assessments, compared to traditional Likert scales, while requiring approximately half the evaluation time of Likert-based methods. This enhanced efficiency, particularly in automated evaluation and non-expert contributions, paves the way for more extensive and cost-effective evaluation of LLMs in health.

Recent advancements in machine learning have spurred growing interests in automated interpreting quality assessment. Nevertheless, existing research suffers from insufficient examination of language use quality, unsatisfactory modeling effectiveness due to data scarcity and imbalance, and a lack of efforts to explain model predictions. To address these gaps, we propose a multi-dimensional modeling framework that integrates feature engineering, data augmentation, and explainable machine learning. This approach prioritizes explainability over ``black box'' predictions by utilizing only construct-relevant, transparent features and conducting Shapley Value (SHAP) analysis. Our results demonstrate strong predictive performance on a novel English-Chinese consecutive interpreting dataset, identifying BLEURT and CometKiwi scores to be the strongest predictive features for fidelity, pause-related features for fluency, and Chinese-specific phraseological diversity metrics for language use. Overall, by placing particular emphasis on explainability, we present a scalable, reliable, and transparent alternative to traditional human evaluation, facilitating the provision of detailed diagnostic feedback for learners and supporting self-regulated learning advantages not afforded by automated scores in isolation.

Recent advances in sequencing technologies have enabled researchers to explore cellular heterogeneity at single-cell resolution. Meanwhile, interpretability has gained prominence parallel to the rapid increase in the complexity and performance of deep learning models. In recent years, topic models have been widely used for interpretable single-cell embedding learning and clustering analysis, which we refer to as single-cell embedded topic models. However, previous studies evaluated the interpretability of the models mainly through qualitative analysis, and these single-cell embedded topic models suffer from the potential problem of interpretation collapse. Furthermore, their neglect of external biological knowledge constrains analytical performance. Here, we present scE2TM, an external knowledge-guided single-cell embedded topic model that provides a high-quality cell embedding and strong interpretation, contributing to comprehensive scRNA-seq data analysis. Our comprehensive evaluation across 20 scRNA-seq datasets demonstrates that scE2TM achieves significant clustering performance gains compared to 7 state-of-the-art methods. In addition, we propose a new interpretability evaluation benchmark that introduces 10 metrics to quantitatively assess the interpretability of single-cell embedded topic models. The results show that the interpretation provided by scE2TM performs encouragingly in terms of diversity and consistency with the underlying biological signals, contributing to a better revealing of the underlying biological mechanisms.

Neural metrics for machine translation evaluation, such as COMET, exhibit significant improvements in their correlation with human judgments, as compared to traditional metrics based on lexical overlap, such as BLEU. Yet, neural metrics are, to a great extent, "black boxes" returning a single sentence-level score without transparency about the decision-making process. In this work, we develop and compare several neural explainability methods and demonstrate their effectiveness for interpreting state-of-the-art fine-tuned neural metrics. Our study reveals that these metrics leverage token-level information that can be directly attributed to translation errors, as assessed through comparison of token-level neural saliency maps with Multidimensional Quality Metrics (MQM) annotations and with synthetically-generated critical translation errors. To ease future research, we release our code at: https://github.com/Unbabel/COMET/tree/explainable-metrics.

Automated metrics for machine translation attempt to replicate human judgment. Unlike humans, who often assess a translation in the context of multiple alternatives, these metrics typically consider only the source sentence and a single translation. This discrepancy in the evaluation setup may negatively impact the performance of automated metrics. We propose two automated metrics that incorporate additional information beyond the single translation. COMET-polycand uses alternative translations of the same source sentence to compare and contrast with the translation at hand, thereby providing a more informed assessment of its quality. COMET-polyic, inspired by retrieval-based in-context learning, takes in translations of similar source texts along with their human-labeled quality scores to guide the evaluation. We find that including a single additional translation in COMET-polycand improves the segment-level metric performance (0.079 to 0.118 Kendall's tau-b correlation), with further gains when more translations are added. Incorporating retrieved examples in COMET-polyic yields similar improvements (0.079 to 0.116 Kendall's tau-b correlation). We release our models publicly.

