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As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry…

计算与语言 · 计算机科学 2024-02-21 Yin Fang , Kangwei Liu , Ningyu Zhang , Xinle Deng , Penghui Yang , Zhuo Chen , Xiangru Tang , Mark Gerstein , Xiaohui Fan , Huajun Chen

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex…

计算与语言 · 计算机科学 2024-12-05 Junhao Liu , Siwei Xu , Lei Zhang , Jing Zhang

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…

计算与语言 · 计算机科学 2025-10-10 Krinos Li , Xianglu Xiao , Shenglong Deng , Lucas He , Zijun Zhong , Yuanjie Zou , Zhonghao Zhan , Zheng Hui , Weiye Bao , Guang Yang

Recent studies have demonstrated the feasibility of modeling single-cell data as natural languages and the potential of leveraging powerful large language models (LLMs) for understanding cell biology. However, a comprehensive evaluation of…

定量方法 · 定量生物学 2025-05-14 Fan Zhang , Tianyu Liu , Zhihong Zhu , Hao Wu , Haixin Wang , Donghao Zhou , Yefeng Zheng , Kun Wang , Xian Wu , Pheng-Ann Heng

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a…

计算与语言 · 计算机科学 2025-10-21 Ming Hu , Chenglong Ma , Wei Li , Wanghan Xu , Jiamin Wu , Jucheng Hu , Tianbin Li , Guohang Zhuang , Jiaqi Liu , Yingzhou Lu , Ying Chen , Chaoyang Zhang , Cheng Tan , Jie Ying , Guocheng Wu , Shujian Gao , Pengcheng Chen , Jiashi Lin , Haitao Wu , Lulu Chen , Fengxiang Wang , Yuanyuan Zhang , Xiangyu Zhao , Feilong Tang , Encheng Su , Junzhi Ning , Xinyao Liu , Ye Du , Changkai Ji , Pengfei Jiang , Cheng Tang , Ziyan Huang , Jiyao Liu , Jiaqi Wei , Yuejin Yang , Xiang Zhang , Guangshuai Wang , Yue Yang , Huihui Xu , Ziyang Chen , Yizhou Wang , Chen Tang , Jianyu Wu , Yuchen Ren , Siyuan Yan , Zhonghua Wang , Zhongxing Xu , Shiyan Su , Shangquan Sun , Runkai Zhao , Zhisheng Zhang , Dingkang Yang , Jinjie Wei , Jiaqi Wang , Jiahao Xu , Jiangtao Yan , Wenhao Tang , Hongze Zhu , Yu Liu , Fudi Wang , Yiqing Shen , Yuanfeng Ji , Yanzhou Su , Tong Xie , Hongming Shan , Chun-Mei Feng , Zhi Hou , Diping Song , Lihao Liu , Yanyan Huang , Lequan Yu , Bin Fu , Shujun Wang , Xiaomeng Li , Xiaowei Hu , Yun Gu , Ben Fei , Benyou Wang , Yuewen Cao , Minjie Shen , Jie Xu , Haodong Duan , Fang Yan , Hongxia Hao , Jielan Li , Jiajun Du , Yanbo Wang , Imran Razzak , Zhongying Deng , Chi Zhang , Lijun Wu , Conghui He , Zhaohui Lu , Jinhai Huang , Wenqi Shao , Yihao Liu , Siqi Luo , Yi Xin , Xiaohong Liu , Fenghua Ling , Yuqiang Li , Aoran Wang , Siqi Sun , Qihao Zheng , Nanqing Dong , Tianfan Fu , Dongzhan Zhou , Yan Lu , Wenlong Zhang , Jin Ye , Jianfei Cai , Yirong Chen , Wanli Ouyang , Yu Qiao , Zongyuan Ge , Shixiang Tang , Junjun He , Chunfeng Song , Lei Bai , Bowen Zhou

Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life…

基因组学 · 定量生物学 2024-12-25 Cong Li , Qingqing Long , Yuanchun Zhou , Meng Xiao

The pursuit of human-level artificial intelligence (AI) has significantly advanced the development of autonomous agents and Large Language Models (LLMs). LLMs are now widely utilized as decision-making agents for their ability to interpret…

