English
Related papers

Related papers: BioAgents: Democratizing Bioinformatics Analysis w…

200 papers

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

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of…

Quantitative Methods · Quantitative Biology 2025-02-04 Jiajia Liu , Mengyuan Yang , Yankai Yu , Haixia Xu , Tiangang Wang , Kang Li , Xiaobo Zhou

Large language model (LLM)-based multi-agent systems (MAS) have demonstrated exceptional capabilities in solving complex tasks, yet their effectiveness depends heavily on the underlying communication topology that coordinates agent…

Machine Learning · Computer Science 2026-03-23 Hongjiang Chen , Xin Zheng , Yixin Liu , Pengfei Jiao , Shiyuan Li , Huan Liu , Zhidong Zhao , Ziqi Xu , Ibrahim Khalil , Shirui Pan

The global demand for sustainable protein sources has accelerated the need for intelligent tools that can rapidly process and synthesise domain-specific scientific knowledge. In this study, we present a proof-of-concept multi-agent…

Artificial Intelligence · Computer Science 2025-06-26 Alexander D. Kalian , Jaewook Lee , Stefan P. Johannesson , Lennart Otte , Christer Hogstrand , Miao Guo

Large language model (LLM)-based multi-agent systems (MASs) are a recent but rapidly evolving technology with the potential to transform chemical engineering by decomposing complex workflows into teams of collaborative agents with…

Multiagent Systems · Computer Science 2025-08-12 Sophia Rupprecht , Qinghe Gao , Tanuj Karia , Artur M. Schweidtmann

Knowledge-intensive conversations supported by large language models (LLMs) have become one of the most popular and helpful applications that can assist people in different aspects. Many current knowledge-intensive applications are centered…

Artificial Intelligence · Computer Science 2025-02-14 Zitao Li , Fei Wei , Yuexiang Xie , Dawei Gao , Weirui Kuang , Zhijian Ma , Bingchen Qian , Yaliang Li , Bolin Ding

Large Language Model (LLM) agents, acting on their users' behalf to manipulate and analyze data, are likely to become the dominant workload for data systems in the future. When working with data, agents employ a high-throughput process of…

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…

Large language models (LLMs) are widely used in retrieval-augmented generation (RAG) to incorporate external knowledge at inference time. However, when retrieved contexts are noisy, incomplete, or heterogeneous, a single generation process…

Computation and Language · Computer Science 2026-04-22 Xingchen Xiao , Heyan Huang , Runheng Liu , Jincheng Xie

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,…

While contemporary large language models (LLMs) are increasingly capable in isolation, there are still many difficult problems that lie beyond the abilities of a single LLM. For such tasks, there is still uncertainty about how best to take…

Artificial Intelligence · Computer Science 2026-02-27 Ryan Liu , Dilip Arumugam , Cedegao E. Zhang , Sean Escola , Xaq Pitkow , Thomas L. Griffiths

We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. Rather than taking…

Long-horizon large language model (LLM) agents are fundamentally limited by context. As interactions become longer, tool descriptions, retrieved memories, and raw environmental feedback accumulate and push out the information needed for…

This paper surveys the development of large language model (LLM)-based agents for question answering (QA). Traditional agents face significant limitations, including substantial data requirements and difficulty in generalizing to new…

Computation and Language · Computer Science 2025-03-26 Murong Yue

To improve the reasoning and question-answering capabilities of Large Language Models (LLMs), several multi-agent approaches have been introduced. While these methods enhance performance, the application of collective intelligence-based…

Artificial Intelligence · Computer Science 2024-07-10 Ciaran Regan , Alexandre Gournail , Mizuki Oka

Drug discovery is a complex, multi-step pipeline that remains heavily dependent on manual, experience-driven operations; meanwhile, existing customized artificial intelligence tools are fragmented across web applications, desktop software,…

Biomolecules · Quantitative Biology 2026-03-03 Qihua Pan , Dong Xu , Qianwei Yang , Jenna Xinyi Yao , Sisi Yuan , Zexuan Zhu , Jianqiang Li , Junkai Ji

There are two main barriers to using large language models (LLMs) in clinical reasoning. Firstly, while LLMs exhibit significant promise in Natural Language Processing (NLP) tasks, their performance in complex reasoning and planning falls…

Artificial Intelligence · Computer Science 2024-12-31 Shengxin Hong , Liang Xiao , Xin Zhang , Jianxia Chen

Graphical User Interface (GUI) agents possess significant commercial and social value, and GUI agents powered by advanced multimodal large language models (MLLMs) have demonstrated remarkable potential. Currently, existing GUI agents…

Artificial Intelligence · Computer Science 2025-09-05 Weizhi Chen , Ziwei Wang , Leyang Yang , Sheng Zhou , Xiaoxuan Tang , Jiajun Bu , Yong Li , Wei Jiang

Large Language Model (LLM)-empowered multi-agent systems extend the cognitive boundaries of individual agents through disciplined collaboration and interaction, while constructing these systems often requires labor-intensive manual designs.…

Machine Learning · Computer Science 2025-06-10 Guibin Zhang , Luyang Niu , Junfeng Fang , Kun Wang , Lei Bai , Xiang Wang

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding…

Artificial Intelligence · Computer Science 2026-01-28 Lukas Weidener , Marko Brkić , Mihailo Jovanović , Ritvik Singh , Chiara Baccin , Emre Ulgac , Alex Dobrin , Aakaash Meduri