Daily Papers

Solving complex real-world tasks requires cycles of actions and observations. This is particularly true in science, where tasks require many cycles of analysis, tool use, and experimentation. Language agents are promising for automating intellectual tasks in science because they can interact with tools via natural language or code. Yet their flexibility creates conceptual and practical challenges for software implementations, since agents may comprise non-standard components such as internal reasoning, planning, tool usage, as well as the inherent stochasticity of temperature-sampled language models. Here, we introduce Aviary, an extensible gymnasium for language agents. We formalize agents as policies solving language-grounded partially observable Markov decision processes, which we term language decision processes. We then implement five environments, including three challenging scientific environments: (1) manipulating DNA constructs for molecular cloning, (2) answering research questions by accessing scientific literature, and (3) engineering protein stability. These environments were selected for their focus on multi-step reasoning and their relevance to contemporary biology research. Finally, with online training and scaling inference-time compute, we show that language agents backed by open-source, non-frontier LLMs can match and exceed both frontier LLM agents and human experts on multiple tasks at up to 100x lower inference cost.

Social science NLP tasks, such as emotion or humor detection, are required to capture the semantics along with the implicit pragmatics from text, often with limited amounts of training data. Instruction tuning has been shown to improve the many capabilities of large language models (LLMs) such as commonsense reasoning, reading comprehension, and computer programming. However, little is known about the effectiveness of instruction tuning on the social domain where implicit pragmatic cues are often needed to be captured. We explore the use of instruction tuning for social science NLP tasks and introduce Socialite-Llama -- an open-source, instruction-tuned Llama. On a suite of 20 social science tasks, Socialite-Llama improves upon the performance of Llama as well as matches or improves upon the performance of a state-of-the-art, multi-task finetuned model on a majority of them. Further, Socialite-Llama also leads to improvement on 5 out of 6 related social tasks as compared to Llama, suggesting instruction tuning can lead to generalized social understanding. All resources including our code, model and dataset can be found through bit.ly/socialitellama.

Large language models (LLMs) have had a transformative impact on a variety of scientific tasks across disciplines such as biology, chemistry, medicine, and physics. However, ensuring the safety alignment of these models in scientific research remains an underexplored area, with existing benchmarks primarily focus on textual content and overlooking key scientific representations such as molecular, protein, and genomic languages. Moreover, the safety mechanisms of LLMs in scientific tasks are insufficiently studied. To address these limitations, we introduce SciSafeEval, a comprehensive benchmark designed to evaluate the safety alignment of LLMs across a range of scientific tasks. SciSafeEval spans multiple scientific languages - including textual, molecular, protein, and genomic - and covers a wide range of scientific domains. We evaluate LLMs in zero-shot, few-shot and chain-of-thought settings, and introduce a 'jailbreak' enhancement feature that challenges LLMs equipped with safety guardrails, rigorously testing their defenses against malicious intention. Our benchmark surpasses existing safety datasets in both scale and scope, providing a robust platform for assessing the safety and performance of LLMs in scientific contexts. This work aims to facilitate the responsible development and deployment of LLMs, promoting alignment with safety and ethical standards in scientific research.

We present SciArena, an open and collaborative platform for evaluating foundation models on scientific literature tasks. Unlike traditional benchmarks for scientific literature understanding and synthesis, SciArena engages the research community directly, following the Chatbot Arena evaluation approach of community voting on model comparisons. By leveraging collective intelligence, SciArena offers a community-driven evaluation of model performance on open-ended scientific tasks that demand literature-grounded, long-form responses. The platform currently supports 23 open-source and proprietary foundation models and has collected over 13,000 votes from trusted researchers across diverse scientific domains. We analyze the data collected so far and confirm that the submitted questions are diverse, aligned with real-world literature needs, and that participating researchers demonstrate strong self-consistency and inter-annotator agreement in their evaluations. We discuss the results and insights based on the model ranking leaderboard. To further promote research in building model-based automated evaluation systems for literature tasks, we release SciArena-Eval, a meta-evaluation benchmark based on our collected preference data. The benchmark measures the accuracy of models in judging answer quality by comparing their pairwise assessments with human votes. Our experiments highlight the benchmark's challenges and emphasize the need for more reliable automated evaluation methods.

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

Peer review is fundamental to scientific research, but the growing volume of publications has intensified the challenges of this expertise-intensive process. While LLMs show promise in various scientific tasks, their potential to assist with peer review, particularly in identifying paper limitations, remains understudied. We first present a comprehensive taxonomy of limitation types in scientific research, with a focus on AI. Guided by this taxonomy, for studying limitations, we present LimitGen, the first comprehensive benchmark for evaluating LLMs' capability to support early-stage feedback and complement human peer review. Our benchmark consists of two subsets: LimitGen-Syn, a synthetic dataset carefully created through controlled perturbations of high-quality papers, and LimitGen-Human, a collection of real human-written limitations. To improve the ability of LLM systems to identify limitations, we augment them with literature retrieval, which is essential for grounding identifying limitations in prior scientific findings. Our approach enhances the capabilities of LLM systems to generate limitations in research papers, enabling them to provide more concrete and constructive feedback.

While Large Language Models (LLMs) have demonstrated remarkable capabilities in scientific tasks, existing evaluation frameworks primarily assess their performance using rich contextual inputs, overlooking their ability to generate novel ideas from minimal information. We introduce LiveIdeaBench, a comprehensive benchmark that evaluates LLMs' scientific creativity and divergent thinking capabilities using single-keyword prompts. Drawing from Guilford's creativity theory, our framework employs a dynamic panel of state-of-the-art LLMs to assess generated ideas across four key dimensions: originality, feasibility, fluency, and flexibility. Through extensive experimentation with 20 leading models across 1,180 keywords spanning 18 scientific domains, we reveal that scientific creative ability shows distinct patterns from general intelligence metrics. Notably, our results demonstrate that models like QwQ-32B-preview achieve comparable creative performance to top-tier models like o1-preview, despite significant gaps in their general intelligence scores. These findings highlight the importance of specialized evaluation frameworks for scientific creativity and suggest that the development of creative capabilities in LLMs may follow different trajectories than traditional problem-solving abilities.

We present SciRIFF (Scientific Resource for Instruction-Following and Finetuning), a dataset of 137K instruction-following demonstrations for 54 tasks covering five essential scientific literature understanding capabilities: information extraction, summarization, question answering, claim verification, and classification. SciRIFF demonstrations are notable for their long input contexts, detailed task specifications, and complex structured outputs. While instruction-following resources are available in specific domains such as clinical medicine and chemistry, SciRIFF is the first dataset focused on extracting and synthesizing information from research literature across a wide range of scientific fields. To demonstrate the utility of SciRIFF, we develop a sample-efficient strategy to adapt a general instruction-following model for science by performing additional finetuning on a mix of general-domain and SciRIFF demonstrations. In evaluations on nine held-out scientific tasks, our model -- called SciTulu -- improves over a strong LLM baseline by 28.1% and 6.5% at the 7B and 70B scales respectively, while maintaining general instruction-following performance within 2% of the baseline. We are optimistic that SciRIFF will facilitate the development and evaluation of LLMs to help researchers navigate the ever-growing body of scientific literature. We release our dataset, model checkpoints, and data processing and evaluation code to enable further research.

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

With the rapid development of Large Language Models (LLMs), it is crucial to have benchmarks which can evaluate the ability of LLMs on different domains. One common use of LLMs is performing tasks on scientific topics, such as writing algorithms, querying databases or giving mathematical proofs. Inspired by the way university students are evaluated on such tasks, in this paper, we propose SciEx - a benchmark consisting of university computer science exam questions, to evaluate LLMs ability on solving scientific tasks. SciEx is (1) multilingual, containing both English and German exams, and (2) multi-modal, containing questions that involve images, and (3) contains various types of freeform questions with different difficulty levels, due to the nature of university exams. We evaluate the performance of various state-of-the-art LLMs on our new benchmark. Since SciEx questions are freeform, it is not straightforward to evaluate LLM performance. Therefore, we provide human expert grading of the LLM outputs on SciEx. We show that the free-form exams in SciEx remain challenging for the current LLMs, where the best LLM only achieves 59.4\% exam grade on average. We also provide detailed comparisons between LLM performance and student performance on SciEx. To enable future evaluation of new LLMs, we propose using LLM-as-a-judge to grade the LLM answers on SciEx. Our experiments show that, although they do not perform perfectly on solving the exams, LLMs are decent as graders, achieving 0.948 Pearson correlation with expert grading.

The rapid advancement of Large Language Models (LLMs) and Large Multimodal Models (LMMs) has heightened the demand for AI-based scientific assistants capable of understanding scientific articles and figures. Despite progress, there remains a significant gap in evaluating models' comprehension of professional, graduate-level, and even PhD-level scientific content. Current datasets and benchmarks primarily focus on relatively simple scientific tasks and figures, lacking comprehensive assessments across diverse advanced scientific disciplines. To bridge this gap, we collected a multimodal, multidisciplinary dataset from open-access scientific articles published in Nature Communications journals. This dataset spans 72 scientific disciplines, ensuring both diversity and quality. We created benchmarks with various tasks and settings to comprehensively evaluate LMMs' capabilities in understanding scientific figures and content. Our evaluation revealed that these tasks are highly challenging: many open-source models struggled significantly, and even GPT-4V and GPT-4o faced difficulties. We also explored using our dataset as training resources by constructing visual instruction-following data, enabling the 7B LLaVA model to achieve performance comparable to GPT-4V/o on our benchmark. Additionally, we investigated the use of our interleaved article texts and figure images for pre-training LMMs, resulting in improvements on the material generation task. The source dataset, including articles, figures, constructed benchmarks, and visual instruction-following data, is open-sourced.

Scientific discovery is a complex cognitive process that has driven human knowledge and technological progress for centuries. While artificial intelligence (AI) has made significant advances in automating aspects of scientific reasoning, simulation, and experimentation, we still lack integrated AI systems capable of performing autonomous long-term scientific research and discovery. This paper examines the current state of AI for scientific discovery, highlighting recent progress in large language models and other AI techniques applied to scientific tasks. We then outline key challenges and promising research directions toward developing more comprehensive AI systems for scientific discovery, including the need for science-focused AI agents, improved benchmarks and evaluation metrics, multimodal scientific representations, and unified frameworks combining reasoning, theorem proving, and data-driven modeling. Addressing these challenges could lead to transformative AI tools to accelerate progress across disciplines towards scientific discovery.

Recent advancements in large language model (LLM) agents have significantly accelerated scientific discovery automation, yet concurrently raised critical ethical and safety concerns. To systematically address these challenges, we introduce SafeScientist, an innovative AI scientist framework explicitly designed to enhance safety and ethical responsibility in AI-driven scientific exploration. SafeScientist proactively refuses ethically inappropriate or high-risk tasks and rigorously emphasizes safety throughout the research process. To achieve comprehensive safety oversight, we integrate multiple defensive mechanisms, including prompt monitoring, agent-collaboration monitoring, tool-use monitoring, and an ethical reviewer component. Complementing SafeScientist, we propose SciSafetyBench, a novel benchmark specifically designed to evaluate AI safety in scientific contexts, comprising 240 high-risk scientific tasks across 6 domains, alongside 30 specially designed scientific tools and 120 tool-related risk tasks. Extensive experiments demonstrate that SafeScientist significantly improves safety performance by 35\% compared to traditional AI scientist frameworks, without compromising scientific output quality. Additionally, we rigorously validate the robustness of our safety pipeline against diverse adversarial attack methods, further confirming the effectiveness of our integrated approach. The code and data will be available at https://github.com/ulab-uiuc/SafeScientist. red{Warning: this paper contains example data that may be offensive or harmful.}

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.

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.

Information overload is a major obstacle to scientific progress. The explosive growth in scientific literature and data has made it ever harder to discover useful insights in a large mass of information. Today scientific knowledge is accessed through search engines, but they are unable to organize scientific knowledge alone. In this paper we introduce Galactica: a large language model that can store, combine and reason about scientific knowledge. We train on a large scientific corpus of papers, reference material, knowledge bases and many other sources. We outperform existing models on a range of scientific tasks. On technical knowledge probes such as LaTeX equations, Galactica outperforms the latest GPT-3 by 68.2% versus 49.0%. Galactica also performs well on reasoning, outperforming Chinchilla on mathematical MMLU by 41.3% to 35.7%, and PaLM 540B on MATH with a score of 20.4% versus 8.8%. It also sets a new state-of-the-art on downstream tasks such as PubMedQA and MedMCQA dev of 77.6% and 52.9%. And despite not being trained on a general corpus, Galactica outperforms BLOOM and OPT-175B on BIG-bench. We believe these results demonstrate the potential for language models as a new interface for science. We open source the model for the benefit of the scientific community.

Satellite remote sensing missions have gained popularity over the past fifteen years due to their ability to cover large swaths of land at regular intervals, making them ideal for monitoring environmental trends. The FINCH mission, a 3U+ CubeSat equipped with a hyperspectral camera, aims to monitor crop residue cover in agricultural fields. Although hyperspectral imaging captures both spectral and spatial information, it is prone to various types of noise, including random noise, stripe noise, and dead pixels. Effective denoising of these images is crucial for downstream scientific tasks. Traditional methods, including hand-crafted techniques encoding strong priors, learned 2D image denoising methods applied across different hyperspectral bands, or diffusion generative models applied independently on bands, often struggle with varying noise strengths across spectral bands, leading to significant spectral distortion. This paper presents a novel approach to hyperspectral image denoising using latent diffusion models that integrate spatial and spectral information. We particularly do so by building a 3D diffusion model and presenting a 3-stage training approach on real and synthetically crafted datasets. The proposed method preserves image structure while reducing noise. Evaluations on both popular hyperspectral denoising datasets and synthetically crafted datasets for the FINCH mission demonstrate the effectiveness of this approach.

Large Language Models (LLMs) have demonstrated impressive capabilities across a range of scientific tasks including mathematics, physics, and chemistry. Despite their successes, the effectiveness of LLMs in handling complex statistical tasks remains systematically under-explored. To bridge this gap, we introduce StatQA, a new benchmark designed for statistical analysis tasks. StatQA comprises 11,623 examples tailored to evaluate LLMs' proficiency in specialized statistical tasks and their applicability assessment capabilities, particularly for hypothesis testing methods. We systematically experiment with representative LLMs using various prompting strategies and show that even state-of-the-art models such as GPT-4o achieve a best performance of only 64.83%, indicating significant room for improvement. Notably, while open-source LLMs (e.g. LLaMA-3) show limited capability, those fine-tuned ones exhibit marked improvements, outperforming all in-context learning-based methods (e.g. GPT-4o). Moreover, our comparative human experiments highlight a striking contrast in error types between LLMs and humans: LLMs primarily make applicability errors, whereas humans mostly make statistical task confusion errors. This divergence highlights distinct areas of proficiency and deficiency, suggesting that combining LLM and human expertise could lead to complementary strengths, inviting further investigation into their collaborative potential.

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

Transformer-based masked language models trained on general corpora, such as BERT and RoBERTa, have shown impressive performance on various downstream tasks. Increasingly, researchers are "finetuning" these models to improve performance on domain-specific tasks. Here, we report a broad study in which we applied 14 transformer-based models to 11 scientific tasks in order to evaluate how downstream performance is affected by changes along various dimensions (e.g., training data, model size, pretraining time, finetuning length). In this process, we created the largest and most diverse scientific language model to date, ScholarBERT, by training a 770M-parameter BERT model on an 221B token scientific literature dataset spanning many disciplines. Counterintuitively, our evaluation of the 14 BERT-based models (seven versions of ScholarBERT, five science-specific large language models from the literature, BERT-Base, and BERT-Large) reveals little difference in performance across the 11 science-focused tasks, despite major differences in model size and training data. We argue that our results establish an upper bound for the performance achievable with BERT-based architectures on tasks from the scientific domain.

Critical peer review of scientific manuscripts presents a significant challenge for Large Language Models (LLMs), partly due to data limitations and the complexity of expert reasoning. This report introduces Persistent Workflow Prompting (PWP), a potentially broadly applicable prompt engineering methodology designed to bridge this gap using standard LLM chat interfaces (zero-code, no APIs). We present a proof-of-concept PWP prompt for the critical analysis of experimental chemistry manuscripts, featuring a hierarchical, modular architecture (structured via Markdown) that defines detailed analysis workflows. We develop this PWP prompt through iterative application of meta-prompting techniques and meta-reasoning aimed at systematically codifying expert review workflows, including tacit knowledge. Submitted once at the start of a session, this PWP prompt equips the LLM with persistent workflows triggered by subsequent queries, guiding modern reasoning LLMs through systematic, multimodal evaluations. Demonstrations show the PWP-guided LLM identifying major methodological flaws in a test case while mitigating LLM input bias and performing complex tasks, including distinguishing claims from evidence, integrating text/photo/figure analysis to infer parameters, executing quantitative feasibility checks, comparing estimates against claims, and assessing a priori plausibility. To ensure transparency and facilitate replication, we provide full prompts, detailed demonstration analyses, and logs of interactive chats as supplementary resources. Beyond the specific application, this work offers insights into the meta-development process itself, highlighting the potential of PWP, informed by detailed workflow formalization, to enable sophisticated analysis using readily available LLMs for complex scientific tasks.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

sec:abstract Large Language Models (LLMs) have shown promise in assisting scientific discovery. However, such applications are currently limited by LLMs' deficiencies in understanding intricate scientific concepts, deriving symbolic equations, and solving advanced numerical calculations. To bridge these gaps, we introduce SciGLM, a suite of scientific language models able to conduct college-level scientific reasoning. Central to our approach is a novel self-reflective instruction annotation framework to address the data scarcity challenge in the science domain. This framework leverages existing LLMs to generate step-by-step reasoning for unlabelled scientific questions, followed by a process of self-reflective critic-and-revise. Applying this framework, we curated SciInstruct, a diverse and high-quality dataset encompassing mathematics, physics, chemistry, and formal proofs. We fine-tuned the ChatGLM family of language models with SciInstruct, enhancing their capabilities in scientific and mathematical reasoning. Remarkably, SciGLM consistently improves both the base model (ChatGLM3-6B-Base) and larger-scale models (12B and 32B), without sacrificing the language understanding capabilities of the base model. This makes SciGLM a suitable foundational model to facilitate diverse scientific discovery tasks. For the benefit of the wider research community, we release SciInstruct, SciGLM, alongside a self-reflective framework and fine-tuning code at https://github.com/THUDM/SciGLM.

Scientific literature serves as a high-quality corpus, supporting a lot of Natural Language Processing (NLP) research. However, existing datasets are centered around the English language, which restricts the development of Chinese scientific NLP. In this work, we present CSL, a large-scale Chinese Scientific Literature dataset, which contains the titles, abstracts, keywords and academic fields of 396k papers. To our knowledge, CSL is the first scientific document dataset in Chinese. The CSL can serve as a Chinese corpus. Also, this semi-structured data is a natural annotation that can constitute many supervised NLP tasks. Based on CSL, we present a benchmark to evaluate the performance of models across scientific domain tasks, i.e., summarization, keyword generation and text classification. We analyze the behavior of existing text-to-text models on the evaluation tasks and reveal the challenges for Chinese scientific NLP tasks, which provides a valuable reference for future research. Data and code are available at https://github.com/ydli-ai/CSL

Despite a surge collection of XAI methods, users still struggle to obtain required AI explanations. Previous research suggests chatbots as dynamic solutions, but the effective design of conversational XAI agents for practical human needs remains under-explored. This paper focuses on Conversational XAI for AI-assisted scientific writing tasks. Drawing from human linguistic theories and formative studies, we identify four design rationales: "multifaceted", "controllability", "mix-initiative", "context-aware drill-down". We incorporate them into an interactive prototype, ConvXAI, which facilitates heterogeneous AI explanations for scientific writing through dialogue. In two studies with 21 users, ConvXAI outperforms a GUI-based baseline on improving human-perceived understanding and writing improvement. The paper further discusses the practical human usage patterns in interacting with ConvXAI for scientific co-writing.

Obtaining large-scale annotated data for NLP tasks in the scientific domain is challenging and expensive. We release SciBERT, a pretrained language model based on BERT (Devlin et al., 2018) to address the lack of high-quality, large-scale labeled scientific data. SciBERT leverages unsupervised pretraining on a large multi-domain corpus of scientific publications to improve performance on downstream scientific NLP tasks. We evaluate on a suite of tasks including sequence tagging, sentence classification and dependency parsing, with datasets from a variety of scientific domains. We demonstrate statistically significant improvements over BERT and achieve new state-of-the-art results on several of these tasks. The code and pretrained models are available at https://github.com/allenai/scibert/.

We introduce SciVer, the first benchmark specifically designed to evaluate the ability of foundation models to verify claims within a multimodal scientific context. SciVer consists of 3,000 expert-annotated examples over 1,113 scientific papers, covering four subsets, each representing a common reasoning type in multimodal scientific claim verification. To enable fine-grained evaluation, each example includes expert-annotated supporting evidence. We assess the performance of 21 state-of-the-art multimodal foundation models, including o4-mini, Gemini-2.5-Flash, Llama-3.2-Vision, and Qwen2.5-VL. Our experiment reveals a substantial performance gap between these models and human experts on SciVer. Through an in-depth analysis of retrieval-augmented generation (RAG), and human-conducted error evaluations, we identify critical limitations in current open-source models, offering key insights to advance models' comprehension and reasoning in multimodal scientific literature tasks.

Reliable evaluation of large language models (LLMs) is impeded by two key challenges: objective metrics often fail to reflect human perception of natural language, and exhaustive human labeling is prohibitively expensive. Here, we propose a sample-efficient human evaluation method for LLMs based on the principle of MAximum Discrepancy (MAD) Competition. Our method automatically and adaptively selects a compact set of input instructions that maximize semantic discrepancy between pairs of LLM responses. Human evaluators then perform three-alternative forced choices on these paired responses, which are aggregated into a global ranking using Elo rating. We apply our approach to compare eight widely used LLMs across four tasks: scientific knowledge understanding, mathematical reasoning, creative and functional writing, and code generation and explanation. Experimental results show that our sample-efficient evaluation method recovers "gold-standard" model rankings with a handful of MAD-selected instructions, reveals respective strengths and weaknesses of each LLM, and offers nuanced insights to guide future LLM development. Code is available at https://github.com/weiji-Feng/MAD-Eval .

Artificial Intelligence (AI) is accelerating the transformation of scientific research paradigms, not only enhancing research efficiency but also driving innovation. We introduce NovelSeek, a unified closed-loop multi-agent framework to conduct Autonomous Scientific Research (ASR) across various scientific research fields, enabling researchers to tackle complicated problems in these fields with unprecedented speed and precision. NovelSeek highlights three key advantages: 1) Scalability: NovelSeek has demonstrated its versatility across 12 scientific research tasks, capable of generating innovative ideas to enhance the performance of baseline code. 2) Interactivity: NovelSeek provides an interface for human expert feedback and multi-agent interaction in automated end-to-end processes, allowing for the seamless integration of domain expert knowledge. 3) Efficiency: NovelSeek has achieved promising performance gains in several scientific fields with significantly less time cost compared to human efforts. For instance, in reaction yield prediction, it increased from 27.6% to 35.4% in just 12 hours; in enhancer activity prediction, accuracy rose from 0.52 to 0.79 with only 4 hours of processing; and in 2D semantic segmentation, precision advanced from 78.8% to 81.0% in a mere 30 hours.

The rapid advancement of perovskite solar cells (PSCs) has led to an exponential growth in research publications, creating an urgent need for efficient knowledge management and reasoning systems in this domain. We present a comprehensive knowledge-enhanced system for PSCs that integrates three key components. First, we develop Perovskite-KG, a domain-specific knowledge graph constructed from 1,517 research papers, containing 23,789 entities and 22,272 relationships. Second, we create two complementary datasets: Perovskite-Chat, comprising 55,101 high-quality question-answer pairs generated through a novel multi-agent framework, and Perovskite-Reasoning, containing 2,217 carefully curated materials science problems. Third, we introduce two specialized large language models: Perovskite-Chat-LLM for domain-specific knowledge assistance and Perovskite-Reasoning-LLM for scientific reasoning tasks. Experimental results demonstrate that our system significantly outperforms existing models in both domain-specific knowledge retrieval and scientific reasoning tasks, providing researchers with effective tools for literature review, experimental design, and complex problem-solving in PSC research.

