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As Large Language Models (LLMs) become ubiquitous across various scientific domains, their lack of ability to perform complex tasks like running simulations or to make complex decisions limits their utility. LLM-based agents bridge this gap…

Computation and Language · Computer Science 2026-01-21 Anurag Acharya , Timothy Vega , Rizwan A. Ashraf , Anshu Sharma , Derek Parker , Robert Rallo

Large Language Models (LLMs) have emerged as powerful tools for accelerating scientific discovery, yet their static knowledge and hallucination issues hinder autonomous research applications. Recent advances integrate LLMs into agentic…

Artificial Intelligence · Computer Science 2025-12-23 Zeyu Xia , Jinzhe Ma , Congjie Zheng , Shufei Zhang , Yuqiang Li , Hang Su , P. Hu , Changshui Zhang , Xingao Gong , Wanli Ouyang , Lei Bai , Dongzhan Zhou , Mao Su

Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug…

Artificial Intelligence · Computer Science 2025-12-12 Salomé Guilbert , Cassandra Masschelein , Jeremy Goumaz , Bohdan Naida , Philippe Schwaller

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers,…

Computation and Language · Computer Science 2025-06-02 Georg Wölflein , Dyke Ferber , Daniel Truhn , Ognjen Arandjelović , Jakob Nikolas Kather

The automation of scientific discovery represents a critical milestone in Artificial Intelligence (AI) research. However, existing agentic systems for science suffer from two fundamental limitations: rigid, pre-programmed workflows that…

Artificial Intelligence · Computer Science 2025-10-20 Ed Li , Junyu Ren , Xintian Pan , Cat Yan , Chuanhao Li , Dirk Bergemann , Zhuoran Yang

Scientific workflow systems automate execution -- scheduling, fault tolerance, resource management -- but not the semantic translation that precedes it. Scientists still manually convert research questions into workflow specifications, a…

Artificial Intelligence · Computer Science 2026-04-24 Bartosz Balis , Michal Orzechowski , Piotr Kica , Michal Dygas , Michal Kuszewski

Autonomous data science, from raw data sources to analyst-grade deep research reports, has been a long-standing challenge, and is now becoming feasible with the emergence of powerful large language models (LLMs). Recent workflow-based data…

Artificial Intelligence · Computer Science 2025-10-21 Shaolei Zhang , Ju Fan , Meihao Fan , Guoliang Li , Xiaoyong Du

Automatic research with Large Language Models (LLMs) is rapidly gaining importance, driving the development of increasingly complex workflows involving multi-agent systems, planning, tool usage, code execution, and human-agent interaction…

Computation and Language · Computer Science 2025-10-09 Haofei Yu , Keyang Xuan , Fenghai Li , Kunlun Zhu , Zijie Lei , Jiaxun Zhang , Ziheng Qi , Kyle Richardson , Jiaxuan You

Large language models (LLMs) excel at solving complex tasks by executing agentic workflows composed of detailed instructions and structured operations. Yet, building general-purpose agents by manually embedding foundation models into…

Artificial Intelligence · Computer Science 2025-08-08 Chia-Tung Ho , Jing Gong , Xufeng Yao , Yunsheng Bai , Abhishek B Akkur , Haoxing Ren

Agent systems based on large language models (LLMs) have shown great potential in complex reasoning tasks, but building efficient and generalizable workflows remains a major challenge. Most existing approaches rely on manually designed…

Computation and Language · Computer Science 2025-10-01 Yanbo Wang , Zixiang Xu , Yue Huang , Xiangqi Wang , Zirui Song , Lang Gao , Chenxi Wang , Xiangru Tang , Yue Zhao , Arman Cohan , Xiangliang Zhang , Xiuying Chen

Large Language Model (LLM)-based agents have demonstrated strong capabilities across a wide range of tasks, and their application in the medical domain holds particular promise due to the demand for high generalizability and reliance on…

Artificial Intelligence · Computer Science 2025-08-18 Yangyang Zhuang , Wenjia Jiang , Jiayu Zhang , Ze Yang , Joey Tianyi Zhou , Chi Zhang

Developing machine learning interatomic potentials (MLIPs) for complex materials systems remains challenging because it requires expertise in atomistic simulations, machine learning, and workflow design, as well as iterative active learning…

Machine Learning · Computer Science 2026-05-15 Wenwen Li , Yuki Orimo , Nontawat Charoenphakdee

Large language models (LLMs) are increasingly deployed as agents, expected to decompose goals, invoke tools, and verify results in dynamic environments. Realizing these capabilities requires access to agentic data-structured interaction…

Artificial Intelligence · Computer Science 2025-10-22 Abhigya Verma , Seganrasan Subramanian , Nandhakumar Kandasamy , Naman Gupta

Recent advances in agentic AI have enabled increasingly autonomous workflows, but existing systems still face substantial challenges in achieving reliable deployment in real-world scientific research. In this work, we present a safe,…

Artificial Intelligence · Computer Science 2026-04-16 Qibin Liu , Julia Gonski

Our paper introduces a generative, multiagent AI framework designed to overcome the rigidity, limited flexibility and technical barriers of current bibliometric tools. The objective is to enable researchers to perform fully dynamic,…

Digital Libraries · Computer Science 2026-04-29 Adela Bara , Simona-Vasilica Oprea

Corpus distillation for biomedical large language models (LLMs) seeks to address the pressing challenge of insufficient quantity and quality in open-source annotated scientific corpora, which remains a bottleneck for effective LLM training…

Computation and Language · Computer Science 2025-12-19 Meng Xiao , Xunxin Cai , Qingqing Long , Chengrui Wang , Yuanchun Zhou , Hengshu Zhu

The emergence of LLMs has catalyzed a paradigm shift in autonomous agent development, enabling systems capable of reasoning, planning, and executing complex multi-step tasks. However, existing agent frameworks often suffer from…

Artificial Intelligence · Computer Science 2026-01-21 Akbar Anbar Jafari , Cagri Ozcinar , Gholamreza Anbarjafari

Recent advances in large language models (LLMs) have enabled a new class of AI agents that automate multiple stages of the data science workflow by integrating planning, tool use, and multimodal reasoning across text, code, tables, and…

Drug discovery frequently loses momentum when data, expertise, and tools are scattered, slowing design cycles. To shorten this loop we built a hierarchical, tool using agent framework that automates molecular optimisation. A Principal…

Machine Learning · Computer Science 2025-08-06 Atabey Ünlü , Phil Rohr , Ahmet Celebi

Agentic AI systems integrating large language models (LLMs) with reasoning and tooluse capabilities are transforming various domains - in particular, software development. In contrast, their application in chemical process flowsheet…

Artificial Intelligence · Computer Science 2026-03-16 Pascal Schäfer , Lukas J. Krinke , Martin Wlotzka , Norbert Asprion
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