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Large Language Models (LLMs) have greatly advanced code auto-completion systems, with a potential for substantial productivity enhancements for developers. However, current benchmarks mainly focus on single-file tasks, leaving an assessment…

Computation and Language · Computer Science 2023-10-05 Tianyang Liu , Canwen Xu , Julian McAuley

Although LLM-based agents have attracted significant attention in domains such as software engineering and machine learning research, their role in advancing combinatorial optimization (CO) remains relatively underexplored. This gap…

Computation and Language · Computer Science 2025-08-25 Weiwei Sun , Shengyu Feng , Shanda Li , Yiming Yang

The ability to understand causality significantly impacts the competence of large language models (LLMs) in output explanation and counterfactual reasoning, as causality reveals the underlying data distribution. However, the lack of a…

Machine Learning · Computer Science 2024-09-30 Yu Zhou , Xingyu Wu , Beicheng Huang , Jibin Wu , Liang Feng , Kay Chen Tan

Large Language Models (LLMs) have demonstrated remarkable capabilities on general text; however, their proficiency in specialized scientific domains that require deep, interconnected knowledge remains largely uncharacterized. Metabolomics…

Computation and Language · Computer Science 2025-10-17 Yuxing Lu , Xukai Zhao , J. Ben Tamo , Micky C. Nnamdi , Rui Peng , Shuang Zeng , Xingyu Hu , Jinzhuo Wang , May D. Wang

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated.…

Quantitative Methods · Quantitative Biology 2025-12-30 Dingyi Rong , Zijian Chen , Qi Jia , Kaiwei Zhang , Haotian Lu , Guangtao Zhai , Ning Liu

Large language model (LLM) agents are increasingly deployed to automate productivity tasks (e.g., email, scheduling, document management), but evaluating them on live services is risky due to potentially irreversible changes. Existing…

Evaluating large language models (LLMs) poses significant challenges, particularly due to issues of data contamination and the leakage of correct answers. To address these challenges, we introduce ThinkBench, a novel evaluation framework…

Computation and Language · Computer Science 2025-02-25 Shulin Huang , Linyi Yang , Yan Song , Shuang Chen , Leyang Cui , Ziyu Wan , Qingcheng Zeng , Ying Wen , Kun Shao , Weinan Zhang , Jun Wang , Yue Zhang

Multi-entity question answering (MEQA) represents significant challenges for large language models (LLM) and retrieval-augmented generation (RAG) systems, which frequently struggle to consolidate scattered information across diverse…

Computation and Language · Computer Science 2025-09-25 Teng Lin , Yuyu Luo , Honglin Zhang , Jicheng Zhang , Chunlin Liu , Kaishun Wu , Nan Tang

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and…

Artificial Intelligence · Computer Science 2026-04-24 Qiang Xu , Shengyuan Bai , Yu Wang , He Cao , Leqing Chen , Yuanyuan Liu , Bin Feng , Zijing Liu , Yu Li

Developing artificial intelligence (AI) for clinical research requires a comprehensive data foundation that supports model training and rigorous evaluation. Here, we introduce TrialPanorama, a large-scale structured resource that aggregates…

Artificial Intelligence · Computer Science 2025-12-17 Zifeng Wang , Jiacheng Lin , Qiao Jin , Junyi Gao , Jathurshan Pradeepkumar , Pengcheng Jiang , Zhiyong Lu , Jimeng Sun

Solving topological grid puzzles requires reasoning over global spatial invariants such as connectivity, loop closure, and region symmetry and remains challenging for even the most powerful large language models (LLMs). To study these…

Artificial Intelligence · Computer Science 2026-03-13 Mayug Maniparambil , Nils Hoehing , Janak Kapuriya , Arjun Karuvally , Ellen Rushe , Anthony Ventresque , Noel O'Connor , Fergal Reid

Advances in generative AI point towards a new era of personalized applications that perform diverse tasks on behalf of users. While general AI assistants have yet to fully emerge, their potential to share personal data raises significant…

Artificial Intelligence · Computer Science 2024-09-24 Zhao Cheng , Diane Wan , Matthew Abueg , Sahra Ghalebikesabi , Ren Yi , Eugene Bagdasarian , Borja Balle , Stefan Mellem , Shawn O'Banion

We introduce PaperBench, a benchmark evaluating the ability of AI agents to replicate state-of-the-art AI research. Agents must replicate 20 ICML 2024 Spotlight and Oral papers from scratch, including understanding paper contributions,…

Recent Large Language Model (LLM)-based AutoML systems demonstrate impressive capabilities but face significant limitations such as constrained exploration strategies and a severe execution bottleneck. Exploration is hindered by one-shot…

Artificial Intelligence · Computer Science 2026-04-24 Stepan Kulibaba , Artem Dzhalilov , Roman Pakhomov , Oleg Svidchenko , Alexander Gasnikov , Aleksei Shpilman

Recent advances in large language models (LLMs) have increased the demand for comprehensive benchmarks to evaluate their capabilities as human-like agents. Existing benchmarks, while useful, often focus on specific application scenarios,…

Deep Research Agents are a prominent category of LLM-based agents. By autonomously orchestrating multistep web exploration, targeted retrieval, and higher-order synthesis, they transform vast amounts of online information into…

Computation and Language · Computer Science 2025-06-16 Mingxuan Du , Benfeng Xu , Chiwei Zhu , Xiaorui Wang , Zhendong Mao

While Large Language Models (LLMs) demonstrate remarkable capabilities in scientific tasks such as literature analysis and experimental design (e.g., accurately extracting key findings from papers or generating coherent experimental…

Computation and Language · Computer Science 2026-02-24 Kai Ruan , Xuan Wang , Jixiang Hong , Peng Wang , Yang Liu , Hao Sun

As large language models (LLMs) become integral to code-related tasks, a central question emerges: Do LLMs truly understand program semantics? We introduce EquiBench, a new benchmark for evaluating LLMs through equivalence checking, i.e.,…

Machine Learning · Computer Science 2025-09-23 Anjiang Wei , Jiannan Cao , Ran Li , Hongyu Chen , Yuhui Zhang , Ziheng Wang , Yuan Liu , Thiago S. F. X. Teixeira , Diyi Yang , Ke Wang , Alex Aiken

Breakthroughs in frontier theory often depend on the combination of concrete diagrammatic notations with rigorous logic. While multimodal large language models (MLLMs) show promise in general scientific tasks, current benchmarks often focus…

Artificial Intelligence · Computer Science 2026-04-07 Zeyu Wang , Xiaogang Li , Peiyao Xiao , Qinhao Kong , Ben Wang , Chengliang Xu , Zichao Chen , Bing Zhao , Hu Wei

Automated red teaming holds substantial promise for uncovering and mitigating the risks associated with the malicious use of large language models (LLMs), yet the field lacks a standardized evaluation framework to rigorously assess new…