Approximating nonlinear differential equations using a neural network provides a robust and efficient tool for various scientific computing tasks, including real-time predictions, inverse problems, optimal controls, and surrogate modeling. Previous works have focused on embedding dynamical systems into networks through two approaches: learning a single solution operator (i.e., the mapping from input parametrized functions to solutions) or learning the governing system of equations (i.e., the constitutive model relative to the state variables). Both of these approaches yield different representations for the same underlying data or function. Additionally, observing that families of differential equations often share key characteristics, we seek one network representation across a wide range of equations. Our method, called Predicting Operators and Symbolic Expressions (PROSE), learns maps from multimodal inputs to multimodal outputs, capable of generating both numerical predictions and mathematical equations. By using a transformer structure and a feature fusion approach, our network can simultaneously embed sets of solution operators for various parametric differential equations using a single trained network. Detailed experiments demonstrate that the network benefits from its multimodal nature, resulting in improved prediction accuracy and better generalization. The network is shown to be able to handle noise in the data and errors in the symbolic representation, including noisy numerical values, model misspecification, and erroneous addition or deletion of terms. PROSE provides a new neural network framework for differential equations which allows for more flexibility and generality in learning operators and governing equations from data.

Recent breakthroughs in large language models (LLMs) exemplified by the impressive mathematical and scientific reasoning capabilities of the o1 model have spotlighted the critical importance of high-quality training data in advancing LLM performance across STEM disciplines. While the mathematics community has benefited from a growing body of curated datasets, the scientific domain at the higher education level has long suffered from a scarcity of comparable resources. To address this gap, we present SCP-116K, a new large-scale dataset of 116,756 high-quality problem-solution pairs, automatically extracted from heterogeneous sources using a streamlined and highly generalizable pipeline. Our approach involves stringent filtering to ensure the scientific rigor and educational level of the extracted materials, while maintaining adaptability for future expansions or domain transfers. By openly releasing both the dataset and the extraction pipeline, we seek to foster research on scientific reasoning, enable comprehensive performance evaluations of new LLMs, and lower the barrier to replicating the successes of advanced models like o1 in the broader science community. We believe SCP-116K will serve as a critical resource, catalyzing progress in high-level scientific reasoning tasks and promoting further innovations in LLM development. The dataset and code are publicly available at https://github.com/AQA6666/SCP-116K-open.

Large Language Models (LLMs) have demonstrated impressive reasoning capabilities, yet their performance is highly dependent on the prompting strategy and model scale. While reinforcement learning and fine-tuning have been deployed to boost reasoning, these approaches incur substantial computational and data overhead. In this work, we introduce Adaptive Graph of Thoughts (AGoT), a dynamic, graph-based inference framework that enhances LLM reasoning solely at test time. Rather than relying on fixed-step methods like Chain of Thought (CoT) or Tree of Thoughts (ToT), AGoT recursively decomposes complex queries into structured subproblems, forming an dynamic directed acyclic graph (DAG) of interdependent reasoning steps. By selectively expanding only those subproblems that require further analysis, AGoT unifies the strengths of chain, tree, and graph paradigms into a cohesive framework that allocates computation where it is most needed. We validate our approach on diverse benchmarks spanning multi-hop retrieval, scientific reasoning, and mathematical problem-solving, achieving up to 46.2% improvement on scientific reasoning tasks (GPQA) - comparable to gains achieved through computationally intensive reinforcement learning approaches and outperforming state-of-the-art iterative approaches. These results suggest that dynamic decomposition and structured recursion offer a scalable, cost-effective alternative to post-training modifications, paving the way for more robust, general-purpose reasoning in LLMs.

Generative Flow Networks (GFlowNets) are amortized samplers that learn stochastic policies to sequentially generate compositional objects from a given unnormalized reward distribution. They can generate diverse sets of high-reward objects, which is an important consideration in scientific discovery tasks. However, as they are typically trained from a given extrinsic reward function, it remains an important open challenge about how to leverage the power of pre-training and train GFlowNets in an unsupervised fashion for efficient adaptation to downstream tasks. Inspired by recent successes of unsupervised pre-training in various domains, we introduce a novel approach for reward-free pre-training of GFlowNets. By framing the training as a self-supervised problem, we propose an outcome-conditioned GFlowNet (OC-GFN) that learns to explore the candidate space. Specifically, OC-GFN learns to reach any targeted outcomes, akin to goal-conditioned policies in reinforcement learning. We show that the pre-trained OC-GFN model can allow for a direct extraction of a policy capable of sampling from any new reward functions in downstream tasks. Nonetheless, adapting OC-GFN on a downstream task-specific reward involves an intractable marginalization over possible outcomes. We propose a novel way to approximate this marginalization by learning an amortized predictor enabling efficient fine-tuning. Extensive experimental results validate the efficacy of our approach, demonstrating the effectiveness of pre-training the OC-GFN, and its ability to swiftly adapt to downstream tasks and discover modes more efficiently. This work may serve as a foundation for further exploration of pre-training strategies in the context of GFlowNets.

Fine-tuning pre-trained language models (PLMs), e.g., SciBERT, generally requires large numbers of annotated data to achieve state-of-the-art performance on a range of NLP tasks in the scientific domain. However, obtaining the fine-tune data for scientific NLP task is still challenging and expensive. Inspired by recent advancement in prompt learning, in this paper, we propose the Mix Prompt Tuning (MPT), which is a semi-supervised method to alleviate the dependence on annotated data and improve the performance of multi-granularity academic function recognition tasks with a small number of labeled examples. Specifically, the proposed method provides multi-perspective representations by combining manual prompt templates with automatically learned continuous prompt templates to help the given academic function recognition task take full advantage of knowledge in PLMs. Based on these prompt templates and the fine-tuned PLM, a large number of pseudo labels are assigned to the unlabeled examples. Finally, we fine-tune the PLM using the pseudo training set. We evaluate our method on three academic function recognition tasks of different granularity including the citation function, the abstract sentence function, and the keyword function, with datasets from computer science domain and biomedical domain. Extensive experiments demonstrate the effectiveness of our method and statistically significant improvements against strong baselines. In particular, it achieves an average increase of 5% in Macro-F1 score compared with fine-tuning, and 6% in Macro-F1 score compared with other semi-supervised method under low-resource settings. In addition, MPT is a general method that can be easily applied to other low-resource scientific classification tasks.

Mesh-based simulations are central to modeling complex physical systems in many disciplines across science and engineering. Mesh representations support powerful numerical integration methods and their resolution can be adapted to strike favorable trade-offs between accuracy and efficiency. However, high-dimensional scientific simulations are very expensive to run, and solvers and parameters must often be tuned individually to each system studied. Here we introduce MeshGraphNets, a framework for learning mesh-based simulations using graph neural networks. Our model can be trained to pass messages on a mesh graph and to adapt the mesh discretization during forward simulation. Our results show it can accurately predict the dynamics of a wide range of physical systems, including aerodynamics, structural mechanics, and cloth. The model's adaptivity supports learning resolution-independent dynamics and can scale to more complex state spaces at test time. Our method is also highly efficient, running 1-2 orders of magnitude faster than the simulation on which it is trained. Our approach broadens the range of problems on which neural network simulators can operate and promises to improve the efficiency of complex, scientific modeling tasks.

As the issue of global climate change becomes increasingly severe, the demand for research in climate science continues to grow. Natural language processing technologies, represented by Large Language Models (LLMs), have been widely applied to climate change-specific research, providing essential information support for decision-makers and the public. Some studies have improved model performance on relevant tasks by constructing climate change-related instruction data and instruction-tuning LLMs. However, current research remains inadequate in efficiently producing large volumes of high-precision instruction data for climate change, which limits further development of climate change LLMs. This study introduces an automated method for constructing instruction data. The method generates instructions using facts and background knowledge from documents and enhances the diversity of the instruction data through web scraping and the collection of seed instructions. Using this method, we constructed a climate change instruction dataset, named ClimateChat-Corpus, which was used to fine-tune open-source LLMs, resulting in an LLM named ClimateChat. Evaluation results show that ClimateChat significantly improves performance on climate change question-and-answer tasks. Additionally, we evaluated the impact of different base models and instruction data on LLM performance and demonstrated its capability to adapt to a wide range of climate change scientific discovery tasks, emphasizing the importance of selecting an appropriate base model for instruction tuning. This research provides valuable references and empirical support for constructing climate change instruction data and training climate change-specific LLMs.

Acronyms are the short forms of longer phrases and they are frequently used in writing, especially scholarly writing, to save space and facilitate the communication of information. As such, every text understanding tool should be capable of recognizing acronyms in text (i.e., acronym identification) and also finding their correct meaning (i.e., acronym disambiguation). As most of the prior works on these tasks are restricted to the biomedical domain and use unsupervised methods or models trained on limited datasets, they fail to perform well for scientific document understanding. To push forward research in this direction, we have organized two shared task for acronym identification and acronym disambiguation in scientific documents, named AI@SDU and AD@SDU, respectively. The two shared tasks have attracted 52 and 43 participants, respectively. While the submitted systems make substantial improvements compared to the existing baselines, there are still far from the human-level performance. This paper reviews the two shared tasks and the prominent participating systems for each of them.

Scientific literature understanding tasks have gained significant attention due to their potential to accelerate scientific discovery. Pre-trained language models (LMs) have shown effectiveness in these tasks, especially when tuned via contrastive learning. However, jointly utilizing pre-training data across multiple heterogeneous tasks (e.g., extreme classification, citation prediction, and literature search) remains largely unexplored. To bridge this gap, we propose a multi-task contrastive learning framework, SciMult, with a focus on facilitating common knowledge sharing across different scientific literature understanding tasks while preventing task-specific skills from interfering with each other. To be specific, we explore two techniques -- task-aware specialization and instruction tuning. The former adopts a Mixture-of-Experts Transformer architecture with task-aware sub-layers; the latter prepends task-specific instructions to the input text so as to produce task-aware outputs. Extensive experiments on a comprehensive collection of benchmark datasets verify the effectiveness of our task-aware specialization strategy in various tasks, where we outperform state-of-the-art scientific LMs.

Language models are known to hallucinate incorrect information, and it is unclear if they are sufficiently accurate and reliable for use in scientific research. We developed a rigorous human-AI comparison methodology to evaluate language model agents on real-world literature search tasks covering information retrieval, summarization, and contradiction detection tasks. We show that PaperQA2, a frontier language model agent optimized for improved factuality, matches or exceeds subject matter expert performance on three realistic literature research tasks without any restrictions on humans (i.e., full access to internet, search tools, and time). PaperQA2 writes cited, Wikipedia-style summaries of scientific topics that are significantly more accurate than existing, human-written Wikipedia articles. We also introduce a hard benchmark for scientific literature research called LitQA2 that guided design of PaperQA2, leading to it exceeding human performance. Finally, we apply PaperQA2 to identify contradictions within the scientific literature, an important scientific task that is challenging for humans. PaperQA2 identifies 2.34 +/- 1.99 contradictions per paper in a random subset of biology papers, of which 70% are validated by human experts. These results demonstrate that language model agents are now capable of exceeding domain experts across meaningful tasks on scientific literature.

Large language models (LLMs) have demonstrated potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. To address this gap, we introduce the first large-scale benchmark for evaluating LLMs with a near-sufficient set of sub-tasks of scientific discovery: inspiration retrieval, hypothesis composition, and hypothesis ranking. We develop an automated framework that extracts critical components - research questions, background surveys, inspirations, and hypotheses - from scientific papers across 12 disciplines, with expert validation confirming its accuracy. To prevent data contamination, we focus exclusively on papers published in 2024, ensuring minimal overlap with LLM pretraining data. Our evaluation reveals that LLMs perform well in retrieving inspirations, an out-of-distribution task, suggesting their ability to surface novel knowledge associations. This positions LLMs as "research hypothesis mines", capable of facilitating automated scientific discovery by generating innovative hypotheses at scale with minimal human intervention.

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.

Revising scientific papers based on peer feedback is a challenging task that requires not only deep scientific knowledge and reasoning, but also the ability to recognize the implicit requests in high-level feedback and to choose the best of many possible ways to update the manuscript in response. We introduce this task for large language models and release ARIES, a dataset of review comments and their corresponding paper edits, to enable training and evaluating models. We study two versions of the task: comment-edit alignment and edit generation, and evaluate several baselines, including GPT-4. We find that models struggle even to identify the edits that correspond to a comment, especially in cases where the comment is phrased in an indirect way or where the edit addresses the spirit of a comment but not the precise request. When tasked with generating edits, GPT-4 often succeeds in addressing comments on a surface level, but it rigidly follows the wording of the feedback rather than the underlying intent, and includes fewer technical details than human-written edits. We hope that our formalization, dataset, and analysis will form a foundation for future work in this area.

Despite long-standing efforts in accelerating scientific discovery with AI, building AI co-scientists remains challenging due to limited high-quality data for training and evaluation. To tackle this data scarcity issue, we present AutoSDT, an automatic pipeline that collects high-quality coding tasks in real-world data-driven discovery workflows. AutoSDT leverages the coding capabilities and parametric knowledge of LLMs to search for diverse sources, select ecologically valid tasks, and synthesize accurate task instructions and code solutions. Using our pipeline, we construct AutoSDT-5K, a dataset of 5,404 coding tasks for data-driven discovery that covers four scientific disciplines and 756 unique Python packages. To the best of our knowledge, AutoSDT-5K is the only automatically collected and the largest open dataset for data-driven scientific discovery. Expert feedback on a subset of 256 tasks shows the effectiveness of AutoSDT: 93% of the collected tasks are ecologically valid, and 92.2% of the synthesized programs are functionally correct. Trained on AutoSDT-5K, the Qwen2.5-Coder-Instruct LLM series, dubbed AutoSDT-Coder, show substantial improvement on two challenging data-driven discovery benchmarks, ScienceAgentBench and DiscoveryBench. Most notably, AutoSDT-Coder-32B reaches the same level of performance as GPT-4o on ScienceAgentBench with a success rate of 7.8%, doubling the performance of its base model. On DiscoveryBench, it lifts the hypothesis matching score to 8.1, bringing a 17.4% relative improvement and closing the gap between open-weight models and GPT-4o.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Prompt-based fine-tuning has become an essential method for eliciting information encoded in pre-trained language models for a variety of tasks, including text classification. For multi-class classification tasks, prompt-based fine-tuning under low-resource scenarios has resulted in performance levels comparable to those of fully fine-tuning methods. Previous studies have used crafted prompt templates and verbalizers, mapping from the label terms space to the class space, to solve the classification problem as a masked language modeling task. However, cross-domain and fine-grained prompt-based fine-tuning with an automatically enriched verbalizer remains unexplored, mainly due to the difficulty and costs of manually selecting domain label terms for the verbalizer, which requires humans with domain expertise. To address this challenge, we introduce SciPrompt, a framework designed to automatically retrieve scientific topic-related terms for low-resource text classification tasks. To this end, we select semantically correlated and domain-specific label terms within the context of scientific literature for verbalizer augmentation. Furthermore, we propose a new verbalization strategy that uses correlation scores as additional weights to enhance the prediction performance of the language model during model tuning. Our method outperforms state-of-the-art, prompt-based fine-tuning methods on scientific text classification tasks under few and zero-shot settings, especially in classifying fine-grained and emerging scientific topics.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

Recent studies show the growing significance of document retrieval in the generation of LLMs, i.e., RAG, within the scientific domain by bridging their knowledge gap. However, dense retrievers often struggle with domain-specific retrieval and complex query-document relationships, particularly when query segments correspond to various parts of a document. To alleviate such prevalent challenges, this paper introduces MixGR, which improves dense retrievers' awareness of query-document matching across various levels of granularity in queries and documents using a zero-shot approach. MixGR fuses various metrics based on these granularities to a united score that reflects a comprehensive query-document similarity. Our experiments demonstrate that MixGR outperforms previous document retrieval by 24.7%, 9.8%, and 6.9% on nDCG@5 with unsupervised, supervised, and LLM-based retrievers, respectively, averaged on queries containing multiple subqueries from five scientific retrieval datasets. Moreover, the efficacy of two downstream scientific question-answering tasks highlights the advantage of MixGR to boost the application of LLMs in the scientific domain. The code and experimental datasets are available.

The exponential growth of online textual content across diverse domains has necessitated advanced methods for automated text classification. Large Language Models (LLMs) based on transformer architectures have shown significant success in this area, particularly in natural language processing (NLP) tasks. However, general-purpose LLMs often struggle with domain-specific content, such as scientific texts, due to unique challenges like specialized vocabulary and imbalanced data. In this study, we fine-tune four state-of-the-art LLMs BERT, SciBERT, BioBERT, and BlueBERT on three datasets derived from the WoS-46985 dataset to evaluate their performance in scientific text classification. Our experiments reveal that domain-specific models, particularly SciBERT, consistently outperform general-purpose models in both abstract-based and keyword-based classification tasks. Additionally, we compare our achieved results with those reported in the literature for deep learning models, further highlighting the advantages of LLMs, especially when utilized in specific domains. The findings emphasize the importance of domain-specific adaptations for LLMs to enhance their effectiveness in specialized text classification tasks.

Large language models (LLMs) are increasingly utilized to assist in scientific and academic writing, helping authors enhance the coherence of their articles. Previous studies have highlighted stereotypes and biases present in LLM outputs, emphasizing the need to evaluate these models for their alignment with human narrative styles and potential gender biases. In this study, we assess the alignment of three prominent LLMs - Claude 3 Opus, Mistral AI Large, and Gemini 1.5 Flash - by analyzing their performance on benchmark text-generation tasks for scientific abstracts. We employ the Linguistic Inquiry and Word Count (LIWC) framework to extract lexical, psychological, and social features from the generated texts. Our findings indicate that, while these models generally produce text closely resembling human authored content, variations in stylistic features suggest significant gender biases. This research highlights the importance of developing LLMs that maintain a diversity of writing styles to promote inclusivity in academic discourse.

Learning semantically meaningful representations from scientific documents can facilitate academic literature search and improve performance of recommendation systems. Pre-trained language models have been shown to learn rich textual representations, yet they cannot provide powerful document-level representations for scientific articles. We propose MIReAD, a simple method that learns high-quality representations of scientific papers by fine-tuning transformer model to predict the target journal class based on the abstract. We train MIReAD on more than 500,000 PubMed and arXiv abstracts across over 2,000 journal classes. We show that MIReAD produces representations that can be used for similar papers retrieval, topic categorization and literature search. Our proposed approach outperforms six existing models for representation learning on scientific documents across four evaluation standards.

Scientific data visualization plays a crucial role in research by enabling the direct display of complex information and assisting researchers in identifying implicit patterns. Despite its importance, the use of Large Language Models (LLMs) for scientific data visualization remains rather unexplored. In this study, we introduce MatPlotAgent, an efficient model-agnostic LLM agent framework designed to automate scientific data visualization tasks. Leveraging the capabilities of both code LLMs and multi-modal LLMs, MatPlotAgent consists of three core modules: query understanding, code generation with iterative debugging, and a visual feedback mechanism for error correction. To address the lack of benchmarks in this field, we present MatPlotBench, a high-quality benchmark consisting of 100 human-verified test cases. Additionally, we introduce a scoring approach that utilizes GPT-4V for automatic evaluation. Experimental results demonstrate that MatPlotAgent can improve the performance of various LLMs, including both commercial and open-source models. Furthermore, the proposed evaluation method shows a strong correlation with human-annotated scores.

Large Language Models (LLMs) have shown outstanding performance across wide range of downstream tasks. This competency is attributed to their substantial parameter size and pre-training on extensive corpus. Moreover, LLMs have exhibited enhanced reasoning capabilities in tackling complex reasoning tasks, owing to the utilization of a method named ``Chain-of-Thought (CoT) prompting''. This method is designed to generate intermediate reasoning steps that guide the inference of the final answer. However, it is essential to highlight that these advanced reasoning abilities appear to emerge in models with a minimum of 10 billion parameters, thereby limiting its efficacy in situations where computational resources are constrained. In this paper, we investigate the possibility of transferring the reasoning capabilities of LLMs to smaller models via knowledge distillation. Specifically, we propose Sci-CoT, a two-stage framework that separates the processes of generating rationales and inferring answers. This method enables a more efficient use of rationales during the answer inference stage, leading to improved performance on scientific question-answering tasks. Utilizing Sci-CoT, our 80-million parameter model is able to exceed the performance of BLOOM-176B in the ARC-Easy dataset under the few shot setting.

We present the first systematic investigation of supervised scaling laws outside of an ImageNet-like context - on images of galaxies. We use 840k galaxy images and over 100M annotations by Galaxy Zoo volunteers, comparable in scale to Imagenet-1K. We find that adding annotated galaxy images provides a power law improvement in performance across all architectures and all tasks, while adding trainable parameters is effective only for some (typically more subjectively challenging) tasks. We then compare the downstream performance of finetuned models pretrained on either ImageNet-12k alone vs. additionally pretrained on our galaxy images. We achieve an average relative error rate reduction of 31% across 5 downstream tasks of scientific interest. Our finetuned models are more label-efficient and, unlike their ImageNet-12k-pretrained equivalents, often achieve linear transfer performance equal to that of end-to-end finetuning. We find relatively modest additional downstream benefits from scaling model size, implying that scaling alone is not sufficient to address our domain gap, and suggest that practitioners with qualitatively different images might benefit more from in-domain adaption followed by targeted downstream labelling.

Existing benchmarks have proven effective for assessing the performance of fully trained large language models. However, we find striking differences in the early training stages of small models, where benchmarks often fail to provide meaningful or discriminative signals. To explore how these differences arise, this competition tackles the challenge of designing scientific knowledge evaluation tasks specifically tailored for measuring early training progress of language models. Participants are invited to develop novel evaluation methodologies or adapt existing benchmarks to better capture performance differences among language models. To support this effort, we provide three pre-trained small models (0.5B, 1B, and 3B parameters), along with intermediate checkpoints sampled during training up to 200B tokens. All experiments and development work can be run on widely available free cloud-based GPU platforms, making participation accessible to researchers with limited computational resources. Submissions will be evaluated based on three criteria: the quality of the performance signal they produce, the consistency of model rankings at 1 trillion tokens of training, and their relevance to the scientific knowledge domain. By promoting the design of tailored evaluation strategies for early training, this competition aims to attract a broad range of participants from various disciplines, including those who may not be machine learning experts or have access to dedicated GPU resources. Ultimately, this initiative seeks to make foundational LLM research more systematic and benchmark-informed from the earliest phases of model development.

Recently, test-time scaling Large Language Models (LLMs) have demonstrated exceptional reasoning capabilities across scientific and professional tasks by generating long chains-of-thought (CoT). As a crucial component for developing these reasoning models, reinforcement learning (RL), exemplified by Proximal Policy Optimization (PPO) and its variants, allows models to learn through trial and error. However, PPO can be time-consuming due to its inherent on-policy nature, which is further exacerbated by increasing response lengths. In this work, we propose Truncated Proximal Policy Optimization (T-PPO), a novel extension to PPO that improves training efficiency by streamlining policy update and length-restricted response generation. T-PPO mitigates the issue of low hardware utilization, an inherent drawback of fully synchronized long-generation procedures, where resources often sit idle during the waiting periods for complete rollouts. Our contributions are two-folds. First, we propose Extended Generalized Advantage Estimation (EGAE) for advantage estimation derived from incomplete responses while maintaining the integrity of policy learning. Second, we devise a computationally optimized mechanism that allows for the independent optimization of the policy and value models. By selectively filtering prompt and truncated tokens, this mechanism reduces redundant computations and accelerates the training process without sacrificing convergence performance. We demonstrate the effectiveness and efficacy of T-PPO on AIME 2024 with a 32B base model. The experimental results show that T-PPO improves the training efficiency of reasoning LLMs by up to 2.5x and outperforms its existing competitors.

Large reasoning models (LRMs), such as OpenAI-o1 and DeepSeek-R1, demonstrate impressive long-horizon reasoning capabilities. However, their reliance on static internal knowledge limits their performance on complex, knowledge-intensive tasks and hinders their ability to produce comprehensive research reports requiring synthesis of diverse web information. To address this, we propose WebThinker, a deep research agent that empowers LRMs to autonomously search the web, navigate web pages, and draft research reports during the reasoning process. WebThinker integrates a Deep Web Explorer module, enabling LRMs to dynamically search, navigate, and extract information from the web when encountering knowledge gaps. It also employs an Autonomous Think-Search-and-Draft strategy, allowing the model to seamlessly interleave reasoning, information gathering, and report writing in real time. To further enhance research tool utilization, we introduce an RL-based training strategy via iterative online Direct Preference Optimization (DPO). Extensive experiments on complex reasoning benchmarks (GPQA, GAIA, WebWalkerQA, HLE) and scientific report generation tasks (Glaive) demonstrate that WebThinker significantly outperforms existing methods and strong proprietary systems. Our approach enhances LRM reliability and applicability in complex scenarios, paving the way for more capable and versatile deep research systems. The code is available at https://github.com/RUC-NLPIR/WebThinker.

