arXiv subjects

Arman Cohan

Publications and source records attributed to Arman Cohan.

At least 55 records · Page 3Linked to original sources

arXiv2026

ANCHOR: Branch-Point Data Generation for GUI Agents

End-to-end GUI agents for real desktop environments require large amounts of high-quality interaction data, yet collecting human demonstrations is expensive and existing synthetic pipelines often suffer from limited task diversity or noisy, goal-drifting trajectories. We present a trajectory expansion framework Anchor that bootstraps scalable desktop supervision from a small set of verified seed demonstrations. Starting from each seed, we identify branch points that correspond to meaningful state changes and propose new, state-grounded task variants conditioned on the current GUI context. An executing agent then follows the proposed instructions to generate new trajectories, while a verifier enforces task completion via state-aware checks and trajectory-level consistency. To improve supervision quality, we further apply task-conditioned step-level filtering to remove ungrounded actions and denoise post-branch segments to maintain coherent intent. Experiments on standard desktop benchmarks, OSWorld and WindowsAgentArena, show that models fine-tuned on our expanded corpus achieve consistent improvements over zero-shot agents and representative synthesis baselines, and generalize across applications and operating systems.

cs.AI↗

arXiv2026

Advancing AI Research Assistants with Expert-Involved Learning

Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source evaluation and optimization framework that pairs a curated multimodal biomedical corpus with expert-vetted tasks to probe two capabilities: full-length article summarization and fine-grained figure interpretation. Using uniform protocols and blinded PhD-level evaluation, we find that state-of-the-art models generate fluent but incomplete summaries, whereas LMMs struggle with detailed visual reasoning. We later observe that prompt engineering and lightweight fine-tuning substantially improve textual coverage, and a compute-scaled inference strategy enhances visual question answering. We build an ARIEL agent that integrates textual and visual cues, and we show it can propose testable mechanistic hypotheses. ARIEL delineates current strengths and limitations of foundation models, and provides a reproducible platform for advancing trustworthy AI in biomedicine.

cs.AI↗

arXiv2026

AlphaResearch: Accelerating New Algorithm Discovery with Language Models

LLMs have made significant progress in complex but easy-to-verify problems, yet they still struggle with discovering the unknown. In this paper, we present \textbf{AlphaResearch}, an autonomous research agent designed to discover new algorithms on open-ended problems by iteratively running the following steps: (1) propose new ideas (2) program to verify (3) optimize the research proposals. To synergize the feasibility and innovation of the discovery process, we construct a novel dual environment by combining the execution-based verifiable reward and reward from simulated real-world peer review environment in AlphaResearch. We construct \textbf{\dataset}, a set of questions that includes an eight open-ended algorithmic problems competition to benchmark AlphaResearch. Experimental results show that AlphaResearch achieves stronger discovery performance than other agentic discovery systems on six open-ended problems. Notably, the algorithm discovered by AlphaResearch on the \emph{``packing circles''} problem achieves the best-of-known performance, surpassing the results of human researchers and strong baselines from recent work (e.g., AlphaEvolve). Additionally, we conduct a comprehensive analysis of the benefits and remaining challenges of autonomous research agent, providing valuable insights for future research.

cs.CL↗

arXiv2026

Examining Reasoning LLMs-as-Judges in Non-Verifiable LLM Post-Training

Reasoning LLMs-as-Judges, which can benefit from inference-time scaling, provide a promising path for extending the success of reasoning models to non-verifiable domains where the output correctness/quality cannot be directly checked. However, while reasoning judges have shown better performance on static evaluation benchmarks, their effectiveness in actual policy training has not been systematically examined. Therefore, we conduct a rigorous study to investigate the actual impact of non-reasoning and reasoning judges in reinforcement-learning-based LLM alignment. Our controlled synthetic setting, where a "gold-standard" judge (gpt-oss-120b) provides preference annotations to train smaller judges, reveals key differences between non-reasoning and reasoning judges: non-reasoning judges lead to reward hacking easily, while reasoning judges can lead to policies that achieve strong performance when evaluated by the gold-standard judge. Interestingly, we find that the reasoning-judge-trained policies achieve such strong performance by learning to generate highly effective adversarial outputs that can also score well on popular benchmarks such as Arena-Hard by deceiving other LLM-judges. Combined with our further analysis, our study highlights both important findings and room for improvements for applying (reasoning) LLM-judges in non-verifiable LLM post-training.

