arXiv subjects

Arman Cohan

Publications and source records attributed to Arman Cohan.

At least 91 records · Page 5Linked to original sources

arXiv2025

Can Multimodal Foundation Models Understand Schematic Diagrams? An Empirical Study on Information-Seeking QA over Scientific Papers

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

cs.CL↗

arXiv2025

Can LLMs Identify Critical Limitations within Scientific Research? A Systematic Evaluation on AI Research Papers

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.

cs.CL↗

arXiv2025

SciVer: Evaluating Foundation Models for Multimodal Scientific Claim Verification

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.

cs.CL↗

arXiv2025

SUCEA: Reasoning-Intensive Retrieval for Adversarial Fact-checking through Claim Decomposition and Editing

Automatic fact-checking has recently received more attention as a means of combating misinformation. Despite significant advancements, fact-checking systems based on retrieval-augmented language models still struggle to tackle adversarial claims, which are intentionally designed by humans to challenge fact-checking systems. To address these challenges, we propose a training-free method designed to rephrase the original claim, making it easier to locate supporting evidence. Our modular framework, SUCEA, decomposes the task into three steps: 1) Claim Segmentation and Decontextualization that segments adversarial claims into independent sub-claims; 2) Iterative Evidence Retrieval and Claim Editing that iteratively retrieves evidence and edits the subclaim based on the retrieved evidence; 3) Evidence Aggregation and Label Prediction that aggregates all retrieved evidence and predicts the entailment label. Experiments on two challenging fact-checking datasets demonstrate that our framework significantly improves on both retrieval and entailment label accuracy, outperforming four strong claim-decomposition-based baselines.

cs.CL↗

arXiv2025

TESS 2: A Large-Scale Generalist Diffusion Language Model

We introduce TESS 2, a general instruction-following diffusion language model that outperforms contemporary instruction-tuned diffusion models, as well as matches and sometimes exceeds strong autoregressive (AR) models. We train TESS 2 by first adapting a strong AR model via continued pretraining with the usual cross-entropy as diffusion loss, and then performing further instruction tuning. We find that adaptation training as well as the choice of the base model is crucial for training good instruction-following diffusion models. We further propose reward guidance, a novel and modular inference-time guidance procedure to align model outputs without needing to train the underlying model. Finally, we show that TESS 2 further improves with increased inference-time compute, highlighting the utility of diffusion LMs in having fine-grained controllability over the amount of compute used at inference time. Code and models are available at https://github.com/hamishivi/tess-2.

cs.CL↗

arXiv2025

MIR: Methodology Inspiration Retrieval for Scientific Research Problems

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

cs.AI↗

arXiv2025

IRIS: Interactive Research Ideation System for Accelerating Scientific Discovery

The rapid advancement in capabilities of large language models (LLMs) raises a pivotal question: How can LLMs accelerate scientific discovery? This work tackles the crucial first stage of research, generating novel hypotheses. While recent work on automated hypothesis generation focuses on multi-agent frameworks and extending test-time compute, none of the approaches effectively incorporate transparency and steerability through a synergistic Human-in-the-loop (HITL) approach. To address this gap, we introduce IRIS: Interactive Research Ideation System, an open-source platform designed for researchers to leverage LLM-assisted scientific ideation. IRIS incorporates innovative features to enhance ideation, including adaptive test-time compute expansion via Monte Carlo Tree Search (MCTS), fine-grained feedback mechanism, and query-based literature synthesis. Designed to empower researchers with greater control and insight throughout the ideation process. We additionally conduct a user study with researchers across diverse disciplines, validating the effectiveness of our system in enhancing ideation. We open-source our code at https://github.com/Anikethh/IRIS-Interactive-Research-Ideation-System