While language models are increasingly utilized in materials science, typical models rely on frequency-centric tokenization methods originally developed for natural language processing. However, these methods frequently produce excessive fragmentation and semantic loss, failing to maintain the structural and semantic integrity of material concepts. To address this issue, we propose MATTER, a novel tokenization approach that integrates material knowledge into tokenization. Based on MatDetector trained on our materials knowledge base and a re-ranking method prioritizing material concepts in token merging, MATTER maintains the structural integrity of identified material concepts and prevents fragmentation during tokenization, ensuring their semantic meaning remains intact. The experimental results demonstrate that MATTER outperforms existing tokenization methods, achieving an average performance gain of 4% and 2% in the generation and classification tasks, respectively. These results underscore the importance of domain knowledge for tokenization strategies in scientific text processing. Our code is available at https://github.com/yerimoh/MATTER

Scientific innovation relies on detailed workflows, which include critical steps such as analyzing literature, generating ideas, validating these ideas, interpreting results, and inspiring follow-up research. However, scientific publications that document these workflows are extensive and unstructured. This makes it difficult for both human researchers and AI systems to effectively navigate and explore the space of scientific innovation. To address this issue, we introduce MASSW, a comprehensive text dataset on Multi-Aspect Summarization of Scientific Workflows. MASSW includes more than 152,000 peer-reviewed publications from 17 leading computer science conferences spanning the past 50 years. Using Large Language Models (LLMs), we automatically extract five core aspects from these publications -- context, key idea, method, outcome, and projected impact -- which correspond to five key steps in the research workflow. These structured summaries facilitate a variety of downstream tasks and analyses. The quality of the LLM-extracted summaries is validated by comparing them with human annotations. We demonstrate the utility of MASSW through multiple novel machine-learning tasks that can be benchmarked using this new dataset, which make various types of predictions and recommendations along the scientific workflow. MASSW holds significant potential for researchers to create and benchmark new AI methods for optimizing scientific workflows and fostering scientific innovation in the field. Our dataset is openly available at https://github.com/xingjian-zhang/massw.

We present MatSci-NLP, a natural language benchmark for evaluating the performance of natural language processing (NLP) models on materials science text. We construct the benchmark from publicly available materials science text data to encompass seven different NLP tasks, including conventional NLP tasks like named entity recognition and relation classification, as well as NLP tasks specific to materials science, such as synthesis action retrieval which relates to creating synthesis procedures for materials. We study various BERT-based models pretrained on different scientific text corpora on MatSci-NLP to understand the impact of pretraining strategies on understanding materials science text. Given the scarcity of high-quality annotated data in the materials science domain, we perform our fine-tuning experiments with limited training data to encourage the generalize across MatSci-NLP tasks. Our experiments in this low-resource training setting show that language models pretrained on scientific text outperform BERT trained on general text. MatBERT, a model pretrained specifically on materials science journals, generally performs best for most tasks. Moreover, we propose a unified text-to-schema for multitask learning on \benchmark and compare its performance with traditional fine-tuning methods. In our analysis of different training methods, we find that our proposed text-to-schema methods inspired by question-answering consistently outperform single and multitask NLP fine-tuning methods. The code and datasets are publicly available at https://github.com/BangLab-UdeM-Mila/NLP4MatSci-ACL23.

We present PeerQA, a real-world, scientific, document-level Question Answering (QA) dataset. PeerQA questions have been sourced from peer reviews, which contain questions that reviewers raised while thoroughly examining the scientific article. Answers have been annotated by the original authors of each paper. The dataset contains 579 QA pairs from 208 academic articles, with a majority from ML and NLP, as well as a subset of other scientific communities like Geoscience and Public Health. PeerQA supports three critical tasks for developing practical QA systems: Evidence retrieval, unanswerable question classification, and answer generation. We provide a detailed analysis of the collected dataset and conduct experiments establishing baseline systems for all three tasks. Our experiments and analyses reveal the need for decontextualization in document-level retrieval, where we find that even simple decontextualization approaches consistently improve retrieval performance across architectures. On answer generation, PeerQA serves as a challenging benchmark for long-context modeling, as the papers have an average size of 12k tokens. Our code and data is available at https://github.com/UKPLab/peerqa.

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.

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

Large Language Models (LLMs) are often described as being instances of foundation models - that is, models that transfer strongly across various tasks and conditions in few-show or zero-shot manner, while exhibiting scaling laws that predict function improvement when increasing the pre-training scale. These claims of excelling in different functions and tasks rely on measurements taken across various sets of standardized benchmarks showing high scores for such models. We demonstrate here a dramatic breakdown of function and reasoning capabilities of state-of-the-art models trained at the largest available scales which claim strong function, using a simple, short, conventional common sense problem formulated in concise natural language, easily solvable by humans. The breakdown is dramatic, as models also express strong overconfidence in their wrong solutions, while providing often non-sensical "reasoning"-like explanations akin to confabulations to justify and backup the validity of their clearly failed responses, making them sound plausible. Various standard interventions in an attempt to get the right solution, like various type of enhanced prompting, or urging the models to reconsider the wrong solutions again by multi step re-evaluation, fail. We take these initial observations to the scientific and technological community to stimulate urgent re-assessment of the claimed capabilities of current generation of LLMs, Such re-assessment also requires common action to create standardized benchmarks that would allow proper detection of such basic reasoning deficits that obviously manage to remain undiscovered by current state-of-the-art evaluation procedures and benchmarks. Code for reproducing experiments in the paper and raw experiments data can be found at https://github.com/LAION-AI/AIW

Recent breakthroughs in Large Language Models (LLMs) have revolutionized natural language understanding and generation, igniting a surge of interest in leveraging these technologies in the field of scientific literature analysis. Existing benchmarks, however, inadequately evaluate the proficiency of LLMs in scientific literature analysis, especially in scenarios involving complex comprehension and multimodal data. In response, we introduced SciAssess, a benchmark tailored for the in-depth analysis of scientific literature, crafted to provide a thorough assessment of LLMs' efficacy. SciAssess focuses on evaluating LLMs' abilities in memorization, comprehension, and analysis within the context of scientific literature analysis. It includes representative tasks from diverse scientific fields, such as general chemistry, organic materials, and alloy materials. And rigorous quality control measures ensure its reliability in terms of correctness, anonymization, and copyright compliance. SciAssess evaluates leading LLMs, including GPT-4, GPT-3.5, and Gemini, identifying their strengths and aspects for improvement and supporting the ongoing development of LLM applications in scientific literature analysis. SciAssess and its resources are made available at https://sci-assess.github.io, offering a valuable tool for advancing LLM capabilities in scientific literature analysis.

This paper examines the encoding of analogy in large-scale pretrained language models, such as BERT and GPT-2. Existing analogy datasets typically focus on a limited set of analogical relations, with a high similarity of the two domains between which the analogy holds. As a more realistic setup, we introduce the Scientific and Creative Analogy dataset (SCAN), a novel analogy dataset containing systematic mappings of multiple attributes and relational structures across dissimilar domains. Using this dataset, we test the analogical reasoning capabilities of several widely-used pretrained language models (LMs). We find that state-of-the-art LMs achieve low performance on these complex analogy tasks, highlighting the challenges still posed by analogy understanding.

The exponential growth of academic publications poses challenges for the research process, such as literature review and procedural planning. Large Language Models (LLMs) have emerged as powerful AI tools, especially when combined with additional tools and resources. Recent LLM-powered frameworks offer promising solutions for handling complex domain-specific tasks, yet their domain-specific implementation limits broader applicability. This highlights the need for LLM-integrated systems that can assist in cross-disciplinary tasks, such as streamlining the research process across science and engineering disciplines. To address this need, we introduce Artificial Research Innovator Assistant (ARIA), a four-agent, multi-LLM framework. By emulating a team of expert assistants, ARIA systematically replicates the human research workflow to autonomously search, retrieve, and filter hundreds of papers, subsequently synthesizing relevant literature into actionable research procedures. In a case study on dropwise condensation enhancement, ARIA demonstrates its capability to streamline research tasks within an hour, maintaining user oversight during execution and ultimately liberating researchers from time-intensive tasks.

As scientific research becomes increasingly complex, innovative tools are needed to manage vast data, facilitate interdisciplinary collaboration, and accelerate discovery. Large language models (LLMs) are now evolving into LLM-based scientific agents that automate critical tasks, ranging from hypothesis generation and experiment design to data analysis and simulation. Unlike general-purpose LLMs, these specialized agents integrate domain-specific knowledge, advanced tool sets, and robust validation mechanisms, enabling them to handle complex data types, ensure reproducibility, and drive scientific breakthroughs. This survey provides a focused review of the architectures, design, benchmarks, applications, and ethical considerations surrounding LLM-based scientific agents. We highlight why they differ from general agents and the ways in which they advance research across various scientific fields. By examining their development and challenges, this survey offers a comprehensive roadmap for researchers and practitioners to harness these agents for more efficient, reliable, and ethically sound scientific discovery.

Scientific figure captioning is a complex task that requires generating contextually appropriate descriptions of visual content. However, existing methods often fall short by utilizing incomplete information, treating the task solely as either an image-to-text or text summarization problem. This limitation hinders the generation of high-quality captions that fully capture the necessary details. Moreover, existing data sourced from arXiv papers contain low-quality captions, posing significant challenges for training large language models (LLMs). In this paper, we introduce a framework called Multi-LLM Collaborative Figure Caption Generation (MLBCAP) to address these challenges by leveraging specialized LLMs for distinct sub-tasks. Our approach unfolds in three key modules: (Quality Assessment) We utilize multimodal LLMs to assess the quality of training data, enabling the filtration of low-quality captions. (Diverse Caption Generation) We then employ a strategy of fine-tuning/prompting multiple LLMs on the captioning task to generate candidate captions. (Judgment) Lastly, we prompt a prominent LLM to select the highest quality caption from the candidates, followed by refining any remaining inaccuracies. Human evaluations demonstrate that informative captions produced by our approach rank better than human-written captions, highlighting its effectiveness. Our code is available at https://github.com/teamreboott/MLBCAP

Large Language Models (LLMs) generalize well across language tasks, but suffer from hallucinations and uninterpretability, making it difficult to assess their accuracy without ground-truth. Retrieval-Augmented Generation (RAG) models have been proposed to reduce hallucinations and provide provenance for how an answer was generated. Applying such models to the scientific literature may enable large-scale, systematic processing of scientific knowledge. We present PaperQA, a RAG agent for answering questions over the scientific literature. PaperQA is an agent that performs information retrieval across full-text scientific articles, assesses the relevance of sources and passages, and uses RAG to provide answers. Viewing this agent as a question answering model, we find it exceeds performance of existing LLMs and LLM agents on current science QA benchmarks. To push the field closer to how humans perform research on scientific literature, we also introduce LitQA, a more complex benchmark that requires retrieval and synthesis of information from full-text scientific papers across the literature. Finally, we demonstrate PaperQA's matches expert human researchers on LitQA.

We propose ParaSCI, the first large-scale paraphrase dataset in the scientific field, including 33,981 paraphrase pairs from ACL (ParaSCI-ACL) and 316,063 pairs from arXiv (ParaSCI-arXiv). Digging into characteristics and common patterns of scientific papers, we construct this dataset though intra-paper and inter-paper methods, such as collecting citations to the same paper or aggregating definitions by scientific terms. To take advantage of sentences paraphrased partially, we put up PDBERT as a general paraphrase discovering method. The major advantages of paraphrases in ParaSCI lie in the prominent length and textual diversity, which is complementary to existing paraphrase datasets. ParaSCI obtains satisfactory results on human evaluation and downstream tasks, especially long paraphrase generation.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

Advancements in Large Language Models (LLMs) drive interest in scientific applications, necessitating specialized benchmarks such as Earth science. Existing benchmarks either present a general science focus devoid of Earth science specificity or cover isolated subdomains, lacking holistic evaluation. Furthermore, current benchmarks typically neglect the assessment of LLMs' capabilities in open-ended scientific exploration. In this paper, we present a comprehensive and professional benchmark for the Earth sciences, designed to evaluate the capabilities of LLMs in scientific exploration within this domain, spanning from fundamental to advanced levels. Leveraging a corpus of 100,000 research papers, we first construct two Question Answering (QA) datasets: Earth-Iron, which offers extensive question coverage for broad assessment, and Earth-Silver, which features a higher level of difficulty to evaluate professional depth. These datasets encompass five Earth spheres, 114 disciplines, and 11 task categories, assessing foundational knowledge crucial for scientific exploration. Most notably, we introduce Earth-Gold with new metrics, a dataset comprising open-ended multi-turn dialogues specifically designed to evaluate the advanced capabilities of LLMs in scientific exploration, including methodology induction, limitation analysis, and concept proposal. Extensive experiments reveal limitations in 11 leading LLMs across different domains and tasks, highlighting considerable room for improvement in their scientific exploration capabilities. The benchmark is available on https://huggingface.co/ai-earth .

Tables are among the most widely used tools for representing structured data in research, business, medicine, and education. Although LLMs demonstrate strong performance in downstream tasks, their efficiency in processing tabular data remains underexplored. In this paper, we investigate the effectiveness of both text-based and multimodal LLMs on table understanding tasks through a cross-domain and cross-modality evaluation. Specifically, we compare their performance on tables from scientific vs. non-scientific contexts and examine their robustness on tables represented as images vs. text. Additionally, we conduct an interpretability analysis to measure context usage and input relevance. We also introduce the TableEval benchmark, comprising 3017 tables from scholarly publications, Wikipedia, and financial reports, where each table is provided in five different formats: Image, Dictionary, HTML, XML, and LaTeX. Our findings indicate that while LLMs maintain robustness across table modalities, they face significant challenges when processing scientific tables.

Fully comprehending scientific papers by machines reflects a high level of Artificial General Intelligence, requiring the ability to reason across fragmented and heterogeneous sources of information, presenting a complex and practically significant challenge. While Vision-Language Models (VLMs) have made remarkable strides in various tasks, particularly those involving reasoning with evidence source from single image or text page, their ability to use cross-source information for reasoning remains an open problem. This work presents MMCR, a high-difficulty benchmark designed to evaluate VLMs' capacity for reasoning with cross-source information from scientific papers. The benchmark comprises 276 high-quality questions, meticulously annotated by humans across 7 subjects and 10 task types. Experiments with 18 VLMs demonstrate that cross-source reasoning presents a substantial challenge for existing models. Notably, even the top-performing model, GPT-4o, achieved only 48.55% overall accuracy, with only 20% accuracy in multi-table comprehension tasks, while the second-best model, Qwen2.5-VL-72B, reached 39.86% overall accuracy. Furthermore, we investigated the impact of the Chain-of-Thought (CoT) technique on cross-source reasoning and observed a detrimental effect on small models, whereas larger models demonstrated substantially enhanced performance. These results highlight the pressing need to develop VLMs capable of effectively utilizing cross-source information for reasoning.

Evaluations of Large Language Models (LLMs) on knowledge-intensive tasks and factual accuracy often focus on high-resource languages primarily because datasets for low-resource languages (LRLs) are scarce. In this paper, we present Uhura -- a new benchmark that focuses on two tasks in six typologically-diverse African languages, created via human translation of existing English benchmarks. The first dataset, Uhura-ARC-Easy, is composed of multiple-choice science questions. The second, Uhura-TruthfulQA, is a safety benchmark testing the truthfulness of models on topics including health, law, finance, and politics. We highlight the challenges creating benchmarks with highly technical content for LRLs and outline mitigation strategies. Our evaluation reveals a significant performance gap between proprietary models such as GPT-4o and o1-preview, and Claude models, and open-source models like Meta's LLaMA and Google's Gemma. Additionally, all models perform better in English than in African languages. These results indicate that LMs struggle with answering scientific questions and are more prone to generating false claims in low-resource African languages. Our findings underscore the necessity for continuous improvement of multilingual LM capabilities in LRL settings to ensure safe and reliable use in real-world contexts. We open-source the Uhura Benchmark and Uhura Platform to foster further research and development in NLP for LRLs.

Large multimodal models (LMMs) have proven flexible and generalisable across many tasks and fields. Although they have strong potential to aid scientific research, their capabilities in this domain are not well characterised. A key aspect of scientific research is the ability to understand and interpret figures, which serve as a rich, compressed source of complex information. In this work, we present SciFIBench, a scientific figure interpretation benchmark. Our main benchmark consists of a 1000-question gold set of multiple-choice questions split between two tasks across 12 categories. The questions are curated from CS arXiv paper figures and captions, using adversarial filtering to find hard negatives and human verification for quality control. We evaluate 26 LMMs on SciFIBench, finding it to be a challenging benchmark. Finally, we investigate the alignment and reasoning faithfulness of the LMMs on augmented question sets from our benchmark. We release SciFIBench to encourage progress in this domain.

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.

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

We present a new scientific document similarity model based on matching fine-grained aspects of texts. To train our model, we exploit a naturally-occurring source of supervision: sentences in the full-text of papers that cite multiple papers together (co-citations). Such co-citations not only reflect close paper relatedness, but also provide textual descriptions of how the co-cited papers are related. This novel form of textual supervision is used for learning to match aspects across papers. We develop multi-vector representations where vectors correspond to sentence-level aspects of documents, and present two methods for aspect matching: (1) A fast method that only matches single aspects, and (2) a method that makes sparse multiple matches with an Optimal Transport mechanism that computes an Earth Mover's Distance between aspects. Our approach improves performance on document similarity tasks in four datasets. Further, our fast single-match method achieves competitive results, paving the way for applying fine-grained similarity to large scientific corpora. Code, data, and models available at: https://github.com/allenai/aspire

We present our systems submitted for the shared tasks of Acronym Identification (AI) and Acronym Disambiguation (AD) held under Workshop on SDU. We mainly experiment with BERT and SciBERT. In addition, we assess the effectiveness of "BIOless" tagging and blending along with the prowess of ensembling in AI. For AD, we formulate the problem as a span prediction task, experiment with different training techniques and also leverage the use of external data. Our systems rank 11th and 3rd in AI and AD tasks respectively.

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

Large language models (LLMs) have achieved huge success for their general knowledge and ability to solve a wide spectrum of tasks in natural language processing (NLP). Due to their impressive abilities, LLMs have shed light on potential inter-discipline applications to foster scientific discoveries of a specific domain by using artificial intelligence (AI for science, AI4S). In the meantime, utilizing NLP techniques in geoscience research and practice is wide and convoluted, contributing from knowledge extraction and document classification to question answering and knowledge discovery. In this work, we take the initial step to leverage LLM for science, through a rather straightforward approach. We try to specialize an LLM into geoscience, by further pre-training the model with a vast amount of texts in geoscience, as well as supervised fine-tuning (SFT) the resulting model with our custom collected instruction tuning dataset. These efforts result in a model GeoGalactica consisting of 30 billion parameters. To our best knowledge, it is the largest language model for the geoscience domain. More specifically, GeoGalactica is from further pre-training of Galactica. We train GeoGalactica over a geoscience-related text corpus containing 65 billion tokens curated from extensive data sources in the big science project Deep-time Digital Earth (DDE), preserving as the largest geoscience-specific text corpus. Then we fine-tune the model with 1 million pairs of instruction-tuning data consisting of questions that demand professional geoscience knowledge to answer. In this technical report, we will illustrate in detail all aspects of GeoGalactica, including data collection, data cleaning, base model selection, pre-training, SFT, and evaluation. We open-source our data curation tools and the checkpoints of GeoGalactica during the first 3/4 of pre-training.

Reasoning models are large language models that emit a long chain-of-thought before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained for chemistry without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 640,730 experimentally-grounded chemistry problems across 375 tasks ranging from synthesizability, to blood-brain barrier permeability, to human receptor activity, to scent. Our model exceeds general-purpose chemistry models, frontier models, and human experts on molecular design tasks. It is also more data efficient relative to specialized models. We anticipate that this method can be applied to train data-efficient language models specialized for tasks across a wide variety of scientific domains.

Scientific extreme summarization (TLDR) aims to form ultra-short summaries of scientific papers. Previous efforts on curating scientific TLDR datasets failed to scale up due to the heavy human annotation and domain expertise required. In this paper, we propose a simple yet effective approach to automatically extracting TLDR summaries for scientific papers from their citation texts. Based on the proposed approach, we create a new benchmark CiteSum without human annotation, which is around 30 times larger than the previous human-curated dataset SciTLDR. We conduct a comprehensive analysis of CiteSum, examining its data characteristics and establishing strong baselines. We further demonstrate the usefulness of CiteSum by adapting models pre-trained on CiteSum (named CITES) to new tasks and domains with limited supervision. For scientific extreme summarization, CITES outperforms most fully-supervised methods on SciTLDR without any fine-tuning and obtains state-of-the-art results with only 128 examples. For news extreme summarization, CITES achieves significant gains on XSum over its base model (not pre-trained on CiteSum), e.g., +7.2 ROUGE-1 zero-shot performance and state-of-the-art few-shot performance. For news headline generation, CITES performs the best among unsupervised and zero-shot methods on Gigaword. Our dataset and code can be found at https://github.com/morningmoni/CiteSum.

Scientific researchers need intensive information about datasets to effectively evaluate and develop theories and methodologies. The information needs regarding datasets are implicitly embedded in particular research tasks, rather than explicitly expressed in search queries. However, existing scientific retrieval and question-answering (QA) datasets typically address straightforward questions, which do not align with the distribution of real-world research inquiries. To bridge this gap, we developed ScIRGen, a dataset generation framework for scientific QA \& retrieval that more accurately reflects the information needs of professional science researchers, and uses it to create a large-scale scientific retrieval-augmented generation (RAG) dataset with realistic queries, datasets and papers. Technically, we designed a dataset-oriented information extraction method that leverages academic papers to augment the dataset representation. We then proposed a question generation framework by employing cognitive taxonomy to ensure the quality of synthesized questions. We also design a method to automatically filter synthetic answers based on the perplexity shift of LLMs, which is highly aligned with human judgment of answers' validity. Collectively, these methodologies culminated in the creation of the 61k QA dataset, ScIRGen-Geo. We benchmarked representative methods on the ScIRGen-Geo dataset for their question-answering and retrieval capabilities, finding out that current methods still suffer from reasoning from complex questions. This work advances the development of more sophisticated tools to support the intricate information needs of the scientific community.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.

Multi-modal large language models (MLLMs) have demonstrated promising capabilities across various tasks by integrating textual and visual information to achieve visual understanding in complex scenarios. Despite the availability of several benchmarks aims to evaluating MLLMs in tasks from visual question answering to complex problem-solving, most focus predominantly on mathematics or general visual understanding tasks. This reveals a critical gap in current benchmarks, which often overlook the inclusion of other key scientific disciplines such as physics and chemistry. To address this gap, we meticulously construct a comprehensive benchmark, named VisScience, which is utilized to assess the multi-modal scientific reasoning across the three disciplines of mathematics, physics, and chemistry. This benchmark comprises 3,000 questions drawn from K12 education - spanning elementary school through high school - equally distributed across three disciplines, with 1,000 questions per discipline. The questions within VisScience span 21 distinct subjects and are categorized into five difficulty levels, offering a broad spectrum of topics within each discipline. With VisScience, we present a detailed evaluation of the performance of 25 representative MLLMs in scientific reasoning. Experimental results demonstrate that closed-source MLLMs generally outperform open-source models. The best performance observed include a 53.4\% accuracy in mathematics by Claude3.5-Sonnet, 38.2\% in physics by GPT-4o, and 47.0\% in chemistry by Gemini-1.5-Pro. These results underscore the strengths and limitations of MLLMs, suggesting areas for future improvement and highlighting the importance of developing models that can effectively handle the diverse demands of multi-modal scientific reasoning.

