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Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face…

Artificial Intelligence · Computer Science 2026-01-16 Kimia Abedini , Farzad Shami , Gianmaria Silvello

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem…

Quantitative Methods · Quantitative Biology 2024-02-22 Hengchuang Yin , Zhonghui Gu , Fanhao Wang , Yiparemu Abuduhaibaier , Yanqiao Zhu , Xinming Tu , Xian-Sheng Hua , Xiao Luo , Yizhou Sun

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose…

Computation and Language · Computer Science 2025-11-25 Yanjun Lyu , Zihao Wu , Lu Zhang , Jing Zhang , Yiwei Li , Wei Ruan , Zhengliang Liu , Zeyu Zhang , Xiang Li , Rongjie Liu , Chao Huang , Wentao Li , Tianming Liu , Dajiang Zhu

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

The widespread adoption of REST APIs, coupled with their growing complexity and size, has led to the need for automated REST API testing tools. Current tools focus on the structured data in REST API specifications but often neglect valuable…

Software Engineering · Computer Science 2024-01-31 Myeongsoo Kim , Tyler Stennett , Dhruv Shah , Saurabh Sinha , Alessandro Orso

Large-scale language models (LLMs) like ChatGPT have demonstrated impressive abilities in generating responses based on human instructions. However, their use in the medical field can be challenging due to their lack of specific, in-depth…

Computation and Language · Computer Science 2025-02-25 Yubo Wang , Xueguang Ma , Wenhu Chen

Despite the rapid progress of Large Language Models (LLMs), their application in agriculture remains limited due to the lack of domain-specific models, curated datasets, and robust evaluation frameworks. To address these challenges, we…

Artificial Intelligence · Computer Science 2025-08-13 Bo Yang , Yu Zhang , Lanfei Feng , Yunkui Chen , Jianyu Zhang , Xiao Xu , Nueraili Aierken , Yurui Li , Yuxuan Chen , Guijun Yang , Yong He , Runhe Huang , Shijian Li

Augmenting large language models (LLMs) with external tools has emerged as a promising approach to solving complex problems. However, traditional methods, which finetune LLMs with tool demonstration data, can be both costly and restricted…

Computation and Language · Computer Science 2024-01-17 Shibo Hao , Tianyang Liu , Zhen Wang , Zhiting Hu

Large language models (LLMs) such as ChatGPT have shown remarkable capabilities in code generation. Despite significant achievements, they rely on enormous training data to acquire a broad spectrum of open-domain knowledge. Besides, their…

Software Engineering · Computer Science 2025-02-18 Xiaodong Gu , Meng Chen , Yalan Lin , Yuhan Hu , Hongyu Zhang , Chengcheng Wan , Zhao Wei , Yong Xu , Juhong Wang

Large language models (LLMs) have shown impressive ability for open-domain NLP tasks. However, LLMs are sometimes too footloose for natural language understanding (NLU) tasks which always have restricted output and input format. Their…

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

Large language models (LLMs) have emerged as powerful tools for medical information retrieval, yet their accuracy and depth remain limited in specialized domains such as Alzheimer's disease (AD), a growing global health challenge. To…

The proliferation of Large Language Models like ChatGPT has significantly advanced language understanding and generation, impacting a broad spectrum of applications. However, these models predominantly excel in text-based tasks, overlooking…

Computation and Language · Computer Science 2023-11-23 Xiao Liu , Jianfeng Lin , Jiawei Zhang

This tutorial explores the advancements and challenges in the development of Large Language Models (LLMs) such as ChatGPT and Gemini. It addresses inherent limitations like temporal knowledge cutoffs, mathematical inaccuracies, and the…

Computation and Language · Computer Science 2024-11-13 Giorgio Roffo

Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage…

Computation and Language · Computer Science 2026-05-08 Xin Gao , Ruiyi Zhang , Meixi Du , Peijia Qin , Pengtao Xie

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to…

Computation and Language · Computer Science 2025-09-11 Fengyu She , Nan Wang , Hongfei Wu , Ziyi Wan , Jingmian Wang , Chang Wang

We present WebGLM, a web-enhanced question-answering system based on the General Language Model (GLM). Its goal is to augment a pre-trained large language model (LLM) with web search and retrieval capabilities while being efficient for…

Computation and Language · Computer Science 2023-06-14 Xiao Liu , Hanyu Lai , Hao Yu , Yifan Xu , Aohan Zeng , Zhengxiao Du , Peng Zhang , Yuxiao Dong , Jie Tang

Large language models (LLMs) often lack specialized knowledge for complex bioinformatics applications. We present a reproducible pipeline for fine-tuning LLMs on specialized bioinformatics data, demonstrated through two use cases: PRSGPT,…

Computation and Language · Computer Science 2026-01-21 Muhammad Muneeb , David B. Ascher

Large-scale language models (LLMs) have emerged as a groundbreaking innovation in the realm of question-answering and conversational agents. These models, leveraging different deep learning architectures such as Transformers, are trained on…

Software Engineering · Computer Science 2023-07-18 Fardin Ahsan Sakib , Saadat Hasan Khan , A. H. M. Rezaul Karim

Tool-augmented large language models (LLMs) have achieved remarkable progress in tackling a broad range of tasks. However, existing methods are mainly restricted to specifically designed tools and fail to fulfill complex instructions,…

Computation and Language · Computer Science 2023-08-29 Yifan Song , Weimin Xiong , Dawei Zhu , Wenhao Wu , Han Qian , Mingbo Song , Hailiang Huang , Cheng Li , Ke Wang , Rong Yao , Ye Tian , Sujian Li
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