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The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and…

Computation and Language · Computer Science 2024-07-16 Biqing Qi , Kaiyan Zhang , Kai Tian , Haoxiang Li , Zhang-Ren Chen , Sihang Zeng , Ermo Hua , Hu Jinfang , Bowen Zhou

Machine reasoning has made great progress in recent years owing to large language models (LLMs). In the clinical domain, however, most NLP-driven projects mainly focus on clinical classification or reading comprehension, and under-explore…

Computation and Language · Computer Science 2024-05-13 Taeyoon Kwon , Kai Tzu-iunn Ong , Dongjin Kang , Seungjun Moon , Jeong Ryong Lee , Dosik Hwang , Yongsik Sim , Beomseok Sohn , Dongha Lee , Jinyoung Yeo

We introduce an explainability method for biomedical hypothesis generation systems, built on top of the novel Hypothesis Generation Context Retriever framework. Our approach combines semantic graph-based retrieval and relevant…

Information Retrieval · Computer Science 2025-11-11 Ilya Tyagin , Saeideh Valipour , Aliaksandra Sikirzhytskaya , Michael Shtutman , Ilya Safro

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of…

In response to the growing complexity and volume of scientific literature, this paper introduces the LLMs4Synthesis framework, designed to enhance the capabilities of Large Language Models (LLMs) in generating high-quality scientific…

Computation and Language · Computer Science 2024-09-30 Hamed Babaei Giglou , Jennifer D'Souza , Sören Auer

The exponential growth of scientific knowledge has created significant barriers to cross-disciplinary knowledge discovery, synthesis and research collaboration. In response to this challenge, we present BioSage, a novel compound AI…

Large Language Models (LLMs) are increasingly adopted for applications in healthcare, reaching the performance of domain experts on tasks such as question answering and document summarisation. Despite their success on these tasks, it is…

Computation and Language · Computer Science 2025-05-20 Aishik Nagar , Viktor Schlegel , Thanh-Tung Nguyen , Hao Li , Yuping Wu , Kuluhan Binici , Stefan Winkler

Understanding and reasoning on the large-scale scientific literature is a crucial touchstone for large language model (LLM) based agents. However, existing works are mainly restricted to tool-free tasks within single papers, largely due to…

Artificial Intelligence · Computer Science 2026-02-02 Daoyu Wang , Mingyue Cheng , Shuo Yu , Zirui Liu , Ze Guo , Xin Li , Qi Liu

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where…

Information Retrieval · Computer Science 2025-04-15 David Brett , Anniek Myatt

Large Language Models (LLMs) have transformed how people interact with artificial intelligence (AI) systems, achieving state-of-the-art results in various tasks, including scientific discovery and hypothesis generation. However, the lack of…

Computation and Language · Computer Science 2024-11-06 Sikun Guo , Amir Hassan Shariatmadari , Guangzhi Xiong , Albert Huang , Eric Xie , Stefan Bekiranov , Aidong Zhang

The biomedical field relies heavily on concept linking in various areas such as literature mining, graph alignment, information retrieval, question-answering, data, and knowledge integration. Although large language models (LLMs) have made…

Computation and Language · Computer Science 2023-07-04 Qinyong Wang , Zhenxiang Gao , Rong Xu

Large language models (LLMs) are in the ascendancy for research in drug discovery, offering unprecedented opportunities to reshape drug research by accelerating hypothesis generation, optimizing candidate prioritization, and enabling more…

Machine Learning · Computer Science 2026-04-06 Tianyu Liu , Sihan Jiang , Fan Zhang , Kunyang Sun , Teresa Head-Gordon , Hongyu Zhao

Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…

Genomics · Quantitative Biology 2024-12-25 Zhijian Chen , Chuan Hu , Min Wu , Qingqing Long , Xuezhi Wang , Yuanchun Zhou , Meng Xiao

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to…

Multiagent Systems · Computer Science 2025-07-08 Yi Luo , Linghang Shi , Yihao Li , Aobo Zhuang , Yeyun Gong , Ling Liu , Chen Lin

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…

Computation and Language · Computer Science 2024-05-06 Mingchen Li , Halil Kilicoglu , Hua Xu , Rui Zhang

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and…

Computation and Language · Computer Science 2025-09-03 Ailing Yu , Lan Yao , Jingnan Liu , Zhe Chen , Jiajun Yin , Yuan Wang , Xinhao Liao , Zhiling Ye , Ji Li , Yun Yue , Hansong Xiao , Hualei Zhou , Chunxiao Guo , Peng Wei , Junwei Liu , Jinjie Gu

Large Language Models (LLMs) have exhibited impressive generation capabilities, but they suffer from hallucinations when solely relying on their internal knowledge, especially when answering questions that require less commonly known…

Computation and Language · Computer Science 2023-11-01 Wenting Zhao , Ye Liu , Tong Niu , Yao Wan , Philip S. Yu , Shafiq Joty , Yingbo Zhou , Semih Yavuz

Large language models (LLMs) have emerged as transformative tools in medicine, with strong capabilities in language understanding, reasoning, and structured information extraction. Radiation oncology is particularly well suited for LLM…

This research paper discusses the advances made in the past decade in biomedicine and Large Language Models. To understand how the advances have been made hand-in-hand with one another, the paper also discusses the integration of Natural…

Computation and Language · Computer Science 2024-06-26 Michael Ackerman