This project investigates the efficacy of Large Language Models (LLMs) in understanding and extracting scientific knowledge across specific domains and to create a deep learning framework: Knowledge AI. As a part of this framework, we employ pre-trained models and fine-tune them on datasets in the scientific domain. The models are adapted for four key Natural Language Processing (NLP) tasks: summarization, text generation, question answering, and named entity recognition. Our results indicate that domain-specific fine-tuning significantly enhances model performance in each of these tasks, thereby improving their applicability for scientific contexts. This adaptation enables non-experts to efficiently query and extract information within targeted scientific fields, demonstrating the potential of fine-tuned LLMs as a tool for knowledge discovery in the sciences.

The number of Language Models (LMs) dedicated to processing scientific text is on the rise. Keeping pace with the rapid growth of scientific LMs (SciLMs) has become a daunting task for researchers. To date, no comprehensive surveys on SciLMs have been undertaken, leaving this issue unaddressed. Given the constant stream of new SciLMs, appraising the state-of-the-art and how they compare to each other remain largely unknown. This work fills that gap and provides a comprehensive review of SciLMs, including an extensive analysis of their effectiveness across different domains, tasks and datasets, and a discussion on the challenges that lie ahead.

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

Recent advancements in artificial intelligence (AI), particularly in large language models (LLMs) such as OpenAI-o1 and DeepSeek-R1, have demonstrated remarkable capabilities in complex domains such as logical reasoning and experimental coding. Motivated by these advancements, numerous studies have explored the application of AI in the innovation process, particularly in the context of scientific research. These AI technologies primarily aim to develop systems that can autonomously conduct research processes across a wide range of scientific disciplines. Despite these significant strides, a comprehensive survey on AI for Research (AI4Research) remains absent, which hampers our understanding and impedes further development in this field. To address this gap, we present a comprehensive survey and offer a unified perspective on AI4Research. Specifically, the main contributions of our work are as follows: (1) Systematic taxonomy: We first introduce a systematic taxonomy to classify five mainstream tasks in AI4Research. (2) New frontiers: Then, we identify key research gaps and highlight promising future directions, focusing on the rigor and scalability of automated experiments, as well as the societal impact. (3) Abundant applications and resources: Finally, we compile a wealth of resources, including relevant multidisciplinary applications, data corpora, and tools. We hope our work will provide the research community with quick access to these resources and stimulate innovative breakthroughs in AI4Research.

Large vision-language models (LVLMs), exemplified by GPT-4V, excel across diverse tasks involving concrete images from natural scenes. However, their ability to interpret abstract figures, such as geometry shapes and scientific plots, remains limited due to a scarcity of training datasets in scientific domains. To fill this gap, we introduce Multimodal ArXiv, consisting of ArXivCap and ArXivQA, for enhancing LVLMs scientific comprehension. ArXivCap is a figure-caption dataset comprising 6.4M images and 3.9M captions sourced from 572K ArXiv papers spanning various scientific domains. Drawing from ArXivCap, we introduce ArXivQA, a question-answering dataset generated by prompting GPT-4V based on scientific figures. ArXivQA greatly enhances LVLMs' mathematical reasoning capabilities, achieving a 10.4% absolute accuracy gain on a multimodal mathematical reasoning benchmark. Furthermore, employing ArXivCap, we devise four vision-to-text tasks for benchmarking LVLMs. Evaluation results with state-of-the-art LVLMs underscore their struggle with the nuanced semantics of academic figures, with domain-specific training yielding substantial performance gains. Our error analysis uncovers misinterpretations of visual context, recognition errors, and the production of overly simplified captions by current LVLMs, shedding light on future improvements.

The detection and extraction of abbreviations from unstructured texts can help to improve the performance of Natural Language Processing tasks, such as machine translation and information retrieval. However, in terms of publicly available datasets, there is not enough data for training deep-neural-networks-based models to the point of generalising well over data. This paper presents PLOD, a large-scale dataset for abbreviation detection and extraction that contains 160k+ segments automatically annotated with abbreviations and their long forms. We performed manual validation over a set of instances and a complete automatic validation for this dataset. We then used it to generate several baseline models for detecting abbreviations and long forms. The best models achieved an F1-score of 0.92 for abbreviations and 0.89 for detecting their corresponding long forms. We release this dataset along with our code and all the models publicly in https://github.com/surrey-nlp/PLOD-AbbreviationDetection

Large language models (LLMs) are increasingly being used for complex research tasks such as literature review, idea generation, and scientific paper analysis, yet their ability to truly understand and process the intricate relationships within complex research papers, such as the logical links between claims and supporting evidence remains largely unexplored. In this study, we present CLAIM-BENCH, a comprehensive benchmark for evaluating LLMs' capabilities in scientific claim-evidence extraction and validation, a task that reflects deeper comprehension of scientific argumentation. We systematically compare three approaches which are inspired by divide and conquer approaches, across six diverse LLMs, highlighting model-specific strengths and weaknesses in scientific comprehension. Through evaluation involving over 300 claim-evidence pairs across multiple research domains, we reveal significant limitations in LLMs' ability to process complex scientific content. Our results demonstrate that closed-source models like GPT-4 and Claude consistently outperform open-source counterparts in precision and recall across claim-evidence identification tasks. Furthermore, strategically designed three-pass and one-by-one prompting approaches significantly improve LLMs' abilities to accurately link dispersed evidence with claims, although this comes at increased computational cost. CLAIM-BENCH sets a new standard for evaluating scientific comprehension in LLMs, offering both a diagnostic tool and a path forward for building systems capable of deeper, more reliable reasoning across full-length papers.

The powerful reasoning capabilities of Large Language Models (LLMs) in mathematics and coding, combined with their ability to automate complex tasks through agentic frameworks, present unprecedented opportunities for accelerating scientific innovation. In this paper, we introduce AI-Researcher, a fully autonomous research system that transforms how AI-driven scientific discovery is conducted and evaluated. Our framework seamlessly orchestrates the complete research pipeline--from literature review and hypothesis generation to algorithm implementation and publication-ready manuscript preparation--with minimal human intervention. To rigorously assess autonomous research capabilities, we develop Scientist-Bench, a comprehensive benchmark comprising state-of-the-art papers across diverse AI research domains, featuring both guided innovation and open-ended exploration tasks. Through extensive experiments, we demonstrate that AI-Researcher achieves remarkable implementation success rates and produces research papers that approach human-level quality. This work establishes new foundations for autonomous scientific innovation that can complement human researchers by systematically exploring solution spaces beyond cognitive limitations.

Language Models [LMs] are now playing an increasingly large role in information generation and synthesis; the representation of scientific knowledge in these systems needs to be highly accurate. A prime challenge is hallucination; that is, generating apparently plausible but actually false information, including invented citations and nonexistent research papers. This kind of inaccuracy is dangerous in all the domains that require high levels of factual correctness, such as academia and education. This work presents a pipeline for evaluating the frequency with which language models hallucinate in generating responses in the scientific literature. We propose ArxEval, an evaluation pipeline with two tasks using ArXiv as a repository: Jumbled Titles and Mixed Titles. Our evaluation includes fifteen widely used language models and provides comparative insights into their reliability in handling scientific literature.

Knowledge graphs (KGs) are crucial in the field of artificial intelligence and are widely applied in downstream tasks, such as enhancing Question Answering (QA) systems. The construction of KGs typically requires significant effort from domain experts. Recently, Large Language Models (LLMs) have been used for knowledge graph construction (KGC), however, most existing approaches focus on a local perspective, extracting knowledge triplets from individual sentences or documents. In this work, we introduce Graphusion, a zero-shot KGC framework from free text. The core fusion module provides a global view of triplets, incorporating entity merging, conflict resolution, and novel triplet discovery. We showcase how Graphusion could be applied to the natural language processing (NLP) domain and validate it in the educational scenario. Specifically, we introduce TutorQA, a new expert-verified benchmark for graph reasoning and QA, comprising six tasks and a total of 1,200 QA pairs. Our evaluation demonstrates that Graphusion surpasses supervised baselines by up to 10% in accuracy on link prediction. Additionally, it achieves average scores of 2.92 and 2.37 out of 3 in human evaluations for concept entity extraction and relation recognition, respectively.

In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process. Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality. In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pre-training techniques. To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality. Moreover, we investigate how LLMs have been deployed to benefit scientific discovery. Resources related to this survey are available at https://github.com/yuzhimanhua/Awesome-Scientific-Language-Models.

In this paper, we champion the use of structured and semantic content representation of discourse-based scholarly communication, inspired by tools like Wikipedia infoboxes or structured Amazon product descriptions. These representations provide users with a concise overview, aiding scientists in navigating the dense academic landscape. Our novel automated approach leverages the robust text generation capabilities of LLMs to produce structured scholarly contribution summaries, offering both a practical solution and insights into LLMs' emergent abilities. For LLMs, the prime focus is on improving their general intelligence as conversational agents. We argue that these models can also be applied effectively in information extraction (IE), specifically in complex IE tasks within terse domains like Science. This paradigm shift replaces the traditional modular, pipelined machine learning approach with a simpler objective expressed through instructions. Our results show that finetuned FLAN-T5 with 1000x fewer parameters than the state-of-the-art GPT-davinci is competitive for the task.

We introduce DLSIA (Deep Learning for Scientific Image Analysis), a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing, or for experiment-in-the-loop computing scenarios. DLSIA features easy-to-use architectures such as autoencoders, tunable U-Nets, and parameter-lean mixed-scale dense networks (MSDNets). Additionally, we introduce sparse mixed-scale networks (SMSNets), generated using random graphs and sparse connections. As experimental data continues to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration, and advance research in scientific image analysis.

We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.

Existing benchmarks for evaluating foundation models mainly focus on single-document, text-only tasks. However, they often fail to fully capture the complexity of research workflows, which typically involve interpreting non-textual data and gathering information across multiple documents. To address this gap, we introduce M3SciQA, a multi-modal, multi-document scientific question answering benchmark designed for a more comprehensive evaluation of foundation models. M3SciQA consists of 1,452 expert-annotated questions spanning 70 natural language processing paper clusters, where each cluster represents a primary paper along with all its cited documents, mirroring the workflow of comprehending a single paper by requiring multi-modal and multi-document data. With M3SciQA, we conduct a comprehensive evaluation of 18 foundation models. Our results indicate that current foundation models still significantly underperform compared to human experts in multi-modal information retrieval and in reasoning across multiple scientific documents. Additionally, we explore the implications of these findings for the future advancement of applying foundation models in multi-modal scientific literature analysis.

In an era of exponential scientific growth, identifying novel research ideas is crucial and challenging in academia. Despite potential, the lack of an appropriate benchmark dataset hinders the research of novelty detection. More importantly, simply adopting existing NLP technologies, e.g., retrieving and then cross-checking, is not a one-size-fits-all solution due to the gap between textual similarity and idea conception. In this paper, we propose to harness large language models (LLMs) for scientific novelty detection (ND), associated with two new datasets in marketing and NLP domains. To construct the considerate datasets for ND, we propose to extract closure sets of papers based on their relationship, and then summarize their main ideas based on LLMs. To capture idea conception, we propose to train a lightweight retriever by distilling the idea-level knowledge from LLMs to align ideas with similar conception, enabling efficient and accurate idea retrieval for LLM novelty detection. Experiments show our method consistently outperforms others on the proposed benchmark datasets for idea retrieval and ND tasks. Codes and data are available at https://anonymous.4open.science/r/NoveltyDetection-10FB/.

Leading vision-language models (VLMs) are trained on general Internet content, overlooking scientific journals' rich, domain-specific knowledge. Training on specialty-specific literature could yield high-performance, task-specific tools, enabling generative AI to match generalist models in specialty publishing, educational, and clinical tasks. We created NeuroPubs, a multimodal dataset of 23,000 Neurosurgery Publications articles (134M words, 78K image-caption pairs). Using NeuroPubs, VLMs generated publication-ready graphical abstracts (70% of 100 abstracts) and board-style questions indistinguishable from human-written ones (54% of 89,587 questions). We used these questions to train CNS-Obsidian, a 34B-parameter VLM. In a blinded, randomized controlled trial, our model demonstrated non-inferiority to then state-of-the-art GPT-4o in neurosurgical differential diagnosis (clinical utility, 40.62% upvotes vs. 57.89%, p=0.1150; accuracy, 59.38% vs. 65.79%, p=0.3797). Our pilot study demonstrates how training generative AI models on specialty-specific journal content - without large-scale internet data - results in high-performance academic and clinical tools, enabling domain-tailored AI across diverse fields.

Large language models (LLMs) have ushered in a new era for processing complex information in various fields, including science. The increasing amount of scientific literature allows these models to acquire and understand scientific knowledge effectively, thus improving their performance in a wide range of tasks. Due to the power of LLMs, they require extremely expensive computational resources, intense amounts of data, and training time. Therefore, in recent years, researchers have proposed various methodologies to make scientific LLMs more affordable. The most well-known approaches align in two directions. It can be either focusing on the size of the models or enhancing the quality of data. To date, a comprehensive review of these two families of methods has not yet been undertaken. In this paper, we (I) summarize the current advances in the emerging abilities of LLMs into more accessible AI solutions for science, and (II) investigate the challenges and opportunities of developing affordable solutions for scientific domains using LLMs.

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

We present the MULTIMODAL UNIVERSE, a large-scale multimodal dataset of scientific astronomical data, compiled specifically to facilitate machine learning research. Overall, the MULTIMODAL UNIVERSE contains hundreds of millions of astronomical observations, constituting 100\,TB of multi-channel and hyper-spectral images, spectra, multivariate time series, as well as a wide variety of associated scientific measurements and "metadata". In addition, we include a range of benchmark tasks representative of standard practices for machine learning methods in astrophysics. This massive dataset will enable the development of large multi-modal models specifically targeted towards scientific applications. All codes used to compile the MULTIMODAL UNIVERSE and a description of how to access the data is available at https://github.com/MultimodalUniverse/MultimodalUniverse

The specialized language and complex concepts in physics pose significant challenges for information extraction through Natural Language Processing (NLP). Central to effective NLP applications is the text embedding model, which converts text into dense vector representations for efficient information retrieval and semantic analysis. In this work, we introduce PhysBERT, the first physics-specific text embedding model. Pre-trained on a curated corpus of 1.2 million arXiv physics papers and fine-tuned with supervised data, PhysBERT outperforms leading general-purpose models on physics-specific tasks including the effectiveness in fine-tuning for specific physics subdomains.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

Classification is a core NLP task architecture with many potential applications. While large language models (LLMs) have brought substantial advancements in text generation, their potential for enhancing classification tasks remains underexplored. To address this gap, we propose a framework for thoroughly investigating fine-tuning LLMs for classification, including both generation- and encoding-based approaches. We instantiate this framework in edit intent classification (EIC), a challenging and underexplored classification task. Our extensive experiments and systematic comparisons with various training approaches and a representative selection of LLMs yield new insights into their application for EIC. We investigate the generalizability of these findings on five further classification tasks. To demonstrate the proposed methods and address the data shortage for empirical edit analysis, we use our best-performing EIC model to create Re3-Sci2.0, a new large-scale dataset of 1,780 scientific document revisions with over 94k labeled edits. The quality of the dataset is assessed through human evaluation. The new dataset enables an in-depth empirical study of human editing behavior in academic writing. We make our experimental framework, models and data publicly available.

As the number of open and shared scientific datasets on the Internet increases under the open science movement, efficiently retrieving these datasets is a crucial task in information retrieval (IR) research. In recent years, the development of large models, particularly the pre-training and fine-tuning paradigm, which involves pre-training on large models and fine-tuning on downstream tasks, has provided new solutions for IR match tasks. In this study, we use the original BERT token in the embedding layer, improve the Sentence-BERT model structure in the model layer by introducing the SimCSE and K-Nearest Neighbors method, and use the cosent loss function in the optimization phase to optimize the target output. Our experimental results show that our model outperforms other competing models on both public and self-built datasets through comparative experiments and ablation implementations. This study explores and validates the feasibility and efficiency of pre-training techniques for semantic retrieval of Chinese scientific datasets.

Traditionally, theory and practice of Cognitive Control are linked via literature reviews by human domain experts. This approach, however, is inadequate to track the ever-growing literature. It may also be biased, and yield redundancies and confusion. Here we present an alternative approach. We performed automated text analyses on a large body of scientific texts to create a joint representation of tasks and constructs. More specifically, 385,705 scientific abstracts were first mapped into an embedding space using a transformers-based language model. Document embeddings were then used to identify a task-construct graph embedding that grounds constructs on tasks and supports nuanced meaning of the constructs by taking advantage of constrained random walks in the graph. This joint task-construct graph embedding, can be queried to generate task batteries targeting specific constructs, may reveal knowledge gaps in the literature, and inspire new tasks and novel hypotheses.

Large Language Models (LLMs) have extended their impact beyond Natural Language Processing, substantially fostering the development of interdisciplinary research. Recently, various LLM-based agents have been developed to assist scientific discovery progress across multiple aspects and domains. Among these, computer-using agents, capable of interacting with operating systems as humans do, are paving the way to automated scientific problem-solving and addressing routines in researchers' workflows. Recognizing the transformative potential of these agents, we introduce ScienceBoard, which encompasses two complementary contributions: (i) a realistic, multi-domain environment featuring dynamic and visually rich scientific workflows with integrated professional software, where agents can autonomously interact via different interfaces to accelerate complex research tasks and experiments; and (ii) a challenging benchmark of 169 high-quality, rigorously validated real-world tasks curated by humans, spanning scientific-discovery workflows in domains such as biochemistry, astronomy, and geoinformatics. Extensive evaluations of agents with state-of-the-art backbones (e.g., GPT-4o, Claude 3.7, UI-TARS) show that, despite some promising results, they still fall short of reliably assisting scientists in complex workflows, achieving only a 15% overall success rate. In-depth analysis further provides valuable insights for addressing current agent limitations and more effective design principles, paving the way to build more capable agents for scientific discovery. Our code, environment, and benchmark are at https://qiushisun.github.io/ScienceBoard-Home/.

Recent advances in Multi-Modal Large Language Models (MLLMs) have enabled unified processing of language, vision, and structured inputs, opening the door to complex tasks such as logical deduction, spatial reasoning, and scientific analysis. Despite their promise, the reasoning capabilities of MLLMs, particularly those augmented with intermediate thinking traces (MLLMs-T), remain poorly understood and lack standardized evaluation benchmarks. Existing work focuses primarily on perception or final answer correctness, offering limited insight into how models reason or fail across modalities. To address this gap, we introduce the MMMR, a new benchmark designed to rigorously evaluate multi-modal reasoning with explicit thinking. The MMMR comprises 1) a high-difficulty dataset of 1,083 questions spanning six diverse reasoning types with symbolic depth and multi-hop demands and 2) a modular Reasoning Trace Evaluation Pipeline (RTEP) for assessing reasoning quality beyond accuracy through metrics like relevance, consistency, and structured error annotations. Empirical results show that MLLMs-T overall outperform non-thinking counterparts, but even top models like Claude-3.7-Sonnet and Gemini-2.5 Pro suffer from reasoning pathologies such as inconsistency and overthinking. This benchmark reveals persistent gaps between accuracy and reasoning quality and provides an actionable evaluation pipeline for future model development. Overall, the MMMR offers a scalable foundation for evaluating, comparing, and improving the next generation of multi-modal reasoning systems.

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

High-quality machine learning (ML)-ready datasets play a foundational role in developing new artificial intelligence (AI) models or fine-tuning existing models for scientific applications such as weather and climate analysis. Unfortunately, despite the growing development of new deep learning models for weather and climate, there is a scarcity of curated, pre-processed machine learning (ML)-ready datasets. Curating such high-quality datasets for developing new models is challenging particularly because the modality of the input data varies significantly for different downstream tasks addressing different atmospheric scales (spatial and temporal). Here we introduce WxC-Bench (Weather and Climate Bench), a multi-modal dataset designed to support the development of generalizable AI models for downstream use-cases in weather and climate research. WxC-Bench is designed as a dataset of datasets for developing ML-models for a complex weather and climate system, addressing selected downstream tasks as machine learning phenomenon. WxC-Bench encompasses several atmospheric processes from meso-beta (20 - 200 km) scale to synoptic scales (2500 km), such as aviation turbulence, hurricane intensity and track monitoring, weather analog search, gravity wave parameterization, and natural language report generation. We provide a comprehensive description of the dataset and also present a technical validation for baseline analysis. The dataset and code to prepare the ML-ready data have been made publicly available on Hugging Face -- https://huggingface.co/datasets/nasa-impact/WxC-Bench

We describe the SemEval task of extracting keyphrases and relations between them from scientific documents, which is crucial for understanding which publications describe which processes, tasks and materials. Although this was a new task, we had a total of 26 submissions across 3 evaluation scenarios. We expect the task and the findings reported in this paper to be relevant for researchers working on understanding scientific content, as well as the broader knowledge base population and information extraction communities.

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

Recent advancements have seen Large Language Models (LLMs) and Large Multimodal Models (LMMs) surpassing general human capabilities in various tasks, approaching the proficiency level of human experts across multiple domains. With traditional benchmarks becoming less challenging for these models, new rigorous challenges are essential to gauge their advanced abilities. In this work, we present OlympiadBench, an Olympiad-level bilingual multimodal scientific benchmark, featuring 8,476 problems from Olympiad-level mathematics and physics competitions, including the Chinese college entrance exam. Each problem is detailed with expert-level annotations for step-by-step reasoning. Evaluating top-tier models on OlympiadBench, we implement a comprehensive assessment methodology to accurately evaluate model responses. Notably, the best-performing model, GPT-4V, attains an average score of 17.97% on OlympiadBench, with a mere 10.74% in physics, highlighting the benchmark rigor and the intricacy of physical reasoning. Our analysis orienting GPT-4V points out prevalent issues with hallucinations, knowledge omissions, and logical fallacies. We hope that our challenging benchmark can serve as a valuable resource for helping future AGI research endeavors. The data and evaluation code are available at https://github.com/OpenBMB/OlympiadBench

Recent large language models (LLMs) have advanced table understanding capabilities but rely on converting tables into text sequences. While multimodal large language models (MLLMs) enable direct visual processing, they face limitations in handling scientific tables due to fixed input image resolutions and insufficient numerical reasoning capabilities. We present a comprehensive framework for multimodal scientific table understanding and reasoning with dynamic input image resolutions. Our framework consists of three key components: (1) MMSci-Pre, a domain-specific table structure learning dataset of 52K scientific table structure recognition samples, (2) MMSci-Ins, an instruction tuning dataset with 12K samples across three table-based tasks, and (3) MMSci-Eval, a benchmark with 3,114 testing samples specifically designed to evaluate numerical reasoning capabilities. Extensive experiments demonstrate that our domain-specific approach with 52K scientific table images achieves superior performance compared to 150K general-domain tables, highlighting the importance of data quality over quantity. Our proposed table-based MLLMs with dynamic input resolutions show significant improvements in both general table understanding and numerical reasoning capabilities, with strong generalisation to held-out datasets. Our code and data are publicly available at https://github.com/Bernard-Yang/MMSci_Table.

The advent of next-generation radio telescopes is set to transform radio astronomy by producing massive data volumes that challenge traditional processing methods. Deep learning techniques have shown strong potential in automating radio analysis tasks, yet are often constrained by the limited availability of large annotated datasets. Recent progress in self-supervised learning has led to foundational radio vision models, but adapting them for new tasks typically requires coding expertise, limiting their accessibility to a broader astronomical community. Text-based AI interfaces offer a promising alternative by enabling task-specific queries and example-driven learning. In this context, Large Language Models (LLMs), with their remarkable zero-shot capabilities, are increasingly used in scientific domains. However, deploying large-scale models remains resource-intensive, and there is a growing demand for AI systems that can reason over both visual and textual data in astronomical analysis. This study explores small-scale Vision-Language Models (VLMs) as AI assistants for radio astronomy, combining LLM capabilities with vision transformers. We fine-tuned the LLaVA VLM on a dataset of 59k radio images from multiple surveys, enriched with 38k image-caption pairs from the literature. The fine-tuned models show clear improvements over base models in radio-specific tasks, achieving ~30% F1-score gains in extended source detection, but they underperform pure vision models and exhibit ~20% drop on general multimodal tasks. Inclusion of caption data and LoRA fine-tuning enhances instruction-following and helps recover ~10% accuracy on standard benchmarks. This work lays the foundation for future advancements in radio VLMs, highlighting their potential and limitations, such as the need for better multimodal alignment, higher-quality datasets, and mitigation of catastrophic forgetting.