To evaluate knowledge in large language models (LLMs), current methods query the model and then evaluate its generated responses. In this work, we ask whether evaluation can be done before the model has generated any text. Concretely, is it possible to estimate how knowledgeable a model is about a certain entity, only from its internal computation? We study this question with two tasks: given a subject entity, the goal is to predict (a) the ability of the model to answer common questions about the entity, and (b) the factuality of responses generated by the model about the entity. Experiments with a variety of LLMs show that KEEN, a simple probe trained over internal subject representations, succeeds at both tasks - strongly correlating with both the QA accuracy of the model per-subject and FActScore, a recent factuality metric in open-ended generation. Moreover, KEEN naturally aligns with the model's hedging behavior and faithfully reflects changes in the model's knowledge after fine-tuning. Lastly, we show a more interpretable yet equally performant variant of KEEN, which highlights a small set of tokens that correlates with the model's lack of knowledge. Being simple and lightweight, KEEN can be leveraged to identify gaps and clusters of entity knowledge in LLMs, and guide decisions such as augmenting queries with retrieval.

Retriever-augmented instruction-following models are attractive alternatives to fine-tuned approaches for information-seeking tasks such as question answering (QA). By simply prepending retrieved documents in its input along with an instruction, these models can be adapted to various information domains and tasks without additional fine-tuning. While the model responses tend to be natural and fluent, the additional verbosity makes traditional QA evaluation metrics such as exact match (EM) and F1 unreliable for accurately quantifying model performance. In this work, we investigate the performance of instruction-following models across three information-seeking QA tasks. We use both automatic and human evaluation to evaluate these models along two dimensions: 1) how well they satisfy the user's information need (correctness), and 2) whether they produce a response based on the provided knowledge (faithfulness). Guided by human evaluation and analysis, we highlight the shortcomings of traditional metrics for both correctness and faithfulness. We then propose simple token-overlap based and model-based metrics that reflect the true performance of these models. Our analysis reveals that instruction-following models are competitive, and sometimes even outperform fine-tuned models for correctness. However, these models struggle to stick to the provided knowledge and often hallucinate in their responses. We hope our work encourages a more holistic evaluation of instruction-following models for QA. Our code and data is available at https://github.com/McGill-NLP/instruct-qa

Multiple choice benchmarks have long been the workhorse of language model evaluation because grading multiple choice is objective and easy to automate. However, we show multiple choice questions from popular benchmarks can often be answered without even seeing the question. These shortcuts arise from a fundamental limitation of discriminative evaluation not shared by evaluations of the model's free-form, generative answers. Until recently, there appeared to be no viable, scalable alternative to multiple choice--but, we show that this has changed. We consider generative evaluation via what we call answer matching: Give the candidate model the question without the options, have it generate a free-form response, then use a modern language model with the reference answer to determine if the response matches the reference. To compare the validity of different evaluation strategies, we annotate MMLU-Pro and GPQA-Diamond to obtain human grading data, and measure the agreement of each evaluation approach. We find answer matching using recent models--even small ones--achieves near-perfect agreement, in the range of inter-annotator agreement. In contrast, both multiple choice evaluation and using LLM-as-a-judge without reference answers aligns poorly with human grading. Improving evaluations via answer matching is not merely a conceptual concern: the rankings of several models change significantly when evaluating their free-form responses with answer matching. In light of these findings, we discuss how to move the evaluation ecosystem from multiple choice to answer matching.

Question Answering (QA) datasets are crucial in assessing reading comprehension skills for both machines and humans. While numerous datasets have been developed in English for this purpose, a noticeable void exists in less-resourced languages. To alleviate this gap, our paper introduces machine-translated versions of FairytaleQA, a renowned QA dataset designed to assess and enhance narrative comprehension skills in young children. By employing fine-tuned, modest-scale models, we establish benchmarks for both Question Generation (QG) and QA tasks within the translated datasets. In addition, we present a case study proposing a model for generating question-answer pairs, with an evaluation incorporating quality metrics such as question well-formedness, answerability, relevance, and children suitability. Our evaluation prioritizes quantifying and describing error cases, along with providing directions for future work. This paper contributes to the advancement of QA and QG research in less-resourced languages, promoting accessibility and inclusivity in the development of these models for reading comprehension. The code and data is publicly available at github.com/bernardoleite/fairytaleqa-translated.