Empirical grammar research has become increasingly data-driven, but the systematic analysis of annotated corpora still requires substantial methodological and technical effort. We explore how agentic large language models (LLMs) can…

计算与语言 · 计算机科学 2025-12-02 Matej Klemen , Tjaša Arčon , Luka Terčon , Marko Robnik-Šikonja , Kaja Dobrovoljc

Evaluating large language models (LLM) in clinical scenarios is crucial to assessing their potential clinical utility. Existing benchmarks rely heavily on static question-answering, which does not accurately depict the complex, sequential…

人机交互 · 计算机科学 2025-05-27 Samuel Schmidgall , Rojin Ziaei , Carl Harris , Eduardo Reis , Jeffrey Jopling , Michael Moor

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. Driven by the growing need for standardized evaluation and integration, we…

人工智能 · 计算机科学 2026-03-10 Mohamed Amine Ferrag , Norbert Tihanyi , Merouane Debbah

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs…

人工智能 · 计算机科学 2026-02-27 Jiahao Zhao , Feng Jiang , Shaowei Qin , Zhonghui Zhang , Junhao Liu , Guibing Guo , Hamid Alinejad-Rokny , Min Yang

Objective: To demonstrate the capabilities of Large Language Models (LLMs) as autonomous agents to reproduce findings of published research studies using the same or similar dataset. Materials and Methods: We used the "Quick Access" dataset…

计算与语言 · 计算机科学 2025-06-02 Nic Dobbins , Christelle Xiong , Kristine Lan , Meliha Yetisgen

Artificial Intelligence is moving from models that only generate text to Agentic AI, where systems behave as autonomous entities that can perceive, reason, plan, and act. Large Language Models (LLMs) are no longer used only as passive…

人工智能 · 计算机科学 2026-01-21 Arunkumar V , Gangadharan G. R. , Rajkumar Buyya

The evolution of Large Language Models (LLMs) from passive text generators to autonomous, goal-driven systems represents a fundamental shift in artificial intelligence. This chapter examines the emergence of agentic AI systems that…

人工智能 · 计算机科学 2026-01-07 Nadia Sibai , Yara Ahmed , Serry Sibaee , Sawsan AlHalawani , Adel Ammar , Wadii Boulila

Reasoning is a fundamental cognitive process underlying inference, problem-solving, and decision-making. While large language models (LLMs) demonstrate strong reasoning capabilities in closed-world settings, they struggle in open-ended and…

With the recent emergence of revolutionary autonomous agentic systems, research community is witnessing a significant shift from traditional static, passive, and domain-specific AI agents toward more dynamic, proactive, and generalizable…

计算机视觉与模式识别 · 计算机科学 2025-10-14 Huanjin Yao , Ruifei Zhang , Jiaxing Huang , Jingyi Zhang , Yibo Wang , Bo Fang , Ruolin Zhu , Yongcheng Jing , Shunyu Liu , Guanbin Li , Dacheng Tao

This scoping review examines the emerging field of Large Language Model (LLM)-based pedagogical agents in educational settings. While traditional pedagogical agents have been extensively studied, the integration of LLMs represents a…

人工智能 · 计算机科学 2026-05-19 Shan Li , Juan Zheng

Large Language Models (LLMs) possess substantial reasoning capabilities and are increasingly applied to optimization tasks, particularly in synergy with evolutionary computation. However, while recent surveys have explored specific aspects…

神经与进化计算 · 计算机科学 2026-01-08 Yisong Zhang , Ran Cheng , Guoxing Yi , Kay Chen Tan

The era of intelligent agents is upon us, driven by revolutionary advancements in large language models. Large Language Model (LLM) agents, with goal-driven behaviors and dynamic adaptation capabilities, potentially represent a critical…

As large language models (LLMs) transition from static tools to fully agentic systems, their potential for transforming social science research has become increasingly evident. This paper introduces a structured framework for understanding…

多智能体系统 · 计算机科学 2026-05-19 Jennifer Haase , Sebastian Pokutta
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