The rapid advancement of scientific progress requires innovative tools that can accelerate discovery. While recent AI methods, particularly large language models (LLMs), have shown promise in tasks such as hypothesis generation and experimental design, they fall short in replicating the collaborative nature of real-world scientific practices, where diverse teams of experts work together to tackle complex problems. To address the limitation, we propose an LLM-based multi-agent system, i.e., Virtual Scientists (VirSci), designed to mimic the teamwork inherent in scientific research. VirSci organizes a team of agents to collaboratively generate, evaluate, and refine research ideas. Through comprehensive experiments, we demonstrate that this multi-agent approach outperforms the state-of-the-art method in producing novel and impactful scientific ideas, showing potential in aligning with key insights in the Science of Science field. Our findings suggest that integrating collaborative agents can lead to more innovative scientific outputs, offering a robust system for autonomous scientific discovery.

Recent neural language models have taken a significant step forward in producing remarkably controllable, fluent, and grammatical text. Although studies have found that AI-generated text is not distinguishable from human-written text for crowd-sourcing workers, there still exist errors in AI-generated text which are even subtler and harder to spot. We primarily focus on the scenario in which scientific AI writing assistant is deeply involved. First, we construct a feature description framework to distinguish between AI-generated text and human-written text from syntax, semantics, and pragmatics based on the human evaluation. Then we utilize the features, i.e., writing style, coherence, consistency, and argument logistics, from the proposed framework to analyze two types of content. Finally, we adopt several publicly available methods to investigate the gap of between AI-generated scientific text and human-written scientific text by AI-generated scientific text detection models. The results suggest that while AI has the potential to generate scientific content that is as accurate as human-written content, there is still a gap in terms of depth and overall quality. The AI-generated scientific content is more likely to contain errors in factual issues. We find that there exists a "writing style" gap between AI-generated scientific text and human-written scientific text. Based on the analysis result, we summarize a series of model-agnostic and distribution-agnostic features for detection tasks in other domains. Findings in this paper contribute to guiding the optimization of AI models to produce high-quality content and addressing related ethical and security concerns.

Multimodal scientific problems (MSPs) involve complex issues that require the integration of multiple modalities, such as text and diagrams, presenting a significant challenge in artificial intelligence. While progress has been made in addressing traditional scientific problems, MSPs still face two primary issues: the challenge of multi-modal comprehensive reasoning in scientific problem-solving and the lack of reflective and rethinking capabilities. To address these issues, we introduce a Multi-Agent framework based on the Big Seven Personality and Socratic guidance (MAPS). This framework employs seven distinct agents that leverage feedback mechanisms and the Socratic method to guide the resolution of MSPs. To tackle the first issue, we propose a progressive four-agent solving strategy, where each agent focuses on a specific stage of the problem-solving process. For the second issue, we introduce a Critic agent, inspired by Socratic questioning, which prompts critical thinking and stimulates autonomous learning. We conduct extensive experiments on the EMMA, Olympiad, and MathVista datasets, achieving promising results that outperform the current SOTA model by 15.84% across all tasks. Meanwhile, the additional analytical experiments also verify the model's progress as well as generalization ability.

Generative pre-trained transformer (GPT) models have revolutionized the field of natural language processing (NLP) with remarkable performance in various tasks and also extend their power to multimodal domains. Despite their success, large GPT models like GPT-4 face inherent limitations such as considerable size, high computational requirements, complex deployment processes, and closed development loops. These constraints restrict their widespread adoption and raise concerns regarding their responsible development and usage. The need for user-friendly, relatively small, and open-sourced alternative GPT models arises from the desire to overcome these limitations while retaining high performance. In this survey paper, we provide an examination of alternative open-sourced models of large GPTs, focusing on user-friendly and relatively small models that facilitate easier deployment and accessibility. Through this extensive survey, we aim to equip researchers, practitioners, and enthusiasts with a thorough understanding of user-friendly and relatively small open-sourced models of large GPTs, their current state, challenges, and future research directions, inspiring the development of more efficient, accessible, and versatile GPT models that cater to the broader scientific community and advance the field of general artificial intelligence. The source contents are continuously updating in https://github.com/GPT-Alternatives/gpt_alternatives.

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

We introduce Agentic Reasoning, a framework that enhances large language model (LLM) reasoning by integrating external tool-using agents. Unlike conventional LLM-based reasoning approaches, which rely solely on internal inference, Agentic Reasoning dynamically engages web search, code execution, and structured reasoning-context memory to solve complex problems requiring deep research and multi-step logical deduction. Our framework introduces the Mind Map agent, which constructs a structured knowledge graph to track logical relationships, improving deductive reasoning. Additionally, the integration of web-search and coding agents enables real-time retrieval and computational analysis, enhancing reasoning accuracy and decision-making. Evaluations on PhD-level scientific reasoning (GPQA) and domain-specific deep research tasks demonstrate that our approach significantly outperforms existing models, including leading retrieval-augmented generation (RAG) systems and closed-source LLMs. Moreover, our results indicate that agentic reasoning improves expert-level knowledge synthesis, test-time scalability, and structured problem-solving. The code is at: https://github.com/theworldofagents/Agentic-Reasoning.

Large Language Models (LLMs) exhibit strong general language capabilities. However, fine-tuning these models on domain-specific tasks often leads to catastrophic forgetting, where the model overwrites or loses essential knowledge acquired during pretraining. This phenomenon significantly limits the broader applicability of LLMs. To address this challenge, we propose a novel approach to compute the element-wise importance of model parameters crucial for preserving general knowledge during fine-tuning. Our method utilizes a dual-objective optimization strategy: (1) regularization loss based on element-wise parameter importance, which constrains the updates to parameters crucial for general knowledge; (2) cross-entropy loss to adapt to domain-specific tasks. Additionally, we introduce layer-wise coefficients to account for the varying contributions of different layers, dynamically balancing the dual-objective optimization. Extensive experiments on scientific, medical, and physical tasks using GPT-J and LLaMA-3 demonstrate that our approach mitigates catastrophic forgetting while enhancing model adaptability. Compared to previous methods, our solution is approximately 20 times faster and requires only 10-15% of the storage, highlighting the practical efficiency. The code will be released.

Rapid development of artificial intelligence has drastically accelerated the development of scientific discovery. Trained with large-scale observation data, deep neural networks extract the underlying patterns in an end-to-end manner and assist human researchers with highly-precised predictions in unseen scenarios. The recent rise of Large Language Models (LLMs) and the empowered autonomous agents enable scientists to gain help through interaction in different stages of their research, including but not limited to literature review, research ideation, idea implementation, and academic writing. However, AI researchers instantiated by foundation model empowered agents with full-process autonomy are still in their infancy. In this paper, we study AI-Generated Science (AIGS), where agents independently and autonomously complete the entire research process and discover scientific laws. By revisiting the definition of scientific research, we argue that falsification is the essence of both human research process and the design of an AIGS system. Through the lens of falsification, prior systems attempting towards AI-Generated Science either lack the part in their design, or rely heavily on existing verification engines that narrow the use in specialized domains. In this work, we propose Baby-AIGS as a baby-step demonstration of a full-process AIGS system, which is a multi-agent system with agents in roles representing key research process. By introducing FalsificationAgent, which identify and then verify possible scientific discoveries, we empower the system with explicit falsification. Experiments on three tasks preliminarily show that Baby-AIGS could produce meaningful scientific discoveries, though not on par with experienced human researchers. Finally, we discuss on the limitations of current Baby-AIGS, actionable insights, and related ethical issues in detail.

When language models (LMs) are trained to forget (or "unlearn'') a skill, how precisely does their behavior change? We study the behavior of transformer LMs in which tasks have been forgotten via fine-tuning on randomized labels. Such LMs learn to generate near-random predictions for individual examples in the "training'' set used for forgetting. Across tasks, however, LMs exhibit extreme variability in whether LM predictions change on examples outside the training set. In some tasks (like entailment classification), forgetting generalizes robustly, and causes models to produce uninformative predictions on new task instances; in other tasks (like physical commonsense reasoning and scientific question answering) forgetting affects only the training examples, and models continue to perform the "forgotten'' task accurately even for examples very similar to those that appeared in the training set. Dataset difficulty is not predictive of whether a behavior can be forgotten; instead, generalization in forgetting is (weakly) predicted by the confidence of LMs' initial task predictions and the variability of LM representations of training data, with low confidence and low variability both associated with greater generalization. Perhaps most surprisingly, random-label forgetting appears to be somewhat insensitive to the contents of the training set: for example, models trained on science questions with random labels continue to answer other science questions accurately, but begin to produce random labels on entailment classification tasks. Finally, we show that even generalizable forgetting is shallow: linear probes trained on LMs' representations can still perform tasks reliably after forgetting. Our results highlight the difficulty and unpredictability of performing targeted skill removal from models via fine-tuning.

Tracking entities in procedural language requires understanding the transformations arising from actions on entities as well as those entities' interactions. While self-attention-based pre-trained language encoders like GPT and BERT have been successfully applied across a range of natural language understanding tasks, their ability to handle the nuances of procedural texts is still untested. In this paper, we explore the use of pre-trained transformer networks for entity tracking tasks in procedural text. First, we test standard lightweight approaches for prediction with pre-trained transformers, and find that these approaches underperform even simple baselines. We show that much stronger results can be attained by restructuring the input to guide the transformer model to focus on a particular entity. Second, we assess the degree to which transformer networks capture the process dynamics, investigating such factors as merged entities and oblique entity references. On two different tasks, ingredient detection in recipes and QA over scientific processes, we achieve state-of-the-art results, but our models still largely attend to shallow context clues and do not form complex representations of intermediate entity or process state.

Humans often use visual aids, for example diagrams or sketches, when solving complex problems. Training multimodal models to do the same, known as Visual Chain of Thought (Visual CoT), is challenging due to: (1) poor off-the-shelf visual CoT performance, which hinders reinforcement learning, and (2) the lack of high-quality visual CoT training data. We introduce Zebra-CoT, a diverse large-scale dataset with 182,384 samples, containing logically coherent interleaved text-image reasoning traces. We focus on four categories of tasks where sketching or visual reasoning is especially natural, spanning scientific questions such as geometry, physics, and algorithms; 2D visual reasoning tasks like visual search and jigsaw puzzles; 3D reasoning tasks including 3D multi-hop inference, embodied and robot planning; visual logic problems and strategic games like chess. Fine-tuning the Anole-7B model on the Zebra-CoT training corpus results in an improvement of +12% in our test-set accuracy and yields up to +13% performance gain on standard VLM benchmark evaluations. Fine-tuning Bagel-7B yields a model that generates high-quality interleaved visual reasoning chains, underscoring Zebra-CoT's effectiveness for developing multimodal reasoning abilities. We open-source our dataset and models to support development and evaluation of visual CoT.

Recent advancements of large language models (LLMs) have led to claims of AI surpassing humans in natural language processing (NLP) tasks such as textual understanding and reasoning. This work investigates these assertions by introducing CAIMIRA, a novel framework rooted in item response theory (IRT) that enables quantitative assessment and comparison of problem-solving abilities of question-answering (QA) agents: humans and AI systems. Through analysis of over 300,000 responses from ~70 AI systems and 155 humans across thousands of quiz questions, CAIMIRA uncovers distinct proficiency patterns in knowledge domains and reasoning skills. Humans outperform AI systems in knowledge-grounded abductive and conceptual reasoning, while state-of-the-art LLMs like GPT-4 and LLaMA show superior performance on targeted information retrieval and fact-based reasoning, particularly when information gaps are well-defined and addressable through pattern matching or data retrieval. These findings highlight the need for future QA tasks to focus on questions that challenge not only higher-order reasoning and scientific thinking, but also demand nuanced linguistic interpretation and cross-contextual knowledge application, helping advance AI developments that better emulate or complement human cognitive abilities in real-world problem-solving.

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, we propose a gating strategy that uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations of adaptations are established to solve specific tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model (LLM) without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics and design. The impact of this work include access to readily expandable, adaptable and changeable models with strong domain knowledge and the capability to integrate across areas of knowledge. With the X-LoRA model featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, and protein mechanics we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, and adversarial agentic modeling including ontological knowledge graphs. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins, but also reasons over the results and correctly predicts likely mechanisms that explain distinct molecular behaviors.

The emergence of generative pre-trained models has facilitated the synthesis of high-quality text, but it has also posed challenges in identifying factual errors in the generated text. In particular: (1) A wider range of tasks now face an increasing risk of containing factual errors when handled by generative models. (2) Generated texts tend to be lengthy and lack a clearly defined granularity for individual facts. (3) There is a scarcity of explicit evidence available during the process of fact checking. With the above challenges in mind, in this paper, we propose FacTool, a task and domain agnostic framework for detecting factual errors of texts generated by large language models (e.g., ChatGPT). Experiments on four different tasks (knowledge-based QA, code generation, mathematical reasoning, and scientific literature review) show the efficacy of the proposed method. We release the code of FacTool associated with ChatGPT plugin interface at https://github.com/GAIR-NLP/factool .

Topic segmentation is important in understanding scientific documents since it can not only provide better readability but also facilitate downstream tasks such as information retrieval and question answering by creating appropriate sections or paragraphs. In the topic segmentation task, topic coherence is critical in predicting segmentation boundaries. Most of the existing models have tried to exploit as many contexts as possible to extract useful topic-related information. However, additional context does not always bring promising results, because the local context between sentences becomes incoherent despite more sentences being supplemented. To alleviate this issue, we propose siamese sentence embedding layers which process two input sentences independently to get appropriate amount of information without being hampered by excessive information. Also, we adopt multi-task learning techniques including Same Topic Prediction (STP), Topic Classification (TC) and Next Sentence Prediction (NSP). When these three classification layers are combined in a multi-task manner, they can make up for each other's limitations, improving performance in all three tasks. We experiment different combinations of the three layers and report how each layer affects other layers in the same combination as well as the overall segmentation performance. The model we proposed achieves the state-of-the-art result in the WikiSection dataset.

Representation learning is a critical ingredient for natural language processing systems. Recent Transformer language models like BERT learn powerful textual representations, but these models are targeted towards token- and sentence-level training objectives and do not leverage information on inter-document relatedness, which limits their document-level representation power. For applications on scientific documents, such as classification and recommendation, the embeddings power strong performance on end tasks. We propose SPECTER, a new method to generate document-level embedding of scientific documents based on pretraining a Transformer language model on a powerful signal of document-level relatedness: the citation graph. Unlike existing pretrained language models, SPECTER can be easily applied to downstream applications without task-specific fine-tuning. Additionally, to encourage further research on document-level models, we introduce SciDocs, a new evaluation benchmark consisting of seven document-level tasks ranging from citation prediction, to document classification and recommendation. We show that SPECTER outperforms a variety of competitive baselines on the benchmark.

Rapid advancements in large language models (LLMs) have the potential to assist in scientific progress. A critical capability toward this endeavor is the ability to reproduce existing work. To evaluate the ability of AI agents to reproduce results in an active research area, we introduce the Automated LLM Speedrunning Benchmark, leveraging the research community contributions on the NanoGPT speedrun, a competition to train a GPT-2 model in the shortest time. Each of the 19 speedrun tasks provides the agent with the previous records training script, optionally paired with one of three hint formats, ranging from pseudocode to paper-like descriptions of the new records improvements. Records execute quickly by design and speedrun improvements encompass diverse code-level changes, ranging from high-level algorithmic advancements to hardware-aware optimizations. These features make the benchmark both accessible and realistic for the frontier problem of improving LLM training. We find that recent reasoning LLMs combined with SoTA scaffolds struggle to reimplement already-known innovations in our benchmark, even when given detailed hints. Our benchmark thus provides a simple, non-saturated measure of an LLMs ability to automate scientific reproduction, a necessary (but not sufficient) skill for an autonomous research agent.

Puzzlehunts are a genre of complex, multi-step puzzles lacking well-defined problem definitions. In contrast to conventional reasoning benchmarks consisting of tasks with clear instructions, puzzlehunts require models to discover the underlying problem structure from multimodal evidence and iterative reasoning, mirroring real-world domains such as scientific discovery, exploratory data analysis, or investigative problem-solving. Despite recent progress in foundation models, their performance on such open-ended settings remains largely untested. In this paper, we introduce PuzzleWorld, a large-scale benchmark of 667 puzzlehunt-style problems designed to assess step-by-step, open-ended, and creative multimodal reasoning. Each puzzle is annotated with the final solution, detailed reasoning traces, and cognitive skill labels, enabling holistic benchmarking and fine-grained diagnostic analysis. Most state-of-the-art models achieve only 1-2% final answer accuracy, with the best model solving only 14% of puzzles and reaching 40% stepwise accuracy. To demonstrate the value of our reasoning annotations, we show that fine-tuning a small model on reasoning traces improves stepwise reasoning from 4% to 11%, while training on final answers alone degrades performance to near zero. Our error analysis reveals that current models exhibit myopic reasoning, are bottlenecked by the limitations of language-based inference, and lack sketching capabilities crucial for visual and spatial reasoning. We release PuzzleWorld at https://github.com/MIT-MI/PuzzleWorld to support future work on building more general, open-ended, and creative reasoning systems.

The emergence of groundbreaking large language models capable of performing complex reasoning tasks holds significant promise for addressing various scientific challenges, including those arising in complex clinical scenarios. To enable their safe and effective deployment in real-world healthcare settings, it is urgently necessary to benchmark the diagnostic capabilities of current models systematically. Given the limitations of existing medical benchmarks in evaluating advanced diagnostic reasoning, we present DiagnosisArena, a comprehensive and challenging benchmark designed to rigorously assess professional-level diagnostic competence. DiagnosisArena consists of 1,113 pairs of segmented patient cases and corresponding diagnoses, spanning 28 medical specialties, deriving from clinical case reports published in 10 top-tier medical journals. The benchmark is developed through a meticulous construction pipeline, involving multiple rounds of screening and review by both AI systems and human experts, with thorough checks conducted to prevent data leakage. Our study reveals that even the most advanced reasoning models, o3-mini, o1, and DeepSeek-R1, achieve only 45.82%, 31.09%, and 17.79% accuracy, respectively. This finding highlights a significant generalization bottleneck in current large language models when faced with clinical diagnostic reasoning challenges. Through DiagnosisArena, we aim to drive further advancements in AIs diagnostic reasoning capabilities, enabling more effective solutions for real-world clinical diagnostic challenges. We provide the benchmark and evaluation tools for further research and development https://github.com/SPIRAL-MED/DiagnosisArena.

Large ground-truth datasets and recent advances in deep learning techniques have been useful for layout detection. However, because of the restricted layout diversity of these datasets, training on them requires a sizable number of annotated instances, which is both expensive and time-consuming. As a result, differences between the source and target domains may significantly impact how well these models function. To solve this problem, domain adaptation approaches have been developed that use a small quantity of labeled data to adjust the model to the target domain. In this research, we introduced a synthetic document dataset called RanLayNet, enriched with automatically assigned labels denoting spatial positions, ranges, and types of layout elements. The primary aim of this endeavor is to develop a versatile dataset capable of training models with robustness and adaptability to diverse document formats. Through empirical experimentation, we demonstrate that a deep layout identification model trained on our dataset exhibits enhanced performance compared to a model trained solely on actual documents. Moreover, we conduct a comparative analysis by fine-tuning inference models using both PubLayNet and IIIT-AR-13K datasets on the Doclaynet dataset. Our findings emphasize that models enriched with our dataset are optimal for tasks such as achieving 0.398 and 0.588 mAP95 score in the scientific document domain for the TABLE class.

The success of neural language models (LMs) on many technological tasks has brought about their potential relevance as scientific theories of language despite some clear differences between LM training and child language acquisition. In this paper we argue that some of the most prominent benchmarks for evaluating the syntactic capacities of LMs may not be sufficiently rigorous. In particular, we show that the template-based benchmarks lack the structural diversity commonly found in the theoretical and psychological studies of language. When trained on small-scale data modeling child language acquisition, the LMs can be readily matched by simple baseline models. We advocate for the use of the readily available, carefully curated datasets that have been evaluated for gradient acceptability by large pools of native speakers and are designed to probe the structural basis of grammar specifically. On one such dataset, the LI-Adger dataset, LMs evaluate sentences in a way inconsistent with human language users. We conclude with suggestions for better connecting LMs with the empirical study of child language acquisition.

Recent studies have shown LLMs possess some ability to improve their responses when given external feedback. However, it remains unclear how effectively and thoroughly these models can incorporate extrinsic feedback. In an ideal scenario, if LLMs receive near-perfect and complete feedback, we would expect them to fully integrate the feedback and change their incorrect answers to correct ones. In this paper, we systematically investigate LLMs' ability to incorporate feedback by designing a controlled experimental environment. For each problem, a solver model attempts a solution, then a feedback generator with access to near-complete ground-truth answers produces targeted feedback, after which the solver tries again. We evaluate this pipeline across a diverse range of tasks, including math reasoning, knowledge reasoning, scientific reasoning, and general multi-domain evaluations with state-of-the-art language models including Claude 3.7 (with and without extended thinking). Surprisingly, even under these near-ideal conditions, solver models consistently show resistance to feedback, a limitation that we term FEEDBACK FRICTION. To mitigate this limitation, we experiment with sampling-based strategies like progressive temperature increases and explicit rejection of previously attempted incorrect answers, which yield improvements but still fail to help models achieve target performance. We also perform a rigorous exploration of potential causes of FEEDBACK FRICTION, ruling out factors such as model overconfidence and data familiarity. We hope that highlighting this issue in LLMs and ruling out several apparent causes will help future research in self-improvement.

Activity and property prediction models are the central workhorses in drug discovery and materials sciences, but currently they have to be trained or fine-tuned for new tasks. Without training or fine-tuning, scientific language models could be used for such low-data tasks through their announced zero- and few-shot capabilities. However, their predictive quality at activity prediction is lacking. In this work, we envision a novel type of activity prediction model that is able to adapt to new prediction tasks at inference time, via understanding textual information describing the task. To this end, we propose a new architecture with separate modules for chemical and natural language inputs, and a contrastive pre-training objective on data from large biochemical databases. In extensive experiments, we show that our method CLAMP yields improved predictive performance on few-shot learning benchmarks and zero-shot problems in drug discovery. We attribute the advances of our method to the modularized architecture and to our pre-training objective.

As black-box models increasingly power high-stakes applications, a variety of data-driven explanation methods have been introduced. Meanwhile, machine learning models are constantly challenged by distributional shifts. A question naturally arises: Are data-driven explanations robust against out-of-distribution data? Our empirical results show that even though predict correctly, the model might still yield unreliable explanations under distributional shifts. How to develop robust explanations against out-of-distribution data? To address this problem, we propose an end-to-end model-agnostic learning framework Distributionally Robust Explanations (DRE). The key idea is, inspired by self-supervised learning, to fully utilizes the inter-distribution information to provide supervisory signals for the learning of explanations without human annotation. Can robust explanations benefit the model's generalization capability? We conduct extensive experiments on a wide range of tasks and data types, including classification and regression on image and scientific tabular data. Our results demonstrate that the proposed method significantly improves the model's performance in terms of explanation and prediction robustness against distributional shifts.

Recent studies customizing Multimodal Large Language Models (MLLMs) for domain-specific tasks have yielded promising results, especially in the field of scientific chart comprehension. These studies generally utilize visual instruction tuning with specialized datasets to enhance question and answer (QA) accuracy within the chart domain. However, they often neglect the fundamental discrepancy between natural image-caption pre-training data and digital chart image-QA data, particularly in the models' capacity to extract underlying numeric values from charts. This paper tackles this oversight by exploring the training processes necessary to improve MLLMs' comprehension of charts. We present three key findings: (1) Incorporating raw data values in alignment pre-training markedly improves comprehension of chart data. (2) Replacing images with their textual representation randomly during end-to-end fine-tuning transfer the language reasoning capability to chart interpretation skills. (3) Requiring the model to first extract the underlying chart data and then answer the question in the fine-tuning can further improve the accuracy. Consequently, we introduce CHOPINLLM, an MLLM tailored for in-depth chart comprehension. CHOPINLLM effectively interprets various types of charts, including unannotated ones, while maintaining robust reasoning abilities. Furthermore, we establish a new benchmark to evaluate MLLMs' understanding of different chart types across various comprehension levels. Experimental results show that CHOPINLLM exhibits strong performance in understanding both annotated and unannotated charts across a wide range of types.