We present an empirical evaluation of various outputs generated by nine of the most widely-available large language models (LLMs). Our analysis is done with off-the-shelf, readily-available tools. We find a correlation between percentage of memorized text, percentage of unique text, and overall output quality, when measured with respect to output pathologies such as counterfactual and logically-flawed statements, and general failures like not staying on topic. Overall, 80.0% of the outputs evaluated contained memorized data, but outputs containing the most memorized content were also more likely to be considered of high quality. We discuss and evaluate mitigation strategies, showing that, in the models evaluated, the rate of memorized text being output is reduced. We conclude with a discussion on potential implications around what it means to learn, to memorize, and to evaluate quality text.

When evaluating large language models (LLMs) with multiple-choice question answering (MCQA), it is common to end the prompt with the string "Answer:" to facilitate automated answer extraction via next-token probabilities. However, there is no consensus on how to tokenize the space following the colon, often overlooked as a trivial choice. In this paper, we uncover accuracy differences of up to 11% due to this (seemingly irrelevant) tokenization variation as well as reshuffled model rankings, raising concerns about the reliability of LLM comparisons in prior work. Surprisingly, we are able to recommend one specific strategy -- tokenizing the space together with the answer letter -- as we observe consistent and statistically significant performance improvements. Additionally, it improves model calibration, enhancing the reliability of the model's confidence estimates. Our findings underscore the importance of careful evaluation design and highlight the need for standardized, transparent evaluation protocols to ensure reliable and comparable results.

Recently, natural language generation (NLG) evaluation has shifted from a single-aspect to a multi-aspect paradigm, allowing for a more accurate assessment. Large language models (LLMs) achieve superior performance on various NLG evaluation tasks. However, current work often employs the LLM to independently evaluate different aspects, which largely ignores the rich correlation between various aspects. To fill this research gap, in this work, we propose an NLG evaluation metric called CoAScore. Powered by LLMs, the CoAScore utilizes multi-aspect knowledge through a CoA (Chain-of-Aspects) prompting framework when assessing the quality of a certain aspect. Specifically, for a given aspect to evaluate, we first prompt the LLM to generate a chain of aspects that are relevant to the target aspect and could be useful for the evaluation. We then collect evaluation scores for each generated aspect, and finally, leverage the knowledge of these aspects to improve the evaluation of the target aspect. We evaluate CoAScore across five NLG evaluation tasks (e.g., summarization, dialog response generation, etc) and nine aspects (e.g., overall quality, relevance, coherence, etc). Our experimental findings highlight that, in comparison to individual aspect evaluation, CoAScore exhibits a higher correlation with human judgments. This improvement significantly outperforms existing unsupervised evaluation metrics, whether for assessing overall quality or other aspects. We also conducted extensive ablation studies to validate the effectiveness of the three stages within the CoAScore framework and conducted case studies to show how the LLM performs in these stages. Our code and scripts are available.

Past work in natural language processing interpretability focused mainly on popular classification tasks while largely overlooking generation settings, partly due to a lack of dedicated tools. In this work, we introduce Inseq, a Python library to democratize access to interpretability analyses of sequence generation models. Inseq enables intuitive and optimized extraction of models' internal information and feature importance scores for popular decoder-only and encoder-decoder Transformers architectures. We showcase its potential by adopting it to highlight gender biases in machine translation models and locate factual knowledge inside GPT-2. Thanks to its extensible interface supporting cutting-edge techniques such as contrastive feature attribution, Inseq can drive future advances in explainable natural language generation, centralizing good practices and enabling fair and reproducible model evaluations.