cs.AI↗

arXiv2025

Diffusion vs. Autoregressive Language Models: A Text Embedding Perspective

Large language model (LLM)-based embedding models, benefiting from large scale pre-training and post-training, have begun to surpass BERT and T5-based models on general-purpose text embedding tasks such as document retrieval. However, a fundamental limitation of LLM embeddings lies in the unidirectional attention used during autoregressive pre-training, which misaligns with the bidirectional nature of text embedding tasks. To this end, We propose adopting diffusion language models for text embeddings, motivated by their inherent bidirectional architecture and recent success in matching or surpassing LLMs especially on reasoning tasks. We present the first systematic study of the diffusion language embedding model, which outperforms the LLM-based embedding model by 20% on long-document retrieval, 8% on reasoning-intensive retrieval, 2% on instruction-following retrieval, and achieve competitive performance on traditional text embedding benchmarks. Our analysis verifies that bidirectional attention is crucial for encoding global context in long and complex text.

cs.CL↗

arXiv2025

LocAgent: Graph-Guided LLM Agents for Code Localization

Code localization--identifying precisely where in a codebase changes need to be made--is a fundamental yet challenging task in software maintenance. Existing approaches struggle to efficiently navigate complex codebases when identifying relevant code sections. The challenge lies in bridging natural language problem descriptions with the appropriate code elements, often requiring reasoning across hierarchical structures and multiple dependencies. We introduce LocAgent, a framework that addresses code localization through graph-based representation. By parsing codebases into directed heterogeneous graphs, LocAgent creates a lightweight representation that captures code structures (files, classes, functions) and their dependencies (imports, invocations, inheritance), enabling LLM agents to effectively search and locate relevant entities through powerful multi-hop reasoning. Experimental results on real-world benchmarks demonstrate that our approach significantly enhances accuracy in code localization. Notably, our method with the fine-tuned Qwen-2.5-Coder-Instruct-32B model achieves comparable results to SOTA proprietary models at greatly reduced cost (approximately 86% reduction), reaching up to 92.7% accuracy on file-level localization while improving downstream GitHub issue resolution success rates by 12% for multiple attempts (Pass@10). Our code is available at https://github.com/gersteinlab/LocAgent.

cs.SE↗

arXiv2025

MDCure: A Scalable Pipeline for Multi-Document Instruction-Following

Multi-document (MD) processing is crucial for LLMs to handle real-world tasks such as summarization and question-answering across large sets of documents. While LLMs have improved at processing long inputs, MD contexts still present unique difficulties, including management of inter-document dependencies, redundancy, and incoherent structures. To address this challenge, we introduce MDCure, a scalable and effective instruction data generation framework to enhance the MD capabilities of LLMs without the computational cost of pre-training or reliance on human-annotated data. MDCure generates high-quality synthetic MD instruction data over sets of articles via targeted prompts. We also introduce MDCureRM, a cost-effective, MD-specific reward model to score and filter generated data based on their training utility for MD settings. MDCure is compatible with open- and closed-source models in addition to policy optimization methods such as PPO, enabling even small open-source models to surpass proprietary LLMs as strong generators of high-quality MD instruction data without further data filtering. With MDCure, we fine-tune a wide variety of LLMs up to 70B parameters in size from the FlanT5, Qwen2, and LLAMA3.1 model families. Extensive evaluations on a wide range of MD and long-context benchmarks spanning various tasks and domains show MDCure consistently improves performance over pre-trained baselines and base models by up to 75.1%. Our code, datasets, and models are available at https://github.com/yale-nlp/MDCure.

cs.CL↗

arXiv2025

The Semantic Scholar Open Data Platform

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

cs.DL↗

arXiv2025

YaleNLP @ PerAnsSumm 2025: Multi-Perspective Integration via Mixture-of-Agents for Enhanced Healthcare QA Summarization