cs.AI↗

arXiv2026

ResearchGym: Evaluating Language Model Agents on Real-World AI Research

We introduce ResearchGym, a benchmark and execution environment for evaluating AI agents on end-to-end research. To instantiate this, we repurpose five oral and spotlight papers from ICML, ICLR, and ACL. From each paper's repository, we preserve the datasets, evaluation harness, and baseline implementations but withhold the paper's proposed method. This results in five containerized task environments comprising 39 sub-tasks in total. Within each environment, agents must propose novel hypotheses, run experiments, and attempt to surpass strong human baselines on the paper's metrics. In a controlled evaluation of an agent powered by GPT-5, we observe a sharp capability--reliability gap. The agent improves over the provided baselines from the repository in just 1 of 15 evaluations (6.7%) by 11.5%, and completes only 26.5% of sub-tasks on average. We identify recurring long-horizon failure modes, including impatience, poor time and resource management, overconfidence in weak hypotheses, difficulty coordinating parallel experiments, and hard limits from context length. Yet in a single run, the agent surpasses the solution of an ICML 2025 Spotlight task, indicating that frontier agents can occasionally reach state-of-the-art performance, but do so unreliably. We additionally evaluate proprietary agent scaffolds including Claude Code (Opus-4.5) and Codex (GPT-5.2) which display a similar gap. ResearchGym provides infrastructure for systematic evaluation and analysis of autonomous agents on closed-loop research.

cs.AI↗

arXiv2026

References Improve LLM Alignment in Non-Verifiable Domains

While Reinforcement Learning with Verifiable Rewards (RLVR) has shown strong effectiveness in reasoning tasks, it cannot be directly applied to non-verifiable domains lacking ground-truth verifiers, such as LLM alignment. In this work, we investigate whether reference-guided LLM-evaluators can bridge this gap by serving as soft "verifiers". First, we design evaluation protocols that enhance LLM-based evaluators for LLM alignment using reference outputs. Through comprehensive experiments, we show that a reference-guided approach substantially improves the accuracy of less capable LLM-judges using references from frontier models; stronger LLM-judges can also be enhanced by high-quality (i.e., human-written) references. Building on these improved judges, we demonstrate the utility of high-quality references in alignment tuning, where LLMs guided with references are used as judges to self-improve. We show that reference-guided self-improvement yields clear gains over both direct SFT on reference outputs and self-improvement with reference-free judges, achieving performance comparable to training with ArmoRM, a strong finetuned reward model. Specifically, our method achieves 73.1% and 58.7% on AlpacaEval and Arena-Hard with Llama-3-8B-Instruct, and 70.0% and 74.1% with Qwen2.5-7B, corresponding to average absolute gains of +20.2 / +17.1 points over SFT distillation and +5.3 / +3.6 points over reference-free self-improvement on AlpacaEval / Arena-Hard. These results highlight the potential of using reference-guided LLM-evaluators to enable effective LLM post-training in non-verifiable domains.

cs.CL↗

arXiv2026

MRMR: A Realistic and Expert-Level Multidisciplinary Benchmark for Reasoning-Intensive Multimodal Retrieval

We introduce MRMR, the first expert-level multidisciplinary multimodal retrieval benchmark requiring intensive reasoning. MRMR contains 1,502 queries spanning 23 domains, with positive documents carefully verified by human experts. Compared to prior benchmarks, MRMR introduces three key advancements. First, it challenges retrieval systems across diverse areas of expertise, enabling fine-grained model comparison across domains. Second, queries are reasoning-intensive, with images requiring deeper interpretation such as diagnosing microscopic slides. We further introduce Contradiction Retrieval, a novel task requiring models to identify conflicting concepts. Finally, queries and documents are constructed as image-text interleaved sequences. Unlike earlier benchmarks restricted to single images or unimodal documents, MRMR offers a realistic setting with multi-image queries and mixed-modality corpus documents. We conduct an extensive evaluation of 4 categories of multimodal retrieval systems and 14 frontier models on MRMR. The text embedding model Qwen3-Embedding with LLM-generated image captions achieves the highest performance, highlighting substantial room for improving multimodal retrieval models. Although latest multimodal models such as Ops-MM-Embedding perform competitively on expert-domain queries, they fall short on reasoning-intensive tasks. We believe that MRMR paves the way for advancing multimodal retrieval in more realistic and challenging scenarios.