We propose a novel VQA dataset, based on picture stories designed for educating young children, that aims to facilitate comprehensive evaluation and characterization of vision-language models on comprehension tasks. Unlike current VQA datasets that often focus on fact-based memorization and simple reasoning tasks without principled scientific grounding, we collect data containing tasks reflecting different levels of comprehension and underlying cognitive processes, as laid out in Bloom's Taxonomy, a classic framework widely adopted in education research. The proposed BloomVQA dataset can be mapped to a hierarchical graph-based representation of visual stories, enabling automatic data augmentation and novel measures characterizing model consistency across the underlying taxonomy. We demonstrate graded evaluation and reliability analysis based on our proposed consistency metrics on state-of-the-art vision-language models. Our results suggest that, while current models achieve the most gain on low-level comprehension tasks, they generally fall short on high-level tasks requiring more advanced comprehension and cognitive skills, as 38.0% drop in VQA accuracy is observed comparing lowest and highest level tasks. Furthermore, current models show consistency patterns misaligned with human comprehension in various scenarios, suggesting emergent structures of model behaviors.

The scientific research paradigm is undergoing a profound transformation owing to the development of Artificial Intelligence (AI). Recent works demonstrate that various AI-assisted research methods can largely improve research efficiency by improving data analysis, accelerating computation, and fostering novel idea generation. To further move towards the ultimate goal (i.e., automatic scientific research), in this paper, we propose Dolphin, the first closed-loop open-ended auto-research framework to further build the entire process of human scientific research. Dolphin can generate research ideas, perform experiments, and get feedback from experimental results to generate higher-quality ideas. More specifically, Dolphin first generates novel ideas based on relevant papers which are ranked by the topic and task attributes. Then, the codes are automatically generated and debugged with the exception-traceback-guided local code structure. Finally, Dolphin automatically analyzes the results of each idea and feeds the results back to the next round of idea generation. Experiments are conducted on the benchmark datasets of different topics and results show that Dolphin can generate novel ideas continuously and complete the experiment in a loop. We highlight that Dolphin can automatically propose methods that are comparable to the state-of-the-art in some tasks such as 2D image classification and 3D point classification.

Artificial intelligence is gradually demonstrating its immense potential, and increasing attention is being given to how AI can be harnessed to advance scientific research. In this vision paper, we present our perspectives on how AI can better assist scientific inquiry and explore corresponding technical approach. We have proposed and open-sourced a large model of our KALE-LM model series, Llama3-KALE-LM-Chem-8B, which has achieved outstanding performance in tasks related to the field of chemistry. We hope that our work serves as a strong starting point, helping to realize more intelligent AI and promoting the advancement of human science and technology, as well as societal development.

The reasoning steps generated by LLMs might be incomplete, as they mimic logical leaps common in everyday communication found in their pre-training data: underlying rationales are frequently left implicit (unstated). To address this challenge, we introduce RATIONALYST, a model for process-supervision of reasoning based on pre-training on a vast collection of rationale annotations extracted from unlabeled data. We extract 79k rationales from web-scale unlabelled dataset (the Pile) and a combination of reasoning datasets with minimal human intervention. This web-scale pre-training for reasoning allows RATIONALYST to consistently generalize across diverse reasoning tasks, including mathematical, commonsense, scientific, and logical reasoning. Fine-tuned from LLaMa-3-8B, RATIONALYST improves the accuracy of reasoning by an average of 3.9% on 7 representative reasoning benchmarks. It also demonstrates superior performance compared to significantly larger verifiers like GPT-4 and similarly sized models fine-tuned on matching training sets.

Chart understanding plays a pivotal role when applying Multimodal Large Language Models (MLLMs) to real-world tasks such as analyzing scientific papers or financial reports. However, existing datasets often focus on oversimplified and homogeneous charts with template-based questions, leading to an over-optimistic measure of progress. We demonstrate that although open-source models can appear to outperform strong proprietary models on these benchmarks, a simple stress test with slightly different charts or questions can deteriorate performance by up to 34.5%. In this work, we propose CharXiv, a comprehensive evaluation suite involving 2,323 natural, challenging, and diverse charts from arXiv papers. CharXiv includes two types of questions: 1) descriptive questions about examining basic chart elements and 2) reasoning questions that require synthesizing information across complex visual elements in the chart. To ensure quality, all charts and questions are handpicked, curated, and verified by human experts. Our results reveal a substantial, previously underestimated gap between the reasoning skills of the strongest proprietary model (i.e., GPT-4o), which achieves 47.1% accuracy, and the strongest open-source model (i.e., InternVL Chat V1.5), which achieves 29.2%. All models lag far behind human performance of 80.5%, underscoring weaknesses in the chart understanding capabilities of existing MLLMs. We hope CharXiv facilitates future research on MLLM chart understanding by providing a more realistic and faithful measure of progress. Project page and leaderboard: https://charxiv.github.io/

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

Ensuring safe and effective use of AI requires understanding and anticipating its performance on novel tasks, from advanced scientific challenges to transformed workplace activities. So far, benchmarking has guided progress in AI, but it has offered limited explanatory and predictive power for general-purpose AI systems, given the low transferability across diverse tasks. In this paper, we introduce general scales for AI evaluation that can explain what common AI benchmarks really measure, extract ability profiles of AI systems, and predict their performance for new task instances, in- and out-of-distribution. Our fully-automated methodology builds on 18 newly-crafted rubrics that place instance demands on general scales that do not saturate. Illustrated for 15 large language models and 63 tasks, high explanatory power is unleashed from inspecting the demand and ability profiles, bringing insights on the sensitivity and specificity exhibited by different benchmarks, and how knowledge, metacognition and reasoning are affected by model size, chain-of-thought and distillation. Surprisingly, high predictive power at the instance level becomes possible using these demand levels, providing superior estimates over black-box baseline predictors based on embeddings or finetuning, especially in out-of-distribution settings (new tasks and new benchmarks). The scales, rubrics, battery, techniques and results presented here represent a major step for AI evaluation, underpinning the reliable deployment of AI in the years ahead. (Collaborative platform: https://kinds-of-intelligence-cfi.github.io/ADELE.)

Flowcharts are graphical tools for representing complex concepts in concise visual representations. This paper introduces the FlowLearn dataset, a resource tailored to enhance the understanding of flowcharts. FlowLearn contains complex scientific flowcharts and simulated flowcharts. The scientific subset contains 3,858 flowcharts sourced from scientific literature and the simulated subset contains 10,000 flowcharts created using a customizable script. The dataset is enriched with annotations for visual components, OCR, Mermaid code representation, and VQA question-answer pairs. Despite the proven capabilities of Large Vision-Language Models (LVLMs) in various visual understanding tasks, their effectiveness in decoding flowcharts - a crucial element of scientific communication - has yet to be thoroughly investigated. The FlowLearn test set is crafted to assess the performance of LVLMs in flowchart comprehension. Our study thoroughly evaluates state-of-the-art LVLMs, identifying existing limitations and establishing a foundation for future enhancements in this relatively underexplored domain. For instance, in tasks involving simulated flowcharts, GPT-4V achieved the highest accuracy (58%) in counting the number of nodes, while Claude recorded the highest accuracy (83%) in OCR tasks. Notably, no single model excels in all tasks within the FlowLearn framework, highlighting significant opportunities for further development.

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

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

The rapid evolution of scientific fields introduces challenges in organizing and retrieving scientific literature. While expert-curated taxonomies have traditionally addressed this need, the process is time-consuming and expensive. Furthermore, recent automatic taxonomy construction methods either (1) over-rely on a specific corpus, sacrificing generalizability, or (2) depend heavily on the general knowledge of large language models (LLMs) contained within their pre-training datasets, often overlooking the dynamic nature of evolving scientific domains. Additionally, these approaches fail to account for the multi-faceted nature of scientific literature, where a single research paper may contribute to multiple dimensions (e.g., methodology, new tasks, evaluation metrics, benchmarks). To address these gaps, we propose TaxoAdapt, a framework that dynamically adapts an LLM-generated taxonomy to a given corpus across multiple dimensions. TaxoAdapt performs iterative hierarchical classification, expanding both the taxonomy width and depth based on corpus' topical distribution. We demonstrate its state-of-the-art performance across a diverse set of computer science conferences over the years to showcase its ability to structure and capture the evolution of scientific fields. As a multidimensional method, TaxoAdapt generates taxonomies that are 26.51% more granularity-preserving and 50.41% more coherent than the most competitive baselines judged by LLMs.

LLM-based Multi-Agent Systems have demonstrated remarkable capabilities in addressing complex, agentic tasks, from generating high-quality presentation slides to even conducting sophisticated scientific research. Meanwhile, RL has been widely recognized for its effectiveness in enhancing agent intelligence, but limited research has investigated the fine-tuning of LaMAS using foundational RL techniques. Moreover, the direct application of MARL methods to LaMAS introduces significant challenges, stemming from the unique characteristics and mechanisms inherent to LaMAS. To address these challenges, this article presents a comprehensive study of LLM-based MARL and proposes a novel paradigm termed Multi-Agent Reinforcement Fine-Tuning (MARFT). We introduce a brand-new POMDP called Flex-POMDP, which aligns with the LaMAS optimization in real-world applications and a universal algorithmic framework tailored specifically for LaMAS, outlining the conceptual foundations, key distinctions, and practical implementation strategies. We review the evolution from RL to RFT, setting the stage for a parallel analysis in the multi-agent domain. In the context of LaMAS, we elucidate critical differences between MARL and MARFT. These differences motivate a transition toward a LaMAS-oriented formulation of RFT. Central to this work is a robust and scalable MARFT framework. We detail the core algorithm and provide a complete, open-source implementation to facilitate adoption and further research. The latter sections of the paper explore real-world application perspectives and opening challenges in MARFT. By bridging theoretical underpinnings with practical methodologies, this work serves as a roadmap for researchers seeking to advance MARFT toward resilient and adaptive solutions in agentic systems. Our implementation of the proposed framework is publicly available at: https://github.com/jwliao-ai/MARFT.

We introduce "pointer-guided segment ordering" (SO), a novel pre-training technique aimed at enhancing the contextual understanding of paragraph-level text representations in large language models. Our methodology leverages a self-attention-driven pointer network to restore the original sequence of shuffled text segments, addressing the challenge of capturing the structural coherence and contextual dependencies within documents. This pre-training approach is complemented by a fine-tuning methodology that incorporates dynamic sampling, augmenting the diversity of training instances and improving sample efficiency for various downstream applications. We evaluate our method on a diverse set of datasets, demonstrating its efficacy in tasks requiring sequential text classification across scientific literature and financial reporting domains. Our experiments show that pointer-guided pre-training significantly enhances the model's ability to understand complex document structures, leading to state-of-the-art performance in downstream classification tasks.

Recent LLM-driven visual agents mainly focus on solving image-based tasks, which limits their ability to understand dynamic scenes, making it far from real-life applications like guiding students in laboratory experiments and identifying their mistakes. Considering the video modality better reflects the ever-changing nature of real-world scenarios, we devise DoraemonGPT, a comprehensive and conceptually elegant system driven by LLMs to handle dynamic video tasks. Given a video with a question/task, DoraemonGPT begins by converting the input video into a symbolic memory that stores task-related attributes. This structured representation allows for spatial-temporal querying and reasoning by well-designed sub-task tools, resulting in concise intermediate results. Recognizing that LLMs have limited internal knowledge when it comes to specialized domains (e.g., analyzing the scientific principles underlying experiments), we incorporate plug-and-play tools to assess external knowledge and address tasks across different domains. Moreover, a novel LLM-driven planner based on Monte Carlo Tree Search is introduced to explore the large planning space for scheduling various tools. The planner iteratively finds feasible solutions by backpropagating the result's reward, and multiple solutions can be summarized into an improved final answer. We extensively evaluate DoraemonGPT's effectiveness on three benchmarks and challenging in-the-wild scenarios. Code will be released at: https://github.com/z-x-yang/DoraemonGPT.

With the recent advances in natural language processing (NLP), a vast number of applications have emerged across various use cases. Among the plethora of NLP applications, many academic researchers are motivated to do work that has a positive social impact, in line with the recent initiatives of NLP for Social Good (NLP4SG). However, it is not always obvious to researchers how their research efforts are tackling today's big social problems. Thus, in this paper, we introduce NLP4SGPAPERS, a scientific dataset with three associated tasks that can help identify NLP4SG papers and characterize the NLP4SG landscape by: (1) identifying the papers that address a social problem, (2) mapping them to the corresponding UN Sustainable Development Goals (SDGs), and (3) identifying the task they are solving and the methods they are using. Using state-of-the-art NLP models, we address each of these tasks and use them on the entire ACL Anthology, resulting in a visualization workspace that gives researchers a comprehensive overview of the field of NLP4SG. Our website is available at https://nlp4sg.vercel.app . We released our data at https://huggingface.co/datasets/feradauto/NLP4SGPapers and code at https://github.com/feradauto/nlp4sg .

Reasoning is a fundamental capability of Large Language Models. While prior research predominantly focuses on enhancing narrow skills like math or code generation, improving performance on many other reasoning tasks remains challenging due to sparse and fragmented training data. To address this issue, we propose CodeI/O, a novel approach that systematically condenses diverse reasoning patterns inherently embedded in contextually-grounded codes, through transforming the original code into a code input-output prediction format. By training models to predict inputs/outputs given code and test cases entirely in natural language as Chain-of-Thought (CoT) rationales, we expose them to universal reasoning primitives -- like logic flow planning, state-space searching, decision tree traversal, and modular decomposition -- while decoupling structured reasoning from code-specific syntax and preserving procedural rigor. Experimental results demonstrate CodeI/O leads to consistent improvements across symbolic, scientific, logic, math & numerical, and commonsense reasoning tasks. By matching the existing ground-truth outputs or re-executing the code with predicted inputs, we can verify each prediction and further enhance the CoTs through multi-turn revision, resulting in CodeI/O++ and achieving higher performance. Our data and models are available at https://github.com/hkust-nlp/CodeIO.

Intelligent Transportation Systems (ITS) allow a drastic expansion of the visibility range and decrease occlusions for autonomous driving. To obtain accurate detections, detailed labeled sensor data for training is required. Unfortunately, high-quality 3D labels of LiDAR point clouds from the infrastructure perspective of an intersection are still rare. Therefore, we provide the A9 Intersection Dataset, which consists of labeled LiDAR point clouds and synchronized camera images. Here, we recorded the sensor output from two roadside cameras and LiDARs mounted on intersection gantry bridges. The point clouds were labeled in 3D by experienced annotators. Furthermore, we provide calibration data between all sensors, which allow the projection of the 3D labels into the camera images and an accurate data fusion. Our dataset consists of 4.8k images and point clouds with more than 57.4k manually labeled 3D boxes. With ten object classes, it has a high diversity of road users in complex driving maneuvers, such as left and right turns, overtaking, and U-turns. In experiments, we provided multiple baselines for the perception tasks. Overall, our dataset is a valuable contribution to the scientific community to perform complex 3D camera-LiDAR roadside perception tasks. Find data, code, and more information at https://a9-dataset.com.

Large language models (LLMs) for code have become indispensable in various domains, including code generation, reasoning tasks and agent systems.While open-access code LLMs are increasingly approaching the performance levels of proprietary models, high-quality code LLMs suitable for rigorous scientific investigation, particularly those with reproducible data processing pipelines and transparent training protocols, remain limited. The scarcity is due to various challenges, including resource constraints, ethical considerations, and the competitive advantages of keeping models advanced. To address the gap, we introduce OpenCoder, a top-tier code LLM that not only achieves performance comparable to leading models but also serves as an ``open cookbook'' for the research community. Unlike most prior efforts, we release not only model weights and inference code, but also the reproducible training data, complete data processing pipeline, rigorous experimental ablation results, and detailed training protocols for open scientific research. Through this comprehensive release, we identify the key ingredients for building a top-tier code LLM: (1) code optimized heuristic rules for data cleaning and methods for data deduplication, (2) recall of text corpus related to code and (3) high-quality synthetic data in both annealing and supervised fine-tuning stages. By offering this level of openness, we aim to broaden access to all aspects of a top-tier code LLM, with OpenCoder serving as both a powerful model and an open foundation to accelerate research, and enable reproducible advancements in code AI.

Math reasoning has become the poster child of progress in large language models (LLMs), with new models rapidly surpassing human-level performance on benchmarks like MATH and AIME. But as math leaderboards improve week by week, it is worth asking: do these gains reflect broader problem-solving ability or just narrow overfitting? To answer this question, we evaluate over 20 open-weight reasoning-tuned models across a broad suite of tasks, including math, scientific QA, agent planning, coding, and standard instruction-following. We surprisingly find that most models that succeed in math fail to transfer their gains to other domains. To rigorously study this phenomenon, we conduct controlled experiments on Qwen3-14B models using math-only data but different tuning methods. We find that reinforcement learning (RL)-tuned models generalize well across domains, while supervised fine-tuning (SFT)-tuned models often forget general capabilities. Latent-space representation and token-space distribution shift analyses reveal that SFT induces substantial representation and output drift, while RL preserves general-domain structure. Our results suggest a need to rethink standard post-training recipes, particularly the reliance on SFT-distilled data for advancing reasoning models.

Large language models (LLMs) have demonstrated remarkable capabilities in code-related tasks, such as code understanding and code generation. However, an equally important yet underexplored question is whether LLMs can serve as general-purpose surrogate code executors, to predict the output and behavior of a program without actually running it. To systematically investigate this capability, we introduce SURGE, a comprehensive benchmark covering eight key aspects: multi-language programming tasks, competition-level programming problems, repository-level code analysis, high-cost scientific computing, time-complexity-intensive algorithms, buggy code analysis, programs dependent on specific compilers or execution environments, and formal mathematical proof verification. We evaluate multiple open-source and proprietary LLMs on SURGE and conduct a scaling study to analyze the impact of model size and training data scale on surrogate execution accuracy. Additionally, we categorize model prediction errors and explore potential areas for improvement. Our findings indicate that while LLMs can predict code execution results in certain cases, they exhibit limitations in general-purpose surrogate execution. This study provides empirical insights into the feasibility of using LLMs as surrogate code executors. Code and dataset are released at https://github.com/Imbernoulli/SURGE.

Humanoid robots hold significant potential in accomplishing daily tasks across diverse environments thanks to their flexibility and human-like morphology. Recent works have made significant progress in humanoid whole-body control and loco-manipulation leveraging optimal control or reinforcement learning. However, these methods require tedious task-specific tuning for each task to achieve satisfactory behaviors, limiting their versatility and scalability to diverse tasks in daily scenarios. To that end, we introduce SkillBlender, a novel hierarchical reinforcement learning framework for versatile humanoid loco-manipulation. SkillBlender first pretrains goal-conditioned task-agnostic primitive skills, and then dynamically blends these skills to accomplish complex loco-manipulation tasks with minimal task-specific reward engineering. We also introduce SkillBench, a parallel, cross-embodiment, and diverse simulated benchmark containing three embodiments, four primitive skills, and eight challenging loco-manipulation tasks, accompanied by a set of scientific evaluation metrics balancing accuracy and feasibility. Extensive simulated experiments show that our method significantly outperforms all baselines, while naturally regularizing behaviors to avoid reward hacking, resulting in more accurate and feasible movements for diverse loco-manipulation tasks in our daily scenarios. Our code and benchmark will be open-sourced to the community to facilitate future research. Project page: https://usc-gvl.github.io/SkillBlender-web/.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

We investigate an emerging setup in which a small, on-device language model (LM) with access to local data communicates with a frontier, cloud-hosted LM to solve real-world tasks involving financial, medical, and scientific reasoning over long documents. Can a local-remote collaboration reduce cloud inference costs while preserving quality? First, we consider a naive collaboration protocol where the local and remote models simply chat back and forth. Because only the local model reads the full context, this protocol achieves a 30.4x reduction in remote costs, but recovers only 87% of the performance of the frontier model. We identify two key limitations of this protocol: the local model struggles to (1) follow the remote model's multi-step instructions and (2) reason over long contexts. Motivated by these observations, we study an extension of this protocol, coined MinionS, in which the remote model decomposes the task into easier subtasks over shorter chunks of the document, that are executed locally in parallel. MinionS reduces costs by 5.7x on average while recovering 97.9% of the performance of the remote model alone. Our analysis reveals several key design choices that influence the trade-off between cost and performance in local-remote systems.

Identifying subtle technical errors within complex scientific and technical documents, especially those requiring multimodal interpretation (e.g., formulas in images), presents a significant hurdle for Large Language Models (LLMs) whose inherent error-correction tendencies can mask inaccuracies. This exploratory proof-of-concept (PoC) study investigates structured LLM context conditioning, informed by Persistent Workflow Prompting (PWP) principles, as a methodological strategy to modulate this LLM behavior at inference time. The approach is designed to enhance the reliability of readily available, general-purpose LLMs (specifically Gemini 2.5 Pro and ChatGPT Plus o3) for precise validation tasks, crucially relying only on their standard chat interfaces without API access or model modifications. To explore this methodology, we focused on validating chemical formulas within a single, complex test paper with known textual and image-based errors. Several prompting strategies were evaluated: while basic prompts proved unreliable, an approach adapting PWP structures to rigorously condition the LLM's analytical mindset appeared to improve textual error identification with both models. Notably, this method also guided Gemini 2.5 Pro to repeatedly identify a subtle image-based formula error previously overlooked during manual review, a task where ChatGPT Plus o3 failed in our tests. These preliminary findings highlight specific LLM operational modes that impede detail-oriented validation and suggest that PWP-informed context conditioning offers a promising and highly accessible technique for developing more robust LLM-driven analytical workflows, particularly for tasks requiring meticulous error detection in scientific and technical documents. Extensive validation beyond this limited PoC is necessary to ascertain broader applicability.

Recent works successfully leveraged Large Language Models' (LLM) abilities to capture abstract knowledge about world's physics to solve decision-making problems. Yet, the alignment between LLMs' knowledge and the environment can be wrong and limit functional competence due to lack of grounding. In this paper, we study an approach (named GLAM) to achieve this alignment through functional grounding: we consider an agent using an LLM as a policy that is progressively updated as the agent interacts with the environment, leveraging online Reinforcement Learning to improve its performance to solve goals. Using an interactive textual environment designed to study higher-level forms of functional grounding, and a set of spatial and navigation tasks, we study several scientific questions: 1) Can LLMs boost sample efficiency for online learning of various RL tasks? 2) How can it boost different forms of generalization? 3) What is the impact of online learning? We study these questions by functionally grounding several variants (size, architecture) of FLAN-T5.

This paper introduces a method for adapting LoRA adapters in smaller-sized language models to arbitrary downstream tasks. Unlike standard mixture-of-expert architectures, our method employs a gradient-free routing function to choose a weighted combination of experts without increasing the compute requirements for training or inference. The results show that token-level adaptation of LoRA adapters outperforms the base Llama-2-7b model across mathematical (GSM8K), scientific (ARC-Challenge), reading comprehension (SQuAD), and coding (CodeAlpaca-20k) tasks. Further evaluations also show that the average performance of token-level adaptation outperforms individual models fine-tuned for each of the tasks with the best performance observed in adaptation of every-other token during inference. The code for this study is made available through a public repository.

Traditional foundation models are pre-trained on broad datasets to reduce the training resources (e.g., time, energy, labeled samples) needed for fine-tuning a wide range of downstream tasks. However, traditional foundation models struggle with out-of-distribution prediction and can produce outputs that are unrealistic and physically infeasible. We propose the notation of physics-guided foundation models (PGFM), that is, foundation models integrated with broad or general domain (e.g., scientific) physical knowledge applicable to a wide range of downstream tasks.

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.

Artificial intelligence is transforming computational materials science, improving the prediction of material properties, and accelerating the discovery of novel materials. Recently, publicly available material data repositories have grown rapidly. This growth encompasses not only more materials, but also a greater variety and quantity of their associated properties. Existing machine learning efforts in materials science focus primarily on single-modality tasks, i.e., relationships between materials and a single physical property, thus not taking advantage of the rich and multimodal set of material properties. Here, we introduce Multimodal Learning for Materials (MultiMat), which enables self-supervised multi-modality training of foundation models for materials. We demonstrate our framework's potential using data from the Materials Project database on multiple axes: (i) MultiMat achieves state-of-the-art performance for challenging material property prediction tasks; (ii) MultiMat enables novel and accurate material discovery via latent space similarity, enabling screening for stable materials with desired properties; and (iii) MultiMat encodes interpretable emergent features that may provide novel scientific insights.