Retrieval-Augmented Generation (RAG) aims to enhance large language models (LLMs) to generate more accurate and reliable answers with the help of the retrieved context from external knowledge sources, thereby reducing the incidence of hallucinations. Despite the advancements, evaluating these systems remains a crucial research area due to the following issues: (1) Limited data diversity: The insufficient diversity of knowledge sources and query types constrains the applicability of RAG systems; (2) Obscure problems location: Existing evaluation methods have difficulty in locating the stage of the RAG pipeline where problems occur; (3) Unstable retrieval evaluation: These methods often fail to effectively assess retrieval performance, particularly when the chunking strategy changes. To tackle these challenges, we propose a Comprehensive Full-chain Evaluation (CoFE-RAG) framework to facilitate thorough evaluation across the entire RAG pipeline, including chunking, retrieval, reranking, and generation. To effectively evaluate the first three phases, we introduce multi-granularity keywords, including coarse-grained and fine-grained keywords, to assess the retrieved context instead of relying on the annotation of golden chunks. Moreover, we release a holistic benchmark dataset tailored for diverse data scenarios covering a wide range of document formats and query types. We demonstrate the utility of the CoFE-RAG framework by conducting experiments to evaluate each stage of RAG systems. Our evaluation method provides unique insights into the effectiveness of RAG systems in handling diverse data scenarios, offering a more nuanced understanding of their capabilities and limitations.

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genome. As GFMs scale up and reshape the landscape of AI-driven genomics, the field faces an urgent need for rigorous and reproducible evaluation. We present OmniGenBench, a modular benchmarking platform designed to unify the data, model, benchmarking, and interpretability layers across GFMs. OmniGenBench enables standardized, one-command evaluation of any GFM across five benchmark suites, with seamless integration of over 31 open-source models. Through automated pipelines and community-extensible features, the platform addresses critical reproducibility challenges, including data transparency, model interoperability, benchmark fragmentation, and black-box interpretability. OmniGenBench aims to serve as foundational infrastructure for reproducible genomic AI research, accelerating trustworthy discovery and collaborative innovation in the era of genome-scale modeling.

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

We present TIGERScore, a Trained metric that follows Instruction Guidance to perform Explainable, and Reference-free evaluation over a wide spectrum of text generation tasks. Different from other automatic evaluation methods that only provide arcane scores, TIGERScore is guided by the natural language instruction to provide error analysis to pinpoint the mistakes in the generated text. Our metric is based on LLaMA, trained on our meticulously curated instruction-tuning dataset MetricInstruct which covers 6 text generation tasks and 23 text generation datasets. The dataset consists of 48K quadruple in the form of (instruction, input, system output rightarrow error analysis). We collected the `system outputs' through diverse channels to cover different types of errors. To quantitatively assess our metric, we evaluate its correlation with human ratings on 5 held-in datasets, 2 held-out datasets and show that TIGERScore can achieve the highest overall Spearman's correlation with human ratings across these datasets and outperforms other metrics significantly. As a reference-free metric, its correlation can even surpass the best existing reference-based metrics. To further qualitatively assess the rationale generated by our metric, we conduct human evaluation on the generated explanations and found that the explanations are 70.8\% accurate. Through these experimental results, we believe TIGERScore demonstrates the possibility of building universal explainable metrics to evaluate any text generation task.

We present our submission to the Task 5 of SemEval-2025 that aims to aid librarians in assigning subject tags to the library records by producing a list of likely relevant tags for a given document. We frame the task as an information retrieval problem, where the document content is used to retrieve subject tags from a large subject taxonomy. We leverage two types of encoder models to build a two-stage information retrieval system -- a bi-encoder for coarse-grained candidate extraction at the first stage, and a cross-encoder for fine-grained re-ranking at the second stage. This approach proved effective, demonstrating significant improvements in recall compared to single-stage methods and showing competitive results according to qualitative evaluation.

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

Enabling a computer to understand a document so that it can answer comprehension questions is a central, yet unsolved goal of NLP. A key factor impeding its solution by machine learned systems is the limited availability of human-annotated data. Hermann et al. (2015) seek to solve this problem by creating over a million training examples by pairing CNN and Daily Mail news articles with their summarized bullet points, and show that a neural network can then be trained to give good performance on this task. In this paper, we conduct a thorough examination of this new reading comprehension task. Our primary aim is to understand what depth of language understanding is required to do well on this task. We approach this from one side by doing a careful hand-analysis of a small subset of the problems and from the other by showing that simple, carefully designed systems can obtain accuracies of 73.6% and 76.6% on these two datasets, exceeding current state-of-the-art results by 7-10% and approaching what we believe is the ceiling for performance on this task.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