cs.IR↗

arXiv2026

SAGE: Benchmarking and Improving Retrieval for Deep Research Agents

Deep research agents have emerged as powerful systems for addressing complex queries. Meanwhile, LLM-based retrievers have demonstrated strong capability in following instructions or reasoning. This raises a critical question: can LLM-based retrievers effectively contribute to deep research agent workflows? To investigate this, we introduce SAGE, a benchmark for scientific literature retrieval comprising 1,200 queries across four scientific domains, with a 200,000 paper retrieval corpus. We evaluate six deep research agents and find that all systems struggle with reasoning-intensive retrieval. Using DR Tulu as backbone, we further compare BM25 and LLM-based retrievers (i.e., ReasonIR and gte-Qwen2-7B-instruct) as alternative search tools. Surprisingly, BM25 significantly outperforms LLM-based retrievers by approximately 30%, as existing agents generate keyword-oriented sub-queries. To improve performance, we propose a corpus-level test-time scaling framework that uses LLMs to augment documents with metadata and keywords, making retrieval easier for off-the-shelf retrievers. This yields 8% and 2% gains on short-form and open-ended questions, respectively.

cs.IR↗

arXiv2026

CellForge: Agentic Design of Virtual Cell Models

Virtual cell modeling aims to predict cellular responses to diverse perturbations but faces challenges from biological complexity, multimodal data heterogeneity, and the need for interdisciplinary expertise. We introduce CellForge, a multi-agent framework that autonomously designs and synthesizes neural network architectures tailored to specific single-cell datasets and perturbation tasks. Given raw multi-omics data and task descriptions, CellForge discovers candidate architectures through collaborative reasoning among specialized agents, then generates executable implementations. Our core contribution is the framework itself: showing that multi-agent collaboration mechanisms - rather than manual human design or single-LLM prompting - can autonomously produce executable, high-quality computational methods. This approach goes beyond conventional hyperparameter tuning by enabling entirely new architectural components such as trajectory-aware encoders and perturbation diffusion modules to emerge from agentic deliberation. We evaluate CellForge on six datasets spanning gene knockouts, drug treatments, and cytokine stimulations across multiple modalities (scRNA-seq, scATAC-seq, CITE-seq). The results demonstrate that the models generated by CellForge are highly competitive with established baselines, while revealing systematic patterns of architectural innovation. CellForge highlights the scientific value of multi-agent frameworks: collaboration among specialized agents enables genuine methodological innovation and executable solutions that single agents or human experts cannot achieve. This represents a paradigm shift toward autonomous scientific method development in computational biology. Code is available at https://github.com/gersteinlab/CellForge.

cs.LG↗

arXiv2026

From Scores to Steps: Diagnosing and Improving LLM Performance in Evidence-Based Medical Calculations

Large language models (LLMs) have demonstrated promising performance on medical benchmarks; however, their ability to perform medical calculations, a crucial aspect of clinical decision-making, remains underexplored and poorly evaluated. Existing benchmarks often assess only the final answer with a wide numerical tolerance, overlooking systematic reasoning failures and potentially causing serious clinical misjudgments. In this work, we revisit medical calculation evaluation with a stronger focus on clinical trustworthiness. First, we clean and restructure the MedCalc-Bench dataset and propose a new step-by-step evaluation pipeline that independently assesses formula selection, entity extraction, and arithmetic computation. Under this granular framework, the accuracy of GPT-4o drops from 62.7% to 43.6%, revealing errors masked by prior evaluations. Second, we introduce an automatic error analysis framework that generates structured attribution for each failure mode. Human evaluation confirms its alignment with expert judgment, enabling scalable and explainable diagnostics. Finally, we propose a modular agentic pipeline, MedRaC, that combines retrieval-augmented generation and Python-based code execution. Without any fine-tuning, MedRaC improves the accuracy of different LLMs from 16.35% up to 53.19%. Our work highlights the limitations of current benchmark practices and proposes a more clinically faithful methodology. By enabling transparent and transferable reasoning evaluation, we move closer to making LLM-based systems trustworthy for real-world medical applications.

