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Rapid advancements in imaging techniques and analytical methods over the past decade have revolutionized our ability to comprehensively probe the biological world at multiple scales, pinpointing the type, quantity, location, and even…

Artificial Intelligence · Computer Science 2025-10-02 Shanghang Zhang , Gaole Dai , Tiejun Huang , Jianxu Chen

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…

Artificial Intelligence · Computer Science 2026-02-03 Shuo Ren , Can Xie , Pu Jian , Zhenjiang Ren , Chunlin Leng , Jiajun Zhang

We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large…

Multi-agent language systems are often built as hand-designed workflows, where agents are assigned semantic roles and communication protocols are specified in advance. We propose NeuroMAS, a method that first treats a multi-agent language…

Artificial Intelligence · Computer Science 2026-05-19 Haoran Lu , Luyang Fang , Wenxuan Zhong , Ping Ma

Transformer-based large language models are rapidly advancing in the field of machine learning research, with applications spanning natural language, biology, chemistry, and computer programming. Extreme scaling and reinforcement learning…

Chemical Physics · Physics 2023-04-12 Daniil A. Boiko , Robert MacKnight , Gabe Gomes

To fully expedite AI-powered chemical research, high-quality chemical databases are the foundation. Automatic extraction of chemical information from the literature is essential for constructing reaction databases, but it is currently…

Artificial Intelligence · Computer Science 2026-03-09 Yufan Chen , Ching Ting Leung , Bowen Yu , Jianwei Sun , Yong Huang , Linyan Li , Hao Chen , Hanyu Gao

Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…

Computation and Language · Computer Science 2025-10-10 Krinos Li , Xianglu Xiao , Shenglong Deng , Lucas He , Zijun Zhong , Yuanjie Zou , Zhonghao Zhan , Zheng Hui , Weiye Bao , Guang Yang

The adoption of machine learning (ML) and deep learning methods has revolutionized molecular medicine by driving breakthroughs in genomics, transcriptomics, drug discovery, and biological systems modeling. The increasing quantity,…

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

This paper introduces Agent-Based Auto Research, a structured multi-agent framework designed to automate, coordinate, and optimize the full lifecycle of scientific research. Leveraging the capabilities of large language models (LLMs) and…

Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…

Quantitative Methods · Quantitative Biology 2025-10-03 Ching-Huei Tsou , Michal Ozery-Flato , Ella Barkan , Diwakar Mahajan , Ben Shapira

Computing has long served as a cornerstone of scientific discovery. Recently, a paradigm shift has emerged with the rise of large language models (LLMs), introducing autonomous systems, referred to as agents, that accelerate discovery…

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…

Biological laboratory automation can reduce repetitive manual work and improve reproducibility, but reliable embodied execution in wet-lab environments remains challenging. Protocols are often unstructured, labware is frequently transparent…

Robotics · Computer Science 2026-05-11 Zhaohui Du , Zhe Wang , Hongmei Fei , Xiwen Cao , Ting Xiao , Qi Wang , Huanbo Jin , Jiaming Gu , Quan Lu , Zhe Liu

Recent advancements in multimodal large language models and vision-languageaction models have significantly driven progress in Embodied AI. As the field transitions toward more complex task scenarios, multi-agent system frameworks are…

The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges.…

Artificial Intelligence · Computer Science 2025-10-01 Gihan Panapitiya , Emily Saldanha , Heather Job , Olivia Hess

Agent-based modeling (ABM) is a well-established paradigm for simulating complex systems via interactions between constituent entities. Machine learning (ML) refers to approaches whereby statistical algorithms 'learn' from data on their…

Quantitative Methods · Quantitative Biology 2022-11-10 Nikita Sivakumar , Cameron Mura , Shayn M. Peirce

The integration of large language models (LLMs) into materials science offers a transformative opportunity to streamline computational workflows, yet current agentic systems remain constrained by rigid, carefully crafted domain-specific…

Materials Science · Physics 2026-04-08 Fengxu Yang , Jack D. Evans

We present a refined approach to biomedical question-answering (QA) services by integrating large language models (LLMs) with Multi-BERT configurations. By enhancing the ability to process and prioritize vast amounts of complex biomedical…

Computation and Language · Computer Science 2024-10-18 Cheng Qian , Xianglong Shi , Shanshan Yao , Yichen Liu , Fengming Zhou , Zishu Zhang , Junaid Akram , Ali Braytee , Ali Anaissi

Intelligent agents stand out as a potential path toward artificial general intelligence (AGI). Thus, researchers have dedicated significant effort to diverse implementations for them. Benefiting from recent progress in large language models…

Artificial Intelligence · Computer Science 2024-01-09 Yuheng Cheng , Ceyao Zhang , Zhengwen Zhang , Xiangrui Meng , Sirui Hong , Wenhao Li , Zihao Wang , Zekai Wang , Feng Yin , Junhua Zhao , Xiuqiang He