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Genomic question answering often requires complex reasoning and integration across diverse biomedical sources. GeneGPT addressed this challenge by combining domain-specific APIs with OpenAI's code-davinci-002 large language model to enable…

Artificial Intelligence · Computer Science 2025-11-20 Haodong Chen , Guido Zuccon , Teerapong Leelanupab

Creating end-to-end bioinformatics workflows requires diverse domain expertise, which poses challenges for both junior and senior researchers as it demands a deep understanding of both genomics concepts and computational techniques. While…

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise…

Computation and Language · Computer Science 2024-04-10 Qiao Jin , Yifan Yang , Qingyu Chen , Zhiyong Lu

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject…

Artificial Intelligence · Computer Science 2024-05-28 Zhizheng Wang , Qiao Jin , Chih-Hsuan Wei , Shubo Tian , Po-Ting Lai , Qingqing Zhu , Chi-Ping Day , Christina Ross , Zhiyong Lu

Emerging 6G networks rely on complex cross-layer optimization, yet manually translating high-level intents into mathematical formulations remains a bottleneck. While Large Language Models (LLMs) offer promise, monolithic approaches often…

Artificial Intelligence · Computer Science 2026-01-28 Haoyun Li , Ming Xiao , Kezhi Wang , Robert Schober , Dong In Kim , Yong Liang Guan

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the…

Computation and Language · Computer Science 2024-07-23 Ling Yue , Sixue Xing , Jintai Chen , Tianfan Fu

Recent advancements in machine learning have significantly improved the identification of disease-associated genes from gene expression datasets. However, these processes often require extensive expertise and manual effort, limiting their…

Machine Learning · Computer Science 2025-04-09 Haoyang Liu , Shuyu Chen , Ye Zhang , Haohan Wang

Large language models (LLMs) excel at natural language tasks but are limited by their static parametric knowledge, especially in knowledge-intensive task. Retrieval-augmented generation (RAG) mitigates this by integrating external…

Artificial Intelligence · Computer Science 2025-10-10 Yi Jiang , Lei Shen , Lujie Niu , Sendong Zhao , Wenbo Su , Bo Zheng

Advancements in large language models (LLMs) allow them to address diverse questions using human-like interfaces. Still, limitations in their training prevent them from answering accurately in scenarios that could benefit from multiple…

Artificial Intelligence · Computer Science 2025-04-09 Yoshitaka Inoue , Tianci Song , Xinling Wang , Augustin Luna , Tianfan Fu

Large language models (LLMs) show promise for healthcare question answering, but clinical use is limited by weak verification, insufficient evidence grounding, and unreliable confidence signalling. We propose a multi-agent medical QA…

Computation and Language · Computer Science 2026-02-17 Naeimeh Nourmohammadi , Md Meem Hossain , The Anh Han , Safina Showkat Ara , Zia Ush Shamszaman

Retrieval-Augmented Generation (RAG) enhances Large Language Models (LLMs) by incorporating external, domain-specific data into the generative process. While LLMs are highly capable, they often rely on static, pre-trained datasets, limiting…

Artificial Intelligence · Computer Science 2024-12-10 Aniruddha Salve , Saba Attar , Mahesh Deshmukh , Sayali Shivpuje , Arnab Mitra Utsab

Large Language Models (LLMs) excel in traditional natural language processing tasks but struggle with problems that require complex domain-specific calculations or simulations. While equipping LLMs with external tools to build LLM-based…

Software Engineering · Computer Science 2025-06-11 Bohan Lyu , Xin Cong , Heyang Yu , Pan Yang , Yujia Qin , Yining Ye , Yaxi Lu , Zhong Zhang , Yukun Yan , Yankai Lin , Zhiyuan Liu , Maosong Sun

In this paper, we aim to improve the reasoning ability of large language models (LLMs) over knowledge graphs (KGs) to answer complex questions. Inspired by existing methods that design the interaction strategy between LLMs and KG, we…

Computation and Language · Computer Science 2024-02-20 Jinhao Jiang , Kun Zhou , Wayne Xin Zhao , Yang Song , Chen Zhu , Hengshu Zhu , Ji-Rong Wen

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…

Recent progress in Large Language Models (LLMs) has drawn attention to their potential for accelerating drug discovery. However, a central problem remains: translating theoretical ideas into robust implementations in the highly specialized…

Machine Learning · Computer Science 2025-03-06 Sizhe Liu , Yizhou Lu , Siyu Chen , Xiyang Hu , Jieyu Zhao , Yingzhou Lu , Yue Zhao

We introduce GenAgent, unifying visual understanding and generation through an agentic multimodal model. Unlike unified models that face expensive training costs and understanding-generation trade-offs, GenAgent decouples these capabilities…

Computer Vision and Pattern Recognition · Computer Science 2026-01-29 Kaixun Jiang , Yuzheng Wang , Junjie Zhou , Pandeng Li , Zhihang Liu , Chen-Wei Xie , Zhaoyu Chen , Yun Zheng , Wenqiang Zhang

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

In this paper, we present a novel framework for enhancing the capabilities of large language models (LLMs) by leveraging the power of multi-agent systems. Our framework introduces a collaborative environment where multiple intelligent agent…

Artificial Intelligence · Computer Science 2023-06-07 Yashar Talebirad , Amirhossein Nadiri

Driven by curiosity, humans have continually sought to explore and understand the world around them, leading to the invention of various tools to satiate this inquisitiveness. Despite not having the capacity to process and memorize vast…

Artificial Intelligence · Computer Science 2024-01-11 Haojie Pan , Zepeng Zhai , Hao Yuan , Yaojia Lv , Ruiji Fu , Ming Liu , Zhongyuan Wang , Bing Qin

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling…

Computation and Language · Computer Science 2025-01-14 Xiangru Tang , Tianyu Hu , Muyang Ye , Yanjun Shao , Xunjian Yin , Siru Ouyang , Wangchunshu Zhou , Pan Lu , Zhuosheng Zhang , Yilun Zhao , Arman Cohan , Mark Gerstein
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