cs.CL↗

arXiv2026

MedTutor: A Retrieval-Augmented LLM System for Case-Based Medical Education

The learning process for medical residents presents significant challenges, demanding both the ability to interpret complex case reports and the rapid acquisition of accurate medical knowledge from reliable sources. Residents typically study case reports and engage in discussions with peers and mentors, but finding relevant educational materials and evidence to support their learning from these cases is often time-consuming and challenging. To address this, we introduce MedTutor, a novel system designed to augment resident training by automatically generating evidence-based educational content and multiple-choice questions from clinical case reports. MedTutor leverages a Retrieval-Augmented Generation (RAG) pipeline that takes clinical case reports as input and produces targeted educational materials. The system's architecture features a hybrid retrieval mechanism that synergistically queries a local knowledge base of medical textbooks and academic literature (using PubMed, Semantic Scholar APIs) for the latest related research, ensuring the generated content is both foundationally sound and current. The retrieved evidence is filtered and ordered using a state-of-the-art reranking model and then an LLM generates the final long-form output describing the main educational content regarding the case-report. We conduct a rigorous evaluation of the system. First, three radiologists assessed the quality of outputs, finding them to be of high clinical and educational value. Second, we perform a large scale evaluation using an LLM-as-a Judge to understand if LLMs can be used to evaluate the output of the system. Our analysis using correlation between LLMs outputs and human expert judgments reveals a moderate alignment and highlights the continued necessity of expert oversight.

cs.CL↗

arXiv2026

SciArena: An Open Evaluation Platform for Non-Verifiable Scientific Literature-Grounded Tasks

We present SciArena, an open and collaborative platform for evaluating foundation models on scientific literature-grounded 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 47 foundation models and has collected over 20,000 votes from human researchers across diverse scientific domains. Our analysis of the data collected so far confirms its high quality. 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 collected preference data. It 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.

cs.CL↗

arXiv2026

Investigating Retrieval-Augmented Generation Systems on Unanswerable, Uncheatable, Realistic, Multi-hop Queries

Real-world use cases often present RAG systems with complex queries for which relevant information is missing from the corpus or is incomplete. In these settings, RAG systems must be able to reject unanswerable, out-of-scope queries and identify failures of retrieval and multi-hop reasoning. Despite this, existing RAG benchmarks rarely reflect realistic task complexity for multi-hop or out-of-scope questions, which often can be cheated via disconnected reasoning (i.e., solved without genuine multi-hop inference) or require only simple factual recall. This limits the ability for such benchmarks to uncover limitations of existing RAG systems. To address this gap, we present the first pipeline for automatic, difficulty-controlled creation of un$\underline{c}$heatable, $\underline{r}$ealistic, $\underline{u}$nanswerable, and $\underline{m}$ulti-hop $\underline{q}$uerie$\underline{s}$ (CRUMQs), adaptable to any corpus and domain. We use our pipeline to create CRUMQs over two popular RAG datasets and demonstrate its effectiveness via benchmark experiments on leading retrieval-augmented LLMs. Results show that compared to prior RAG benchmarks, CRUMQs are highly challenging for RAG systems and achieve up to 81.0\% reduction in cheatability scores. More broadly, our pipeline offers a simple way to enhance benchmark difficulty and drive development of more capable RAG systems.

cs.CL↗

arXiv2026

Patient-Similarity Cohort Reasoning in Clinical Text-to-SQL

Real-world clinical text-to-SQL requires reasoning over heterogeneous EHR tables, temporal windows, and patient-similarity cohorts to produce executable queries. We introduce CLINSQL, a benchmark of 633 expert-annotated tasks on MIMIC-IV v3.1 that demands multi-table joins, clinically meaningful filters, and executable SQL. Solving CLINSQL entails navigating schema metadata and clinical coding systems, handling long contexts, and composing multi-step queries beyond traditional text-to-SQL. We evaluate 22 proprietary and open-source models under Chain-of-Thought self-refinement and use rubric-based SQL analysis with execution checks that prioritize critical clinical requirements. Despite recent advances, performance remains far from clinical reliability: on the test set, GPT-5-mini attains 74.7% execution score, DeepSeek-R1 leads open-source at 69.2% and Gemini-2.5-Pro drops from 85.5% on Easy to 67.2% on Hard. Progress on CLINSQL marks tangible advances toward clinically reliable text-to-SQL for real-world EHR analytics.