Hampering the interpretation of benchmark scores, evaluation data contamination has become a growing concern in the evaluation of LLMs, and an active area of research studies its effects. While evaluation data contamination is easily understood intuitively, it is surprisingly difficult to define precisely which samples should be considered contaminated and, consequently, how it impacts benchmark scores. We propose that these questions should be addressed together and that contamination metrics can be assessed based on whether models benefit from the examples they mark contaminated. We propose a novel analysis method called ConTAM, and show with a large scale survey of existing and novel n-gram based contamination metrics across 13 benchmarks and 7 models from 2 different families that ConTAM can be used to better understand evaluation data contamination and its effects. We find that contamination may have a much larger effect than reported in recent LLM releases and benefits models differently at different scales. We also find that considering only the longest contaminated substring provides a better signal than considering a union of all contaminated substrings, and that doing model and benchmark specific threshold analysis greatly increases the specificity of the results. Lastly, we investigate the impact of hyperparameter choices, finding that, among other things, both using larger values of n and disregarding matches that are infrequent in the pre-training data lead to many false negatives. With ConTAM, we provide a method to empirically ground evaluation data contamination metrics in downstream effects. With our exploration, we shed light on how evaluation data contamination can impact LLMs and provide insight into the considerations important when doing contamination analysis. We end our paper by discussing these in more detail and providing concrete suggestions for future work.

The burgeoning utilization of Large Language Models (LLMs) in scientific research necessitates advanced benchmarks capable of evaluating their understanding and application of scientific knowledge comprehensively. To address this need, we introduce the SciKnowEval benchmark, a novel framework that systematically evaluates LLMs across five progressive levels of scientific knowledge: studying extensively, inquiring earnestly, thinking profoundly, discerning clearly, and practicing assiduously. These levels aim to assess the breadth and depth of scientific knowledge in LLMs, including knowledge coverage, inquiry and exploration capabilities, reflection and reasoning abilities, ethic and safety considerations, as well as practice proficiency. Specifically, we take biology and chemistry as the two instances of SciKnowEval and construct a dataset encompassing 50K multi-level scientific problems and solutions. By leveraging this dataset, we benchmark 20 leading open-source and proprietary LLMs using zero-shot and few-shot prompting strategies. The results reveal that despite achieving state-of-the-art performance, the proprietary LLMs still have considerable room for improvement, particularly in addressing scientific computations and applications. We anticipate that SciKnowEval will establish a comprehensive standard for benchmarking LLMs in science research and discovery, and promote the development of LLMs that integrate scientific knowledge with strong safety awareness. The dataset and code are publicly available at https://github.com/hicai-zju/sciknoweval .

Existing frameworks for evaluating long-context language models (LCLM) can be broadly categorized into real-world and synthetic tasks. Despite their utility, both approaches are accompanied by certain intrinsic limitations. Real-world tasks are too complex to interpret or characterize and are susceptible to data contamination. In contrast, synthetic tasks often adopt the needle-in-the-haystack (NIAH) format, wherein a lack of coherence between the "needle" and the "haystack" compromises their validity as proxies for realistic applications. In response to these challenges, we posit that an ideal long-context evaluation framework should be characterized by three essential features: seamless context, controllable setting, and sound evaluation. This study introduces LongBioBench, a novel benchmark that utilizes artificially generated biographies as a controlled environment for assessing LCLMs across dimensions of understanding, reasoning, and trustworthiness. Our experimental evaluation, which includes 18 LCLMs in total, demonstrates that most models still exhibit deficiencies in semantic understanding and elementary reasoning over retrieved results and are less trustworthy as context length increases. Our further analysis indicates some design choices employed by existing synthetic benchmarks, such as contextual non-coherence, numerical needles, and the absence of distractors, rendering them vulnerable to test the model long-context capabilities. Moreover, we also reveal that long-context continual pretraining primarily adjusts RoPE embedding to accommodate extended context lengths. To sum up, compared to previous synthetic benchmarks, LongBioBench achieves a better trade-off between mirroring authentic language tasks and maintaining controllability, and is highly interpretable and configurable.