It remains an open question whether incorporating external knowledge benefits commonsense reasoning while maintaining the flexibility of pretrained sequence models. To investigate this question, we develop generated knowledge prompting, which consists of generating knowledge from a language model, then providing the knowledge as additional input when answering a question. Our method does not require task-specific supervision for knowledge integration, or access to a structured knowledge base, yet it improves performance of large-scale, state-of-the-art models on four commonsense reasoning tasks, achieving state-of-the-art results on numerical commonsense (NumerSense), general commonsense (CommonsenseQA 2.0), and scientific commonsense (QASC) benchmarks. Generated knowledge prompting highlights large-scale language models as flexible sources of external knowledge for improving commonsense reasoning. Our code is available at https://github.com/liujch1998/GKP

Scientific communication is receiving increasing attention in natural language processing, especially to help researches access, summarize, and generate content. One emerging application in this area is Speech-to-Abstract Generation (SAG), which aims to automatically generate abstracts from recorded scientific presentations. SAG enables researchers to efficiently engage with conference talks, but progress has been limited by a lack of large-scale datasets. To address this gap, we introduce NUTSHELL, a novel multimodal dataset of *ACL conference talks paired with their corresponding abstracts. We establish strong baselines for SAG and evaluate the quality of generated abstracts using both automatic metrics and human judgments. Our results highlight the challenges of SAG and demonstrate the benefits of training on NUTSHELL. By releasing NUTSHELL under an open license (CC-BY 4.0), we aim to advance research in SAG and foster the development of improved models and evaluation methods.

Science journalism refers to the task of reporting technical findings of a scientific paper as a less technical news article to the general public audience. We aim to design an automated system to support this real-world task (i.e., automatic science journalism) by 1) introducing a newly-constructed and real-world dataset (SciTechNews), with tuples of a publicly-available scientific paper, its corresponding news article, and an expert-written short summary snippet; 2) proposing a novel technical framework that integrates a paper's discourse structure with its metadata to guide generation; and, 3) demonstrating with extensive automatic and human experiments that our framework outperforms other baseline methods (e.g. Alpaca and ChatGPT) in elaborating a content plan meaningful for the target audience, simplifying the information selected, and producing a coherent final report in a layman's style.

One long-term goal of machine learning research is to produce methods that are applicable to reasoning and natural language, in particular building an intelligent dialogue agent. To measure progress towards that goal, we argue for the usefulness of a set of proxy tasks that evaluate reading comprehension via question answering. Our tasks measure understanding in several ways: whether a system is able to answer questions via chaining facts, simple induction, deduction and many more. The tasks are designed to be prerequisites for any system that aims to be capable of conversing with a human. We believe many existing learning systems can currently not solve them, and hence our aim is to classify these tasks into skill sets, so that researchers can identify (and then rectify) the failings of their systems. We also extend and improve the recently introduced Memory Networks model, and show it is able to solve some, but not all, of the tasks.

The principal goal of the TREC Neural Cross-Language Information Retrieval (NeuCLIR) track is to study the impact of neural approaches to cross-language information retrieval. The track has created four collections, large collections of Chinese, Persian, and Russian newswire and a smaller collection of Chinese scientific abstracts. The principal tasks are ranked retrieval of news in one of the three languages, using English topics. Results for a multilingual task, also with English topics but with documents from all three newswire collections, are also reported. New in this second year of the track is a pilot technical documents CLIR task for ranked retrieval of Chinese technical documents using English topics. A total of 220 runs across all tasks were submitted by six participating teams and, as baselines, by track coordinators. Task descriptions and results are presented.

We introduce Dynatask: an open source system for setting up custom NLP tasks that aims to greatly lower the technical knowledge and effort required for hosting and evaluating state-of-the-art NLP models, as well as for conducting model in the loop data collection with crowdworkers. Dynatask is integrated with Dynabench, a research platform for rethinking benchmarking in AI that facilitates human and model in the loop data collection and evaluation. To create a task, users only need to write a short task configuration file from which the relevant web interfaces and model hosting infrastructure are automatically generated. The system is available at https://dynabench.org/ and the full library can be found at https://github.com/facebookresearch/dynabench.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Scientific reasoning poses an excessive challenge for even the most advanced Large Language Models (LLMs). To make this task more practical and solvable for LLMs, we introduce a new task setting named tool-augmented scientific reasoning. This setting supplements LLMs with scalable toolsets, and shifts the focus from pursuing an omniscient problem solver to a proficient tool-user. To facilitate the research of such setting, we construct a tool-augmented training corpus named MathFunc which encompasses over 30,000 samples and roughly 6,000 tools. Building on MathFunc, we develop SciAgent to retrieve, understand and, if necessary, use tools for scientific problem solving. Additionally, we craft a benchmark, SciToolBench, spanning five scientific domains to evaluate LLMs' abilities with tool assistance. Extensive experiments on SciToolBench confirm the effectiveness of SciAgent. Notably, SciAgent-Mistral-7B surpasses other LLMs with the same size by more than 13% in absolute accuracy. Furthermore, SciAgent-DeepMath-7B shows much superior performance than ChatGPT.

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

Astronomers have typically set out to solve supervised machine learning problems by creating their own representations from scratch. We show that deep learning models trained to answer every Galaxy Zoo DECaLS question learn meaningful semantic representations of galaxies that are useful for new tasks on which the models were never trained. We exploit these representations to outperform several recent approaches at practical tasks crucial for investigating large galaxy samples. The first task is identifying galaxies of similar morphology to a query galaxy. Given a single galaxy assigned a free text tag by humans (e.g. "#diffuse"), we can find galaxies matching that tag for most tags. The second task is identifying the most interesting anomalies to a particular researcher. Our approach is 100% accurate at identifying the most interesting 100 anomalies (as judged by Galaxy Zoo 2 volunteers). The third task is adapting a model to solve a new task using only a small number of newly-labelled galaxies. Models fine-tuned from our representation are better able to identify ring galaxies than models fine-tuned from terrestrial images (ImageNet) or trained from scratch. We solve each task with very few new labels; either one (for the similarity search) or several hundred (for anomaly detection or fine-tuning). This challenges the longstanding view that deep supervised methods require new large labelled datasets for practical use in astronomy. To help the community benefit from our pretrained models, we release our fine-tuning code Zoobot. Zoobot is accessible to researchers with no prior experience in deep learning.

The last decade has seen a significant increase of interest in deep learning research, with many public successes that have demonstrated its potential. As such, these systems are now being incorporated into commercial products. With this comes an additional challenge: how can we build AI systems that solve tasks where there is not a crisp, well-defined specification? While multiple solutions have been proposed, in this competition we focus on one in particular: learning from human feedback. Rather than training AI systems using a predefined reward function or using a labeled dataset with a predefined set of categories, we instead train the AI system using a learning signal derived from some form of human feedback, which can evolve over time as the understanding of the task changes, or as the capabilities of the AI system improve. The MineRL BASALT competition aims to spur forward research on this important class of techniques. We design a suite of four tasks in Minecraft for which we expect it will be hard to write down hardcoded reward functions. These tasks are defined by a paragraph of natural language: for example, "create a waterfall and take a scenic picture of it", with additional clarifying details. Participants must train a separate agent for each task, using any method they want. Agents are then evaluated by humans who have read the task description. To help participants get started, we provide a dataset of human demonstrations on each of the four tasks, as well as an imitation learning baseline that leverages these demonstrations. Our hope is that this competition will improve our ability to build AI systems that do what their designers intend them to do, even when the intent cannot be easily formalized. Besides allowing AI to solve more tasks, this can also enable more effective regulation of AI systems, as well as making progress on the value alignment problem.

We present the results and the main findings of SemEval-2024 Task 8: Multigenerator, Multidomain, and Multilingual Machine-Generated Text Detection. The task featured three subtasks. Subtask A is a binary classification task determining whether a text is written by a human or generated by a machine. This subtask has two tracks: a monolingual track focused solely on English texts and a multilingual track. Subtask B is to detect the exact source of a text, discerning whether it is written by a human or generated by a specific LLM. Subtask C aims to identify the changing point within a text, at which the authorship transitions from human to machine. The task attracted a large number of participants: subtask A monolingual (126), subtask A multilingual (59), subtask B (70), and subtask C (30). In this paper, we present the task, analyze the results, and discuss the system submissions and the methods they used. For all subtasks, the best systems used LLMs.

The 1st Workshop on Data Contamination (CONDA 2024) focuses on all relevant aspects of data contamination in natural language processing, where data contamination is understood as situations where evaluation data is included in pre-training corpora used to train large scale models, compromising evaluation results. The workshop fostered a shared task to collect evidence on data contamination in current available datasets and models. The goal of the shared task and associated database is to assist the community in understanding the extent of the problem and to assist researchers in avoiding reporting evaluation results on known contaminated resources. The shared task provides a structured, centralized public database for the collection of contamination evidence, open to contributions from the community via GitHub pool requests. This first compilation paper is based on 566 reported entries over 91 contaminated sources from a total of 23 contributors. The details of the individual contamination events are available in the platform. The platform continues to be online, open to contributions from the community.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. Recently, a plethora of new AI models and tools has been proposed, promising to empower researchers and academics worldwide to conduct their research more effectively and efficiently. This includes all aspects of the research cycle, especially (1) searching for relevant literature; (2) generating research ideas and conducting experimentation; generating (3) text-based and (4) multimodal content (e.g., scientific figures and diagrams); and (5) AI-based automatic peer review. In this survey, we provide an in-depth overview over these exciting recent developments, which promise to fundamentally alter the scientific research process for good. Our survey covers the five aspects outlined above, indicating relevant datasets, methods and results (including evaluation) as well as limitations and scope for future research. Ethical concerns regarding shortcomings of these tools and potential for misuse (fake science, plagiarism, harms to research integrity) take a particularly prominent place in our discussion. We hope that our survey will not only become a reference guide for newcomers to the field but also a catalyst for new AI-based initiatives in the area of "AI4Science".

Experts in various fields routinely perform methodical writing tasks to plan, organize, and report their work. From a clinician writing a differential diagnosis for a patient, to a teacher writing a lesson plan for students, these tasks are pervasive, requiring to methodically generate structured long-form output for a given input. We develop a typology of methodical tasks structured in the form of a task objective, procedure, input, and output, and introduce DoLoMiTes, a novel benchmark with specifications for 519 such tasks elicited from hundreds of experts from across 25 fields. Our benchmark further contains specific instantiations of methodical tasks with concrete input and output examples (1,857 in total) which we obtain by collecting expert revisions of up to 10 model-generated examples of each task. We use these examples to evaluate contemporary language models highlighting that automating methodical tasks is a challenging long-form generation problem, as it requires performing complex inferences, while drawing upon the given context as well as domain knowledge.

This paper presents teaching materials, particularly assignments and ideas for classroom activities, from a new course on large language models (LLMs) taught at Charles University. The assignments include experiments with LLM inference for weather report generation and machine translation. The classroom activities include class quizzes, focused research on downstream tasks and datasets, and an interactive "best paper" session aimed at reading and comprehension of research papers.

We propose a new shared task for tactical data-to-text generation in the domain of source code libraries. Specifically, we focus on text generation of function descriptions from example software projects. Data is drawn from existing resources used for studying the related problem of semantic parser induction (Richardson and Kuhn, 2017b; Richardson and Kuhn, 2017a), and spans a wide variety of both natural languages and programming languages. In this paper, we describe these existing resources, which will serve as training and development data for the task, and discuss plans for building new independent test sets.

We present the FinCausal 2020 Shared Task on Causality Detection in Financial Documents and the associated FinCausal dataset, and discuss the participating systems and results. Two sub-tasks are proposed: a binary classification task (Task 1) and a relation extraction task (Task 2). A total of 16 teams submitted runs across the two Tasks and 13 of them contributed with a system description paper. This workshop is associated to the Joint Workshop on Financial Narrative Processing and MultiLing Financial Summarisation (FNP-FNS 2020), held at The 28th International Conference on Computational Linguistics (COLING'2020), Barcelona, Spain on September 12, 2020.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

We present SemEval-2025 Task 5: LLMs4Subjects, a shared task on automated subject tagging for scientific and technical records in English and German using the GND taxonomy. Participants developed LLM-based systems to recommend top-k subjects, evaluated through quantitative metrics (precision, recall, F1-score) and qualitative assessments by subject specialists. Results highlight the effectiveness of LLM ensembles, synthetic data generation, and multilingual processing, offering insights into applying LLMs for digital library classification.

Artificial Intelligence (AI) has made incredible progress recently. On the one hand, advanced foundation models like ChatGPT can offer powerful conversation, in-context learning and code generation abilities on a broad range of open-domain tasks. They can also generate high-level solution outlines for domain-specific tasks based on the common sense knowledge they have acquired. However, they still face difficulties with some specialized tasks because they lack enough domain-specific data during pre-training or they often have errors in their neural network computations on those tasks that need accurate executions. On the other hand, there are also many existing models and systems (symbolic-based or neural-based) that can do some domain-specific tasks very well. However, due to the different implementation or working mechanisms, they are not easily accessible or compatible with foundation models. Therefore, there is a clear and pressing need for a mechanism that can leverage foundation models to propose task solution outlines and then automatically match some of the sub-tasks in the outlines to the off-the-shelf models and systems with special functionalities to complete them. Inspired by this, we introduce TaskMatrix.AI as a new AI ecosystem that connects foundation models with millions of APIs for task completion. Unlike most previous work that aimed to improve a single AI model, TaskMatrix.AI focuses more on using existing foundation models (as a brain-like central system) and APIs of other AI models and systems (as sub-task solvers) to achieve diversified tasks in both digital and physical domains. As a position paper, we will present our vision of how to build such an ecosystem, explain each key component, and use study cases to illustrate both the feasibility of this vision and the main challenges we need to address next.

This study evaluates the effectiveness of various large language models (LLMs) in performing tasks common among undergraduate computer science students. Although a number of research studies in the computing education community have explored the possibility of using LLMs for a variety of tasks, there is a lack of comprehensive research comparing different LLMs and evaluating which LLMs are most effective for different tasks. Our research systematically assesses some of the publicly available LLMs such as Google Bard, ChatGPT(3.5), GitHub Copilot Chat, and Microsoft Copilot across diverse tasks commonly encountered by undergraduate computer science students in India. These tasks include code explanation and documentation, solving class assignments, technical interview preparation, learning new concepts and frameworks, and email writing. Evaluation for these tasks was carried out by pre-final year and final year undergraduate computer science students and provides insights into the models' strengths and limitations. This study aims to guide students as well as instructors in selecting suitable LLMs for any specific task and offers valuable insights on how LLMs can be used constructively by students and instructors.

In this community review report, we discuss applications and techniques for fast machine learning (ML) in science -- the concept of integrating power ML methods into the real-time experimental data processing loop to accelerate scientific discovery. The material for the report builds on two workshops held by the Fast ML for Science community and covers three main areas: applications for fast ML across a number of scientific domains; techniques for training and implementing performant and resource-efficient ML algorithms; and computing architectures, platforms, and technologies for deploying these algorithms. We also present overlapping challenges across the multiple scientific domains where common solutions can be found. This community report is intended to give plenty of examples and inspiration for scientific discovery through integrated and accelerated ML solutions. This is followed by a high-level overview and organization of technical advances, including an abundance of pointers to source material, which can enable these breakthroughs.

In populous countries, pending legal cases have been growing exponentially. There is a need for developing NLP-based techniques for processing and automatically understanding legal documents. To promote research in the area of Legal NLP we organized the shared task LegalEval - Understanding Legal Texts at SemEval 2023. LegalEval task has three sub-tasks: Task-A (Rhetorical Roles Labeling) is about automatically structuring legal documents into semantically coherent units, Task-B (Legal Named Entity Recognition) deals with identifying relevant entities in a legal document and Task-C (Court Judgement Prediction with Explanation) explores the possibility of automatically predicting the outcome of a legal case along with providing an explanation for the prediction. In total 26 teams (approx. 100 participants spread across the world) submitted systems paper. In each of the sub-tasks, the proposed systems outperformed the baselines; however, there is a lot of scope for improvement. This paper describes the tasks, and analyzes techniques proposed by various teams.

Can foundation models be guided to execute tasks involving legal reasoning? We believe that building a benchmark to answer this question will require sustained collaborative efforts between the computer science and legal communities. To that end, this short paper serves three purposes. First, we describe how IRAC-a framework legal scholars use to distinguish different types of legal reasoning-can guide the construction of a Foundation Model oriented benchmark. Second, we present a seed set of 44 tasks built according to this framework. We discuss initial findings, and highlight directions for new tasks. Finally-inspired by the Open Science movement-we make a call for the legal and computer science communities to join our efforts by contributing new tasks. This work is ongoing, and our progress can be tracked here: https://github.com/HazyResearch/legalbench.

The SoccerNet 2022 challenges were the second annual video understanding challenges organized by the SoccerNet team. In 2022, the challenges were composed of 6 vision-based tasks: (1) action spotting, focusing on retrieving action timestamps in long untrimmed videos, (2) replay grounding, focusing on retrieving the live moment of an action shown in a replay, (3) pitch localization, focusing on detecting line and goal part elements, (4) camera calibration, dedicated to retrieving the intrinsic and extrinsic camera parameters, (5) player re-identification, focusing on retrieving the same players across multiple views, and (6) multiple object tracking, focusing on tracking players and the ball through unedited video streams. Compared to last year's challenges, tasks (1-2) had their evaluation metrics redefined to consider tighter temporal accuracies, and tasks (3-6) were novel, including their underlying data and annotations. More information on the tasks, challenges and leaderboards are available on https://www.soccer-net.org. Baselines and development kits are available on https://github.com/SoccerNet.

We present the GenAI Content Detection Task~1 -- a shared task on binary machine generated text detection, conducted as a part of the GenAI workshop at COLING 2025. The task consists of two subtasks: Monolingual (English) and Multilingual. The shared task attracted many participants: 36 teams made official submissions to the Monolingual subtask during the test phase and 26 teams -- to the Multilingual. We provide a comprehensive overview of the data, a summary of the results -- including system rankings and performance scores -- detailed descriptions of the participating systems, and an in-depth analysis of submissions. https://github.com/mbzuai-nlp/COLING-2025-Workshop-on-MGT-Detection-Task1

Revision is a crucial step in scientific writing, where authors refine their work to improve clarity, structure, and academic quality. Existing approaches to automated writing assistance often focus on sentence-level revisions, which fail to capture the broader context needed for effective modification. In this paper, we explore the impact of shifting from sentence-level to paragraph-level scope for the task of scientific text revision. The paragraph level definition of the task allows for more meaningful changes, and is guided by detailed revision instructions rather than general ones. To support this task, we introduce ParaRev, the first dataset of revised scientific paragraphs with an evaluation subset manually annotated with revision instructions. Our experiments demonstrate that using detailed instructions significantly improves the quality of automated revisions compared to general approaches, no matter the model or the metric considered.

Energy time-series analysis describes the process of analyzing past energy observations and possibly external factors so as to predict the future. Different tasks are involved in the general field of energy time-series analysis and forecasting, with electric load demand forecasting, personalized energy consumption forecasting, as well as renewable energy generation forecasting being among the most common ones. Following the exceptional performance of Deep Learning (DL) in a broad area of vision tasks, DL models have successfully been utilized in time-series forecasting tasks. This paper aims to provide insight into various DL methods geared towards improving the performance in energy time-series forecasting tasks, with special emphasis in Greek Energy Market, and equip the reader with the necessary knowledge to apply these methods in practice.

We propose a new test to measure a text model's multitask accuracy. The test covers 57 tasks including elementary mathematics, US history, computer science, law, and more. To attain high accuracy on this test, models must possess extensive world knowledge and problem solving ability. We find that while most recent models have near random-chance accuracy, the very largest GPT-3 model improves over random chance by almost 20 percentage points on average. However, on every one of the 57 tasks, the best models still need substantial improvements before they can reach expert-level accuracy. Models also have lopsided performance and frequently do not know when they are wrong. Worse, they still have near-random accuracy on some socially important subjects such as morality and law. By comprehensively evaluating the breadth and depth of a model's academic and professional understanding, our test can be used to analyze models across many tasks and to identify important shortcomings.

We present our submission to the AXOLOTL-24 shared task. The shared task comprises two subtasks: identifying new senses that words gain with time (when comparing newer and older time periods) and producing the definitions for the identified new senses. We implemented a conceptually simple and computationally inexpensive solution to both subtasks. We trained adapter-based binary classification models to match glosses with usage examples and leveraged the probability output of the models to identify novel senses. The same models were used to match examples of novel sense usages with Wiktionary definitions. Our submission attained third place on the first subtask and the first place on the second subtask.

In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible, rerunning and verifying experiments is usually hard due to a lack of standards. Therefore, reusing existing scientific data processing code from state-of-the-art research is hard as well. This is why we introduce CLAIMED, which has a proven track record in scientific research for addressing the repeatability and reusability issues in modern data-driven science. CLAIMED is a framework to build reusable operators and scalable scientific workflows by supporting the scientist to draw from previous work by re-composing workflows from existing libraries of coarse-grained scientific operators. Although various implementations exist, CLAIMED is programming language, scientific library, and execution environment agnostic.

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

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

Science journalism reports current scientific discoveries to non-specialists, aiming to enable public comprehension of the state of the art. However, this task can be challenging as the audience often lacks specific knowledge about the presented research. To address this challenge, we propose a framework that integrates three LLMs mimicking the real-world writing-reading-feedback-revision workflow, with one LLM acting as the journalist, a smaller LLM as the general public reader, and the third LLM as an editor. The journalist's writing is iteratively refined by feedback from the reader and suggestions from the editor. Our experiments demonstrate that by leveraging the collaboration of two 7B and one 1.8B open-source LLMs, we can generate articles that are more accessible than those generated by existing methods, including advanced models such as GPT-4.

This paper describes a system designed to distinguish between AI-generated and human-written scientific excerpts in the DAGPap24 competition hosted within the Fourth Workshop on Scientific Document Processing. In this competition the task is to find artificially generated token-level text fragments in documents of a scientific domain. Our work focuses on the use of a multi-task learning architecture with two heads. The application of this approach is justified by the specificity of the task, where class spans are continuous over several hundred characters. We considered different encoder variations to obtain a state vector for each token in the sequence, as well as a variation in splitting fragments into tokens to further feed into the input of a transform-based encoder. This approach allows us to achieve a 9% quality improvement relative to the baseline solution score on the development set (from 0.86 to 0.95) using the average macro F1-score, as well as a score of 0.96 on a closed test part of the dataset from the competition.

AI is increasingly playing a pivotal role in transforming how scientific discoveries are made. We introduce The AI Scientist-v2, an end-to-end agentic system capable of producing the first entirely AI generated peer-review-accepted workshop paper. This system iteratively formulates scientific hypotheses, designs and executes experiments, analyzes and visualizes data, and autonomously authors scientific manuscripts. Compared to its predecessor (v1, Lu et al., 2024 arXiv:2408.06292), The AI Scientist-v2 eliminates the reliance on human-authored code templates, generalizes effectively across diverse machine learning domains, and leverages a novel progressive agentic tree-search methodology managed by a dedicated experiment manager agent. Additionally, we enhance the AI reviewer component by integrating a Vision-Language Model (VLM) feedback loop for iterative refinement of content and aesthetics of the figures. We evaluated The AI Scientist-v2 by submitting three fully autonomous manuscripts to a peer-reviewed ICLR workshop. Notably, one manuscript achieved high enough scores to exceed the average human acceptance threshold, marking the first instance of a fully AI-generated paper successfully navigating a peer review. This accomplishment highlights the growing capability of AI in conducting all aspects of scientific research. We anticipate that further advancements in autonomous scientific discovery technologies will profoundly impact human knowledge generation, enabling unprecedented scalability in research productivity and significantly accelerating scientific breakthroughs, greatly benefiting society at large. We have open-sourced the code at https://github.com/SakanaAI/AI-Scientist-v2 to foster the future development of this transformative technology. We also discuss the role of AI in science, including AI safety.