Automated summarization of healthcare community question-answering forums is challenging due to diverse perspectives presented across multiple user responses to each question. The PerAnsSumm Shared Task was therefore proposed to tackle this challenge by identifying perspectives from different answers and then generating a comprehensive answer to the question. In this study, we address the PerAnsSumm Shared Task using two complementary paradigms: (i) a training-based approach through QLoRA fine-tuning of LLaMA-3.3-70B-Instruct, and (ii) agentic approaches including zero- and few-shot prompting with frontier LLMs (LLaMA-3.3-70B-Instruct and GPT-4o) and a Mixture-of-Agents (MoA) framework that leverages a diverse set of LLMs by combining outputs from multi-layer feedback aggregation. For perspective span identification/classification, GPT-4o zero-shot achieves an overall score of 0.57, substantially outperforming the 0.40 score of the LLaMA baseline. With a 2-layer MoA configuration, we were able to improve LLaMA performance up by 28 percent to 0.51. For perspective-based summarization, GPT-4o zero-shot attains an overall score of 0.42 compared to 0.28 for the best LLaMA zero-shot, and our 2-layer MoA approach boosts LLaMA performance by 32 percent to 0.37. Furthermore, in few-shot setting, our results show that the sentence-transformer embedding-based exemplar selection provides more gain than manually selected exemplars on LLaMA models, although the few-shot prompting is not always helpful for GPT-4o. The YaleNLP team's approach ranked the overall second place in the shared task.

cs.CL↗

arXiv2025

Z1: Efficient Test-time Scaling with Code

Large Language Models (LLMs) can achieve enhanced complex problem-solving through test-time computing scaling, yet this often entails longer contexts and numerous reasoning token costs. In this paper, we propose an efficient test-time scaling method that trains LLMs on code-related reasoning trajectories, facilitating their reduction of excess thinking tokens while maintaining performance. First, we create Z1-Code-Reasoning-107K, a curated dataset of simple and complex coding problems paired with their short and long solution trajectories. Second, we present a novel Shifted Thinking Window to mitigate overthinking overhead by removing context-delimiting tags (e.g., . . . ) and capping reasoning tokens. Trained with long and short trajectory data and equipped with Shifted Thinking Window, our model, Z1-7B, demonstrates the ability to adjust its reasoning level as the complexity of problems and exhibits efficient test-time scaling across different reasoning tasks that matches R1-Distill-Qwen-7B performance with about 30% of its average thinking tokens. Notably, fine-tuned with only code trajectories, Z1-7B demonstrates generalization to broader reasoning tasks (47.5% on GPQA Diamond). Our analysis of efficient reasoning elicitation also provides valuable insights for future research.

cs.CL↗

arXiv2025

PHYSICS: Benchmarking Foundation Models on University-Level Physics Problem Solving

We introduce PHYSICS, a comprehensive benchmark for university-level physics problem solving. It contains 1297 expert-annotated problems covering six core areas: classical mechanics, quantum mechanics, thermodynamics and statistical mechanics, electromagnetism, atomic physics, and optics. Each problem requires advanced physics knowledge and mathematical reasoning. We develop a robust automated evaluation system for precise and reliable validation. Our evaluation of leading foundation models reveals substantial limitations. Even the most advanced model, o3-mini, achieves only 59.9% accuracy, highlighting significant challenges in solving high-level scientific problems. Through comprehensive error analysis, exploration of diverse prompting strategies, and Retrieval-Augmented Generation (RAG)-based knowledge augmentation, we identify key areas for improvement, laying the foundation for future advancements.

cs.AI↗

arXiv2025

ATEB: Evaluating and Improving Advanced NLP Tasks for Text Embedding Models

Traditional text embedding benchmarks primarily evaluate embedding models' capabilities to capture semantic similarity. However, more advanced NLP tasks require a deeper understanding of text, such as safety and factuality. These tasks demand an ability to comprehend and process complex information, often involving the handling of sensitive content, or the verification of factual statements against reliable sources. We introduce a new benchmark designed to assess and highlight the limitations of embedding models trained on existing information retrieval data mixtures on advanced capabilities, which include factuality, safety, instruction following, reasoning and document-level understanding. This benchmark includes a diverse set of tasks that simulate real-world scenarios where these capabilities are critical and leads to identification of the gaps of the currently advanced embedding models. Furthermore, we propose a novel method that reformulates these various tasks as retrieval tasks. By framing tasks like safety or factuality classification as retrieval problems, we leverage the strengths of retrieval models in capturing semantic relationships while also pushing them to develop a deeper understanding of context and content. Using this approach with single-task fine-tuning, we achieved performance gains of 8\% on factuality classification and 13\% on safety classification. Our code and data will be publicly available.