Automatically evaluating the quality of language generation is critical. Although recent learned metrics show high correlation with human judgement, these metrics can not explain their verdict or associate the scores with defects in generated text. To address this limitation, we present InstructScore, an explainable evaluation metric for text generation. By harnessing both explicit human instruction and the implicit knowledge of GPT-4, we fine-tune a text evaluation metric based on LLaMA, producing both a score for generated text and a human readable diagnostic report. We evaluate InstructScore on a variety of generation tasks, including translation, captioning, data-to-text and commonsense generation. Experiments show that our 7B model surpasses all other unsupervised metrics, including those based on 175B GPT-3 and GPT-4. Surprisingly, our InstructScore, even without direct supervision from human-rated data, achieves performance levels on par with state-of-the-art metrics like COMET22, which were fine-tuned on human ratings.

The reliance on translated or adapted datasets from English or multilingual resources introduces challenges regarding linguistic and cultural suitability. This study addresses the need for robust and culturally appropriate benchmarks by evaluating the quality of 17 commonly used Turkish benchmark datasets. Using a comprehensive framework that assesses six criteria, both human and LLM-judge annotators provide detailed evaluations to identify dataset strengths and shortcomings. Our results reveal that 70% of the benchmark datasets fail to meet our heuristic quality standards. The correctness of the usage of technical terms is the strongest criterion, but 85% of the criteria are not satisfied in the examined datasets. Although LLM judges demonstrate potential, they are less effective than human annotators, particularly in understanding cultural common sense knowledge and interpreting fluent, unambiguous text. GPT-4o has stronger labeling capabilities for grammatical and technical tasks, while Llama3.3-70B excels at correctness and cultural knowledge evaluation. Our findings emphasize the urgent need for more rigorous quality control in creating and adapting datasets for low-resource languages.

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

Recent large language models (LLMs) support long contexts ranging from 128K to 1M tokens. A popular method for evaluating these capabilities is the needle-in-a-haystack (NIAH) test, which involves retrieving a "needle" (relevant information) from a "haystack" (long irrelevant context). Extensions of this approach include increasing distractors, fact chaining, and in-context reasoning. However, in these benchmarks, models can exploit existing literal matches between the needle and haystack to simplify the task. To address this, we introduce NoLiMa, a benchmark extending NIAH with a carefully designed needle set, where questions and needles have minimal lexical overlap, requiring models to infer latent associations to locate the needle within the haystack. We evaluate 12 popular LLMs that claim to support contexts of at least 128K tokens. While they perform well in short contexts (<1K), performance degrades significantly as context length increases. At 32K, for instance, 10 models drop below 50% of their strong short-length baselines. Even GPT-4o, one of the top-performing exceptions, experiences a reduction from an almost-perfect baseline of 99.3% to 69.7%. Our analysis suggests these declines stem from the increased difficulty the attention mechanism faces in longer contexts when literal matches are absent, making it harder to retrieve relevant information.

Representation and learning of commonsense knowledge is one of the foundational problems in the quest to enable deep language understanding. This issue is particularly challenging for understanding casual and correlational relationships between events. While this topic has received a lot of interest in the NLP community, research has been hindered by the lack of a proper evaluation framework. This paper attempts to address this problem with a new framework for evaluating story understanding and script learning: the 'Story Cloze Test'. This test requires a system to choose the correct ending to a four-sentence story. We created a new corpus of ~50k five-sentence commonsense stories, ROCStories, to enable this evaluation. This corpus is unique in two ways: (1) it captures a rich set of causal and temporal commonsense relations between daily events, and (2) it is a high quality collection of everyday life stories that can also be used for story generation. Experimental evaluation shows that a host of baselines and state-of-the-art models based on shallow language understanding struggle to achieve a high score on the Story Cloze Test. We discuss these implications for script and story learning, and offer suggestions for deeper language understanding.

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.