State-of-the-art space science missions increasingly rely on automation due to spacecraft complexity and the costs of human oversight. The high volume of data, including scientific and telemetry data, makes manual inspection challenging. Machine learning offers significant potential to meet these demands. The Euclid space telescope, in its survey phase since February 2024, exemplifies this shift. Euclid's success depends on accurate monitoring and interpretation of housekeeping telemetry and science-derived data. Thousands of telemetry parameters, monitored as time series, may or may not impact the quality of scientific data. These parameters have complex interdependencies, often due to physical relationships (e.g., proximity of temperature sensors). Optimising science operations requires careful anomaly detection and identification of hidden parameter states. Moreover, understanding the interactions between known anomalies and physical quantities is crucial yet complex, as related parameters may display anomalies with varied timing and intensity. We address these challenges by analysing temperature anomalies in Euclid's telemetry from February to August 2024, focusing on eleven temperature parameters and 35 covariates. We use a predictive XGBoost model to forecast temperatures based on historical values, detecting anomalies as deviations from predictions. A second XGBoost model predicts anomalies from covariates, capturing their relationships to temperature anomalies. We identify the top three anomalies per parameter and analyse their interactions with covariates using SHAP (Shapley Additive Explanations), enabling rapid, automated analysis of complex parameter relationships. Our method demonstrates how machine learning can enhance telemetry monitoring, offering scalable solutions for other missions with similar data challenges.

We present the results and the main findings of SemEval-2020 Task 11 on Detection of Propaganda Techniques in News Articles. The task featured two subtasks. Subtask SI is about Span Identification: given a plain-text document, spot the specific text fragments containing propaganda. Subtask TC is about Technique Classification: given a specific text fragment, in the context of a full document, determine the propaganda technique it uses, choosing from an inventory of 14 possible propaganda techniques. The task attracted a large number of participants: 250 teams signed up to participate and 44 made a submission on the test set. In this paper, we present the task, analyze the results, and discuss the system submissions and the methods they used. For both subtasks, the best systems used pre-trained Transformers and ensembles.

Citations in scientific papers not only help us trace the intellectual lineage but also are a useful indicator of the scientific significance of the work. Citation intents prove beneficial as they specify the role of the citation in a given context. In this paper, we present CitePrompt, a framework which uses the hitherto unexplored approach of prompt-based learning for citation intent classification. We argue that with the proper choice of the pretrained language model, the prompt template, and the prompt verbalizer, we can not only get results that are better than or comparable to those obtained with the state-of-the-art methods but also do it with much less exterior information about the scientific document. We report state-of-the-art results on the ACL-ARC dataset, and also show significant improvement on the SciCite dataset over all baseline models except one. As suitably large labelled datasets for citation intent classification can be quite hard to find, in a first, we propose the conversion of this task to the few-shot and zero-shot settings. For the ACL-ARC dataset, we report a 53.86% F1 score for the zero-shot setting, which improves to 63.61% and 66.99% for the 5-shot and 10-shot settings, respectively.

We introduce WIQA, the first large-scale dataset of "What if..." questions over procedural text. WIQA contains three parts: a collection of paragraphs each describing a process, e.g., beach erosion; a set of crowdsourced influence graphs for each paragraph, describing how one change affects another; and a large (40k) collection of "What if...?" multiple-choice questions derived from the graphs. For example, given a paragraph about beach erosion, would stormy weather result in more or less erosion (or have no effect)? The task is to answer the questions, given their associated paragraph. WIQA contains three kinds of questions: perturbations to steps mentioned in the paragraph; external (out-of-paragraph) perturbations requiring commonsense knowledge; and irrelevant (no effect) perturbations. We find that state-of-the-art models achieve 73.8% accuracy, well below the human performance of 96.3%. We analyze the challenges, in particular tracking chains of influences, and present the dataset as an open challenge to the community.

Scientific question answering (SQA) is an important task aimed at answering questions based on papers. However, current SQA datasets have limited reasoning types and neglect the relevance between tables and text, creating a significant gap with real scenarios. To address these challenges, we propose a QA benchmark for scientific tables and text with diverse reasoning types (SciTaT). To cover more reasoning types, we summarize various reasoning types from real-world questions. To involve both tables and text, we require the questions to incorporate tables and text as much as possible. Based on SciTaT, we propose a strong baseline (CaR), which combines various reasoning methods to address different reasoning types and process tables and text at the same time. CaR brings average improvements of 12.9% over other baselines on SciTaT, validating its effectiveness. Error analysis reveals the challenges of SciTaT, such as complex numerical calculations and domain knowledge.

We introduce a new challenge to test the STEM skills of neural models. The problems in the real world often require solutions, combining knowledge from STEM (science, technology, engineering, and math). Unlike existing datasets, our dataset requires the understanding of multimodal vision-language information of STEM. Our dataset features one of the largest and most comprehensive datasets for the challenge. It includes 448 skills and 1,073,146 questions spanning all STEM subjects. Compared to existing datasets that often focus on examining expert-level ability, our dataset includes fundamental skills and questions designed based on the K-12 curriculum. We also add state-of-the-art foundation models such as CLIP and GPT-3.5-Turbo to our benchmark. Results show that the recent model advances only help master a very limited number of lower grade-level skills (2.5% in the third grade) in our dataset. In fact, these models are still well below (averaging 54.7%) the performance of elementary students, not to mention near expert-level performance. To understand and increase the performance on our dataset, we teach the models on a training split of our dataset. Even though we observe improved performance, the model performance remains relatively low compared to average elementary students. To solve STEM problems, we will need novel algorithmic innovations from the community.

Typically, machine learning systems solve new tasks by training on thousands of examples. In contrast, humans can solve new tasks by reading some instructions, with perhaps an example or two. To take a step toward closing this gap, we introduce a framework for developing NLP systems that solve new tasks after reading their descriptions, synthesizing prior work in this area. We instantiate this framework with a new English language dataset, ZEST, structured for task-oriented evaluation on unseen tasks. Formulating task descriptions as questions, we ensure each is general enough to apply to many possible inputs, thus comprehensively evaluating a model's ability to solve each task. Moreover, the dataset's structure tests specific types of systematic generalization. We find that the state-of-the-art T5 model achieves a score of 12% on ZEST, leaving a significant challenge for NLP researchers.

Task semantics can be expressed by a set of input-to-output examples or a piece of textual instruction. Conventional machine learning approaches for natural language processing (NLP) mainly rely on the availability of large-scale sets of task-specific examples. Two issues arise: first, collecting task-specific labeled examples does not apply to scenarios where tasks may be too complicated or costly to annotate, or the system is required to handle a new task immediately; second, this is not user-friendly since end-users are probably more willing to provide task description rather than a set of examples before using the system. Therefore, the community is paying increasing interest in a new supervision-seeking paradigm for NLP: learning from task instructions. Despite its impressive progress, there are some common issues that the community struggles with. This survey paper tries to summarize and provide insights into the current research on instruction learning, particularly by answering the following questions: (i) What is task instruction, and what instruction types exist? (ii) How to model instructions? (iii) What factors influence and explain the instructions' performance? (iv) What challenges remain in instruction learning? To our knowledge, this is the first comprehensive survey about textual instructions.

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

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Despite the growing adoption of large language models (LLMs) in academic workflows, their capabilities remain limited when it comes to supporting high-quality scientific writing. Most existing systems are designed for general-purpose scientific text generation and fail to meet the sophisticated demands of research communication beyond surface-level polishing, such as conceptual coherence across sections. Furthermore, academic writing is inherently iterative and revision-driven, a process not well supported by direct prompting-based paradigms. To address these scenarios, we propose a human-AI collaboration framework for academic paper revision. We first introduce a comprehensive dataset of 7,040 research papers from top-tier venues annotated with over 140,000 instruction-response pairs that reflect realistic, section-level scientific revisions. Building on the dataset, we develop XtraGPT, the first suite of open-source LLMs, designed to provide context-aware, instruction-guided writing assistance, ranging from 1.5B to 14B parameters. Extensive experiments validate that XtraGPT significantly outperforms same-scale baselines and approaches the quality of proprietary systems. Both automated preference assessments and human evaluations confirm the effectiveness of our models in improving scientific drafts.

Most work in machine reading focuses on question answering problems where the answer is directly expressed in the text to read. However, many real-world question answering problems require the reading of text not because it contains the literal answer, but because it contains a recipe to derive an answer together with the reader's background knowledge. One example is the task of interpreting regulations to answer "Can I...?" or "Do I have to...?" questions such as "I am working in Canada. Do I have to carry on paying UK National Insurance?" after reading a UK government website about this topic. This task requires both the interpretation of rules and the application of background knowledge. It is further complicated due to the fact that, in practice, most questions are underspecified, and a human assistant will regularly have to ask clarification questions such as "How long have you been working abroad?" when the answer cannot be directly derived from the question and text. In this paper, we formalise this task and develop a crowd-sourcing strategy to collect 32k task instances based on real-world rules and crowd-generated questions and scenarios. We analyse the challenges of this task and assess its difficulty by evaluating the performance of rule-based and machine-learning baselines. We observe promising results when no background knowledge is necessary, and substantial room for improvement whenever background knowledge is needed.

This paper presents a new challenging information extraction task in the domain of materials science. We develop an annotation scheme for marking information on experiments related to solid oxide fuel cells in scientific publications, such as involved materials and measurement conditions. With this paper, we publish our annotation guidelines, as well as our SOFC-Exp corpus consisting of 45 open-access scholarly articles annotated by domain experts. A corpus and an inter-annotator agreement study demonstrate the complexity of the suggested named entity recognition and slot filling tasks as well as high annotation quality. We also present strong neural-network based models for a variety of tasks that can be addressed on the basis of our new data set. On all tasks, using BERT embeddings leads to large performance gains, but with increasing task complexity, adding a recurrent neural network on top seems beneficial. Our models will serve as competitive baselines in future work, and analysis of their performance highlights difficult cases when modeling the data and suggests promising research directions.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

We introduce scientific claim verification, a new task to select abstracts from the research literature containing evidence that SUPPORTS or REFUTES a given scientific claim, and to identify rationales justifying each decision. To study this task, we construct SciFact, a dataset of 1.4K expert-written scientific claims paired with evidence-containing abstracts annotated with labels and rationales. We develop baseline models for SciFact, and demonstrate that simple domain adaptation techniques substantially improve performance compared to models trained on Wikipedia or political news. We show that our system is able to verify claims related to COVID-19 by identifying evidence from the CORD-19 corpus. Our experiments indicate that SciFact will provide a challenging testbed for the development of new systems designed to retrieve and reason over corpora containing specialized domain knowledge. Data and code for this new task are publicly available at https://github.com/allenai/scifact. A leaderboard and COVID-19 fact-checking demo are available at https://scifact.apps.allenai.org.

We consider the problem of building an assistive robotic system that can help humans in daily household cleanup tasks. Creating such an autonomous system in real-world environments is inherently quite challenging, as a general solution may not suit the preferences of a particular customer. Moreover, such a system consists of multi-objective tasks comprising -- (i) Detection of misplaced objects and prediction of their potentially correct placements, (ii) Fine-grained manipulation for stable object grasping, and (iii) Room-to-room navigation for transferring objects in unseen environments. This work systematically tackles each component and integrates them into a complete object rearrangement pipeline. To validate our proposed system, we conduct multiple experiments on a real robotic platform involving multi-room object transfer, user preference-based placement, and complex pick-and-place tasks. Project page: https://sites.google.com/eng.ucsd.edu/home-robot

Tables and table-based use cases play a crucial role in many important real-world applications, such as spreadsheets, databases, and computational notebooks, which traditionally require expert-level users like data engineers, data analysts, and database administrators to operate. Although LLMs have shown remarkable progress in working with tables (e.g., in spreadsheet and database copilot scenarios), comprehensive benchmarking of such capabilities remains limited. In contrast to an extensive and growing list of NLP benchmarks, evaluations of table-related tasks are scarce, and narrowly focus on tasks like NL-to-SQL and Table-QA, overlooking the broader spectrum of real-world tasks that professional users face. This gap limits our understanding and model progress in this important area. In this work, we introduce MMTU, a large-scale benchmark with over 30K questions across 25 real-world table tasks, designed to comprehensively evaluate models ability to understand, reason, and manipulate real tables at the expert-level. These tasks are drawn from decades' worth of computer science research on tabular data, with a focus on complex table tasks faced by professional users. We show that MMTU require a combination of skills -- including table understanding, reasoning, and coding -- that remain challenging for today's frontier models, where even frontier reasoning models like OpenAI o4-mini and DeepSeek R1 score only around 60%, suggesting significant room for improvement. We highlight key findings in our evaluation using MMTU and hope that this benchmark drives further advances in understanding and developing foundation models for structured data processing and analysis. Our code and data are available at https://github.com/MMTU-Benchmark/MMTU and https://huggingface.co/datasets/MMTU-benchmark/MMTU.

We introduce MURA, a large dataset of musculoskeletal radiographs containing 40,561 images from 14,863 studies, where each study is manually labeled by radiologists as either normal or abnormal. To evaluate models robustly and to get an estimate of radiologist performance, we collect additional labels from six board-certified Stanford radiologists on the test set, consisting of 207 musculoskeletal studies. On this test set, the majority vote of a group of three radiologists serves as gold standard. We train a 169-layer DenseNet baseline model to detect and localize abnormalities. Our model achieves an AUROC of 0.929, with an operating point of 0.815 sensitivity and 0.887 specificity. We compare our model and radiologists on the Cohen's kappa statistic, which expresses the agreement of our model and of each radiologist with the gold standard. Model performance is comparable to the best radiologist performance in detecting abnormalities on finger and wrist studies. However, model performance is lower than best radiologist performance in detecting abnormalities on elbow, forearm, hand, humerus, and shoulder studies. We believe that the task is a good challenge for future research. To encourage advances, we have made our dataset freely available at https://stanfordmlgroup.github.io/competitions/mura .

Rapid progress in the capabilities of machine learning approaches in natural language processing has culminated in the rise of large language models over the last two years. Recent works have shown unprecedented adoption of these for academic writing, especially in some fields, but their pervasiveness in astronomy has not been studied sufficiently. To remedy this, we extract words that ChatGPT uses more often than humans when generating academic text and search a total of 1 million articles for them. This way, we assess the frequency of word occurrence in published works in astronomy tracked by the NASA Astrophysics Data System since 2000. We then perform a statistical analysis of the occurrences. We identify a list of words favoured by ChatGPT and find a statistically significant increase for these words against a control group in 2024, which matches the trend in other disciplines. These results suggest a widespread adoption of these models in the writing of astronomy papers. We encourage organisations, publishers, and researchers to work together to identify ethical and pragmatic guidelines to maximise the benefits of these systems while maintaining scientific rigour.

The recent success of Large Language Models (LLMs) signifies an impressive stride towards artificial general intelligence. They have shown a promising prospect in automatically completing tasks upon user instructions, functioning as brain-like coordinators. The associated risks will be revealed as we delegate an increasing number of tasks to machines for automated completion. A big question emerges: how can we make machines behave responsibly when helping humans automate tasks as personal copilots? In this paper, we explore this question in depth from the perspectives of feasibility, completeness and security. In specific, we present Responsible Task Automation (ResponsibleTA) as a fundamental framework to facilitate responsible collaboration between LLM-based coordinators and executors for task automation with three empowered capabilities: 1) predicting the feasibility of the commands for executors; 2) verifying the completeness of executors; 3) enhancing the security (e.g., the protection of users' privacy). We further propose and compare two paradigms for implementing the first two capabilities. One is to leverage the generic knowledge of LLMs themselves via prompt engineering while the other is to adopt domain-specific learnable models. Moreover, we introduce a local memory mechanism for achieving the third capability. We evaluate our proposed ResponsibleTA on UI task automation and hope it could bring more attentions to ensuring LLMs more responsible in diverse scenarios. The research project homepage is at https://task-automation-research.github.io/responsible_task_automation.

In this paper, we present a novel approach to knowledge extraction and retrieval using Natural Language Processing (NLP) techniques for material science. Our goal is to automatically mine structured knowledge from millions of research articles in the field of polycrystalline materials and make it easily accessible to the broader community. The proposed method leverages NLP techniques such as entity recognition and document classification to extract relevant information and build an extensive knowledge base, from a collection of 9.5 Million publications. The resulting knowledge base is integrated into a search engine, which enables users to search for information about specific materials, properties, and experiments with greater precision than traditional search engines like Google. We hope our results can enable material scientists quickly locate desired experimental procedures, compare their differences, and even inspire them to design new experiments. Our website will be available at Github https://github.com/Xianjun-Yang/PcMSP.git soon.

We estimate the relative likelihood of success in the searches for primitive versus intelligent life on other planets. Taking into account the larger search volume for detectable artificial electromagnetic signals, we conclude that both searches should be performed concurrently, albeit with significantly more funding dedicated to primitive life. Based on the current federal funding allocated to the search for biosignatures, our analysis suggests that the search for extraterrestrial intelligence (SETI) may merit a federal funding level of at least 10$ million per year, assuming that the average lifetime of technological species exceeds a millennium.

Many natural language processing (NLP) tasks in English or general domains are widely available and are often used to evaluate pre-trained language models. In contrast, there are fewer tasks available for languages other than English and for the financial domain. In particular, tasks in Japanese and the financial domain are limited. We construct two large datasets using materials published by a Japanese central government agency. The datasets provide three Japanese financial NLP tasks, which include a 3-class and 12-class classification for categorizing sentences, as well as a 5-class classification task for sentiment analysis. Our datasets are designed to be comprehensive and up-to-date, leveraging an automatic update framework that ensures the latest task datasets are publicly available anytime.

Writing is a cognitively demanding task involving continuous decision-making, heavy use of working memory, and frequent switching between multiple activities. Scholarly writing is particularly complex as it requires authors to coordinate many pieces of multiform knowledge. To fully understand writers' cognitive thought process, one should fully decode the end-to-end writing data (from individual ideas to final manuscript) and understand their complex cognitive mechanisms in scholarly writing. We introduce ScholaWrite dataset, the first-of-its-kind keystroke logs of an end-to-end scholarly writing process for complete manuscripts, with thorough annotations of cognitive writing intentions behind each keystroke. Our dataset includes LaTeX-based keystroke data from five preprints with nearly 62K total text changes and annotations across 4 months of paper writing. ScholaWrite shows promising usability and applications (e.g., iterative self-writing) for the future development of AI writing assistants for academic research, which necessitate complex methods beyond LLM prompting. Our experiments clearly demonstrated the importance of collection of end-to-end writing data, rather than the final manuscript, for the development of future writing assistants to support the cognitive thinking process of scientists. Our de-identified dataset, demo, and code repository are available on our project page.

With the release of ever more capable large language models (LLMs), researchers in NLP and related disciplines have started to explore the usability of LLMs for a wide variety of different annotation tasks. Very recently, a lot of this attention has shifted to tasks that are subjective in nature. Given that the latest generations of LLMs have digested and encoded extensive knowledge about different human subpopulations and individuals, the hope is that these models can be trained, tuned or prompted to align with a wide range of different human perspectives. While researchers already evaluate the success of this alignment via surveys and tests, there is a lack of resources to evaluate the alignment on what oftentimes matters the most in NLP; the actual downstream tasks. To fill this gap we present SubData, a Python library that offers researchers working on topics related to subjectivity in annotation tasks a convenient way of collecting, combining and using a range of suitable datasets.

Superconductivity allows electrical current to flow without any energy loss, and thus making solids superconducting is a grand goal of physics, material science, and electrical engineering. More than 16 Nobel Laureates have been awarded for their contribution to superconductivity research. Superconductors are valuable for sustainable development goals (SDGs), such as climate change mitigation, affordable and clean energy, industry, innovation and infrastructure, and so on. However, a unified physics theory explaining all superconductivity mechanism is still unknown. It is believed that superconductivity is microscopically due to not only molecular compositions but also the geometric crystal structure. Hence a new dataset, S2S, containing both crystal structures and superconducting critical temperature, is built upon SuperCon and Material Project. Based on this new dataset, we propose a novel model, S2SNet, which utilizes the attention mechanism for superconductivity prediction. To overcome the shortage of data, S2SNet is pre-trained on the whole Material Project dataset with Masked-Language Modeling (MLM). S2SNet makes a new state-of-the-art, with out-of-sample accuracy of 92% and Area Under Curve (AUC) of 0.92. To the best of our knowledge, S2SNet is the first work to predict superconductivity with only information of crystal structures. This work is beneficial to superconductivity discovery and further SDGs. Code and datasets are available in https://github.com/zjuKeLiu/S2SNet

The web provides a rich, open-domain environment with textual, structural, and spatial properties. We propose a new task for grounding language in this environment: given a natural language command (e.g., "click on the second article"), choose the correct element on the web page (e.g., a hyperlink or text box). We collected a dataset of over 50,000 commands that capture various phenomena such as functional references (e.g. "find who made this site"), relational reasoning (e.g. "article by john"), and visual reasoning (e.g. "top-most article"). We also implemented and analyzed three baseline models that capture different phenomena present in the dataset.

We introduce N-LTP, an open-source neural language technology platform supporting six fundamental Chinese NLP tasks: {lexical analysis} (Chinese word segmentation, part-of-speech tagging, and named entity recognition), {syntactic parsing} (dependency parsing), and {semantic parsing} (semantic dependency parsing and semantic role labeling). Unlike the existing state-of-the-art toolkits, such as Stanza, that adopt an independent model for each task, N-LTP adopts the multi-task framework by using a shared pre-trained model, which has the advantage of capturing the shared knowledge across relevant Chinese tasks. In addition, a knowledge distillation method DBLP:journals/corr/abs-1907-04829 where the single-task model teaches the multi-task model is further introduced to encourage the multi-task model to surpass its single-task teacher. Finally, we provide a collection of easy-to-use APIs and a visualization tool to make users to use and view the processing results more easily and directly. To the best of our knowledge, this is the first toolkit to support six Chinese NLP fundamental tasks. Source code, documentation, and pre-trained models are available at https://github.com/HIT-SCIR/ltp.

To facilitate research in the direction of fine-tuning foundation models from human feedback, we held the MineRL BASALT Competition on Fine-Tuning from Human Feedback at NeurIPS 2022. The BASALT challenge asks teams to compete to develop algorithms to solve tasks with hard-to-specify reward functions in Minecraft. Through this competition, we aimed to promote the development of algorithms that use human feedback as channels to learn the desired behavior. We describe the competition and provide an overview of the top solutions. We conclude by discussing the impact of the competition and future directions for improvement.

A major step toward Artificial General Intelligence (AGI) and Super Intelligence is AI's ability to autonomously conduct research - what we term Artificial Research Intelligence (ARI). If machines could generate hypotheses, conduct experiments, and write research papers without human intervention, it would transform science. Sakana recently introduced the 'AI Scientist', claiming to conduct research autonomously, i.e. they imply to have achieved what we term Artificial Research Intelligence (ARI). The AI Scientist gained much attention, but a thorough independent evaluation has yet to be conducted. Our evaluation of the AI Scientist reveals critical shortcomings. The system's literature reviews produced poor novelty assessments, often misclassifying established concepts (e.g., micro-batching for stochastic gradient descent) as novel. It also struggles with experiment execution: 42% of experiments failed due to coding errors, while others produced flawed or misleading results. Code modifications were minimal, averaging 8% more characters per iteration, suggesting limited adaptability. Generated manuscripts were poorly substantiated, with a median of five citations, most outdated (only five of 34 from 2020 or later). Structural errors were frequent, including missing figures, repeated sections, and placeholder text like 'Conclusions Here'. Some papers contained hallucinated numerical results. Despite these flaws, the AI Scientist represents a leap forward in research automation. It generates full research manuscripts with minimal human input, challenging expectations of AI-driven science. Many reviewers might struggle to distinguish its work from human researchers. While its quality resembles a rushed undergraduate paper, its speed and cost efficiency are unprecedented, producing a full paper for USD 6 to 15 with 3.5 hours of human involvement, far outpacing traditional researchers.

Recently, there has been growing interest in using Large Language Models (LLMs) for scientific research. Numerous benchmarks have been proposed to evaluate the ability of LLMs for scientific research. However, current benchmarks are mostly based on pre-collected objective questions. This design suffers from data leakage problem and lacks the evaluation of subjective Q/A ability. In this paper, we propose SciEval, a comprehensive and multi-disciplinary evaluation benchmark to address these issues. Based on Bloom's taxonomy, SciEval covers four dimensions to systematically evaluate scientific research ability. In particular, we design a "dynamic" subset based on scientific principles to prevent evaluation from potential data leakage. Both objective and subjective questions are included in SciEval. These characteristics make SciEval a more effective benchmark for scientific research ability evaluation of LLMs. Comprehensive experiments on most advanced LLMs show that, although GPT-4 achieves SOTA performance compared to other LLMs, there is still substantial room for improvement, especially for dynamic questions. The data and codes are now publicly available.

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