cs.CL↗

arXiv2025

RouterRetriever: Routing over a Mixture of Expert Embedding Models

Information retrieval methods often rely on a single embedding model trained on large, general-domain datasets like MSMARCO. While this approach can produce a retriever with reasonable overall performance, they often underperform models trained on domain-specific data when testing on their respective domains. Prior work in information retrieval has tackled this through multi-task training, but the idea of routing over a mixture of domain-specific expert retrievers remains unexplored despite the popularity of such ideas in language model generation research. In this work, we introduce RouterRetriever, a retrieval model that leverages a mixture of domain-specific experts by using a routing mechanism to select the most appropriate expert for each query. RouterRetriever is lightweight and allows easy addition or removal of experts without additional training. Evaluation on the BEIR benchmark demonstrates that RouterRetriever outperforms both models trained on MSMARCO (+2.1 absolute nDCG@10) and multi-task models (+3.2). This is achieved by employing our routing mechanism, which surpasses other routing techniques (+1.8 on average) commonly used in language modeling. Furthermore, the benefit generalizes well to other datasets, even in the absence of a specific expert on the dataset. RouterRetriever is the first work to demonstrate the advantages of routing over a mixture of domain-specific expert embedding models as an alternative to a single, general-purpose embedding model, especially when retrieving from diverse, specialized domains.

cs.IR↗

arXiv2025

HYBRIDMIND: Meta Selection of Natural Language and Symbolic Language for Enhanced LLM Reasoning

LLMs approach logical and mathematical reasoning through natural or symbolic languages. While natural language offers human-accessible flexibility but suffers from ambiguity, symbolic reasoning provides precise, machine-executable inferences at the cost of strict domain constraints. We introduce HYBRIDMIND, an adaptive strategy that selects the optimal reasoning approach for each reasoning problem. Through extensive experiments, we evaluate both prompting-based approaches with state-of-the-art LLMs and fine-tuned open-source models. We find that fine-tuning LLaMA-3.1-8B-Instruct as a meta-selector outperforms GPT-4o's natural language reasoning by 4.4\% on FOLIO and 1.3\% on MATH. More notably, using GPT-3.5-turbo as a prompted meta-selector yields a 10\% improvement on FOLIO's challenging subset compared to GPT-4o. We will release our code and data to support future research.

cs.CL↗

arXiv2025

Re-evaluating Automatic LLM System Ranking for Alignment with Human Preference

Evaluating and ranking the capabilities of different LLMs is crucial for understanding their performance and alignment with human preferences. Due to the high cost and time-consuming nature of human evaluations, an automatic LLM bencher (i.e., an automatic evaluation framework that aims to rank LLMs based on their alignment with human preferences) is indispensable. An automatic LLM bencher consists of four components: the input set (e.g., a user instruction), the evaluation model (e.g., an LLM), the evaluation type (e.g., pairwise comparison), and the aggregation method (e.g., the ELO rating system). However, previous work has not thoroughly explored how to select these components or how their different combinations influence the results. In this work, through controlled experiments, we provide a series of recommendations on how to choose each component to better automate the evaluation of LLMs. Furthermore, we discovered that when evaluating LLMs with similar performance, the performance of the automatic LLM bencher declines sharply, underscoring the limitations of current benchers and calling for future work. Lastly, we found that the evaluation models' performance at the instance level (e.g., the accuracy of selecting the best output) does not always align with their effectiveness when used as a component of a bencher, highlighting the importance of dedicated system-level evaluation of benchers.

cs.CL↗