cs.CL↗

arXiv2025

On Evaluating LLM Alignment by Evaluating LLMs as Judges

Alignment with human preferences is an important evaluation aspect of LLMs, requiring them to be helpful, honest, safe, and to precisely follow human instructions. Evaluating large language models' (LLMs) alignment typically involves directly assessing their open-ended responses, requiring human annotators or strong LLM judges. Conversely, LLMs themselves have also been extensively evaluated as judges for assessing alignment. In this work, we examine the relationship between LLMs' generation and evaluation capabilities in aligning with human preferences. To this end, we first conduct a comprehensive analysis of the generation-evaluation consistency (GE-consistency) among various LLMs, revealing a strong correlation between their generation and evaluation capabilities when evaluated by a strong LLM preference oracle. Utilizing this finding, we propose a benchmarking paradigm that measures LLM alignment with human preferences without directly evaluating their generated outputs, instead assessing LLMs in their role as evaluators. Our evaluation shows that our proposed benchmark, AlignEval, matches or surpasses widely used automatic LLM evaluation benchmarks, such as AlpacaEval and Arena-Hard, in capturing human preferences when ranking LLMs. Our study offers valuable insights into the connection between LLMs' generation and evaluation capabilities, and introduces a benchmark that assesses alignment without directly evaluating model outputs.

cs.CL↗

arXiv2025

SciRAG: Adaptive, Citation-Aware, and Outline-Guided Retrieval and Synthesis for Scientific Literature

The accelerating growth of scientific publications has intensified the need for scalable, trustworthy systems to synthesize knowledge across diverse literature. While recent retrieval-augmented generation (RAG) methods have improved access to scientific information, they often overlook citation graph structure, adapt poorly to complex queries, and yield fragmented, hard-to-verify syntheses. We introduce SciRAG, an open-source framework for scientific literature exploration that addresses these gaps through three key innovations: (1) adaptive retrieval that flexibly alternates between sequential and parallel evidence gathering; (2) citation-aware symbolic reasoning that leverages citation graphs to organize and filter supporting documents; and (3) outline-guided synthesis that plans, critiques, and refines answers to ensure coherence and transparent attribution. Extensive experiments across multiple benchmarks such as QASA and ScholarQA demonstrate that SciRAG outperforms prior systems in factual accuracy and synthesis quality, establishing a new foundation for reliable, large-scale scientific knowledge aggregation.

cs.DL↗

arXiv2025

Rethinking Retrieval-Augmented Generation for Medicine: A Large-Scale, Systematic Expert Evaluation and Practical Insights

Large language models (LLMs) are transforming the landscape of medicine, yet two fundamental challenges persist: keeping up with rapidly evolving medical knowledge and providing verifiable, evidence-grounded reasoning. Retrieval-augmented generation (RAG) has been widely adopted to address these limitations by supplementing model outputs with retrieved evidence. However, whether RAG reliably achieves these goals remains unclear. Here, we present the most comprehensive expert evaluation of RAG in medicine to date. Eighteen medical experts contributed a total of 80,502 annotations, assessing 800 model outputs generated by GPT-4o and Llama-3.1-8B across 200 real-world patient and USMLE-style queries. We systematically decomposed the RAG pipeline into three components: (i) evidence retrieval (relevance of retrieved passages), (ii) evidence selection (accuracy of evidence usage), and (iii) response generation (factuality and completeness of outputs). Contrary to expectation, standard RAG often degraded performance: only 22% of top-16 passages were relevant, evidence selection remained weak (precision 41-43%, recall 27-49%), and factuality and completeness dropped by up to 6% and 5%, respectively, compared with non-RAG variants. Retrieval and evidence selection remain key failure points for the model, contributing to the overall performance drop. We further show that simple yet effective strategies, including evidence filtering and query reformulation, substantially mitigate these issues, improving performance on MedMCQA and MedXpertQA by up to 12% and 8.2%, respectively. These findings call for re-examining RAG's role in medicine and highlight the importance of stage-aware evaluation and deliberate system design for reliable medical LLM applications.

cs.CL↗

arXiv2025

Measuring what Matters: Construct Validity in Large Language Model Benchmarks

Evaluating large language models (LLMs) is crucial for both assessing their capabilities and identifying safety or robustness issues prior to deployment. Reliably measuring abstract and complex phenomena such as 'safety' and 'robustness' requires strong construct validity, that is, having measures that represent what matters to the phenomenon. With a team of 29 expert reviewers, we conduct a systematic review of 445 LLM benchmarks from leading conferences in natural language processing and machine learning. Across the reviewed articles, we find patterns related to the measured phenomena, tasks, and scoring metrics which undermine the validity of the resulting claims. To address these shortcomings, we provide eight key recommendations and detailed actionable guidance to researchers and practitioners in developing LLM benchmarks.

cs.CL↗