The problem of answering questions using knowledge from pre-trained language models (LMs) and knowledge graphs (KGs) presents two challenges: given a QA context (question and answer choice), methods need to (i) identify relevant knowledge from large KGs, and (ii) perform joint reasoning over the QA context and KG. In this work, we propose a new model, QA-GNN, which addresses the above challenges through two key innovations: (i) relevance scoring, where we use LMs to estimate the importance of KG nodes relative to the given QA context, and (ii) joint reasoning, where we connect the QA context and KG to form a joint graph, and mutually update their representations through graph neural networks. We evaluate our model on QA benchmarks in the commonsense (CommonsenseQA, OpenBookQA) and biomedical (MedQA-USMLE) domains. QA-GNN outperforms existing LM and LM+KG models, and exhibits capabilities to perform interpretable and structured reasoning, e.g., correctly handling negation in questions.

Large Language Models (LLMs) have shown improved generation performance through retrieval-augmented generation (RAG) following the retriever-reader paradigm, which supplements model inputs with externally retrieved knowledge. However, prior work often evaluates RAG holistically, assessing the retriever and reader jointly, making it difficult to isolate the true contribution of retrieval, particularly given the prompt sensitivity of LLMs used as readers. We introduce Spectrum Projection Score (SPS), a lightweight, supervision-free metric that allows the reader to gauge the semantic alignment of a retrieved summary with its hidden representation by comparing the area formed by generated tokens from the summary, and the principal directions of subspace in the reader and to measure the relevance. Building on SPS we present xCompress, an inference time controller framework that dynamically samples, ranks, and compresses retrieval summary candidates. Extensive experiments on five QA benchmarks with four open source LLMs show that SPS not only enhances performance across a range of tasks but also provides a principled perspective on the interaction between retrieval and generation.

English Natural Language Understanding (NLU) systems have achieved great performances and even outperformed humans on benchmarks like GLUE and SuperGLUE. However, these benchmarks contain only textbook Standard American English (SAE). Other dialects have been largely overlooked in the NLP community. This leads to biased and inequitable NLU systems that serve only a sub-population of speakers. To understand disparities in current models and to facilitate more dialect-competent NLU systems, we introduce the VernAcular Language Understanding Evaluation (VALUE) benchmark, a challenging variant of GLUE that we created with a set of lexical and morphosyntactic transformation rules. In this initial release (V.1), we construct rules for 11 features of African American Vernacular English (AAVE), and we recruit fluent AAVE speakers to validate each feature transformation via linguistic acceptability judgments in a participatory design manner. Experiments show that these new dialectal features can lead to a drop in model performance. To run the transformation code and download both synthetic and gold-standard dialectal GLUE benchmarks, see https://github.com/SALT-NLP/value

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

Evaluations are critical for understanding the capabilities of large language models (LLMs). Fundamentally, evaluations are experiments; but the literature on evaluations has largely ignored the literature from other sciences on experiment analysis and planning. This article shows researchers with some training in statistics how to think about and analyze data from language model evaluations. Conceptualizing evaluation questions as having been drawn from an unseen super-population, we present formulas for analyzing evaluation data, measuring differences between two models, and planning an evaluation experiment. We make a number of specific recommendations for running language model evaluations and reporting experiment results in a way that minimizes statistical noise and maximizes informativeness.

This work introduces Salamandra, a suite of open-source decoder-only large language models available in three different sizes: 2, 7, and 40 billion parameters. The models were trained from scratch on highly multilingual data that comprises text in 35 European languages and code. Our carefully curated corpus is made exclusively from open-access data compiled from a wide variety of sources. Along with the base models, supplementary checkpoints that were fine-tuned on public-domain instruction data are also released for chat applications. Additionally, we also share our preliminary experiments on multimodality, which serve as proof-of-concept to showcase potential applications for the Salamandra family. Our extensive evaluations on multilingual benchmarks reveal that Salamandra has strong capabilities, achieving competitive performance when compared to similarly sized open-source models. We provide comprehensive evaluation results both on standard downstream tasks as well as key aspects related to bias and safety.With this technical report, we intend to promote open science by sharing all the details behind our design choices, data curation strategy and evaluation methodology. In addition to that, we deviate from the usual practice by making our training and evaluation scripts publicly accessible. We release all models under a permissive Apache 2.0 license in order to foster future research and facilitate commercial use, thereby contributing to the open-source ecosystem of large language models.

Using Large Language Models (LLMs) for relevance assessments offers promising opportunities to improve Information Retrieval (IR), Natural Language Processing (NLP), and related fields. Indeed, LLMs hold the promise of allowing IR experimenters to build evaluation collections with a fraction of the manual human labor currently required. This could help with fresh topics on which there is still limited knowledge and could mitigate the challenges of evaluating ranking systems in low-resource scenarios, where it is challenging to find human annotators. Given the fast-paced recent developments in the domain, many questions concerning LLMs as assessors are yet to be answered. Among the aspects that require further investigation, we can list the impact of various components in a relevance judgment generation pipeline, such as the prompt used or the LLM chosen. This paper benchmarks and reports on the results of a large-scale automatic relevance judgment evaluation, the LLMJudge challenge at SIGIR 2024, where different relevance assessment approaches were proposed. In detail, we release and benchmark 42 LLM-generated labels of the TREC 2023 Deep Learning track relevance judgments produced by eight international teams who participated in the challenge. Given their diverse nature, these automatically generated relevance judgments can help the community not only investigate systematic biases caused by LLMs but also explore the effectiveness of ensemble models, analyze the trade-offs between different models and human assessors, and advance methodologies for improving automated evaluation techniques. The released resource is available at the following link: https://llm4eval.github.io/LLMJudge-benchmark/

We introduce Korean Language Understanding Evaluation (KLUE) benchmark. KLUE is a collection of 8 Korean natural language understanding (NLU) tasks, including Topic Classification, SemanticTextual Similarity, Natural Language Inference, Named Entity Recognition, Relation Extraction, Dependency Parsing, Machine Reading Comprehension, and Dialogue State Tracking. We build all of the tasks from scratch from diverse source corpora while respecting copyrights, to ensure accessibility for anyone without any restrictions. With ethical considerations in mind, we carefully design annotation protocols. Along with the benchmark tasks and data, we provide suitable evaluation metrics and fine-tuning recipes for pretrained language models for each task. We furthermore release the pretrained language models (PLM), KLUE-BERT and KLUE-RoBERTa, to help reproducing baseline models on KLUE and thereby facilitate future research. We make a few interesting observations from the preliminary experiments using the proposed KLUE benchmark suite, already demonstrating the usefulness of this new benchmark suite. First, we find KLUE-RoBERTa-large outperforms other baselines, including multilingual PLMs and existing open-source Korean PLMs. Second, we see minimal degradation in performance even when we replace personally identifiable information from the pretraining corpus, suggesting that privacy and NLU capability are not at odds with each other. Lastly, we find that using BPE tokenization in combination with morpheme-level pre-tokenization is effective in tasks involving morpheme-level tagging, detection and generation. In addition to accelerating Korean NLP research, our comprehensive documentation on creating KLUE will facilitate creating similar resources for other languages in the future. KLUE is available at https://klue-benchmark.com.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

Recent advances in LLMs have made automated scientific research the next frontline in the path to artificial superintelligence. However, these systems are bound either to tasks of narrow scope or the limited creative capabilities of LLMs. We propose Spacer, a scientific discovery system that develops creative and factually grounded concepts without external intervention. Spacer attempts to achieve this via 'deliberate decontextualization,' an approach that disassembles information into atomic units - keywords - and draws creativity from unexplored connections between them. Spacer consists of (i) Nuri, an inspiration engine that builds keyword sets, and (ii) the Manifesting Pipeline that refines these sets into elaborate scientific statements. Nuri extracts novel, high-potential keyword sets from a keyword graph built with 180,000 academic publications in biological fields. The Manifesting Pipeline finds links between keywords, analyzes their logical structure, validates their plausibility, and ultimately drafts original scientific concepts. According to our experiments, the evaluation metric of Nuri accurately classifies high-impact publications with an AUROC score of 0.737. Our Manifesting Pipeline also successfully reconstructs core concepts from the latest top-journal articles solely from their keyword sets. An LLM-based scoring system estimates that this reconstruction was sound for over 85% of the cases. Finally, our embedding space analysis shows that outputs from Spacer are significantly more similar to leading publications compared with those from SOTA LLMs.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".