English
Related papers

Related papers: ProtChatGPT: Towards Understanding Proteins with L…

200 papers

Large Language Models (LLMs) have demonstrated exceptional natural language understanding abilities and have excelled in a variety of natural language processing (NLP)tasks in recent years. Despite the fact that most LLMs are trained…

Computation and Language · Computer Science 2023-10-25 Xiang Zhang , Senyu Li , Bradley Hauer , Ning Shi , Grzegorz Kondrak

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…

Large language models, pivotal in artificial intelligence, find diverse applications. ChatGPT (Chat Generative Pre-trained Transformer), an OpenAI creation, stands out as a widely adopted, powerful tool. It excels in chatbots, content…

Computation and Language · Computer Science 2025-05-28 Walid Hariri

Logical reasoning is a fundamental aspect of human intelligence and a key component of tasks like problem-solving and decision-making. Recent advancements have enabled Large Language Models (LLMs) to potentially exhibit reasoning…

Computation and Language · Computer Science 2023-11-13 Jiazhan Feng , Ruochen Xu , Junheng Hao , Hiteshi Sharma , Yelong Shen , Dongyan Zhao , Weizhu Chen

Since the launch of ChatGPT, a powerful AI Chatbot developed by OpenAI, large language models (LLMs) have made significant advancements in both academia and industry, bringing about a fundamental engineering paradigm shift in many areas.…

Software Engineering · Computer Science 2023-11-22 Xiaoxia Liu , Jingyi Wang , Jun Sun , Xiaohan Yuan , Guoliang Dong , Peng Di , Wenhai Wang , Dongxia Wang

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated.…

Quantitative Methods · Quantitative Biology 2025-12-30 Dingyi Rong , Zijian Chen , Qi Jia , Kaiwei Zhang , Haotian Lu , Guangtao Zhai , Ning Liu

Large Language Models (LLM) have become sophisticated enough that complex computer programs can be created through interpretation of plain English sentences and implemented in a variety of modern languages such as Python, Java Script, C++…

Software Engineering · Computer Science 2023-09-04 Simon Thorne

Large language models (LLMs) have made significant progress in NLP. However, their ability to memorize, represent, and leverage commonsense knowledge has been a well-known pain point. In this paper, we specifically focus on ChatGPT, a…

Computation and Language · Computer Science 2024-04-22 Ning Bian , Xianpei Han , Le Sun , Hongyu Lin , Yaojie Lu , Ben He , Shanshan Jiang , Bin Dong

This paper introduces DevGPT, a dataset curated to explore how software developers interact with ChatGPT, a prominent large language model (LLM). The dataset encompasses 29,778 prompts and responses from ChatGPT, including 19,106 code…

Software Engineering · Computer Science 2024-02-15 Tao Xiao , Christoph Treude , Hideaki Hata , Kenichi Matsumoto

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

Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key…

Computational Engineering, Finance, and Science · Computer Science 2026-05-29 Yi Zhou , Haohao Qu , Yunqing Liu , Shanru Lin , Le Song , Wenqi Fan

The use of large language models (LLMs) in natural language processing (NLP) tasks is rapidly increasing, leading to changes in how researchers approach problems in the field. To fully utilize these models' abilities, a better understanding…

Computation and Language · Computer Science 2023-11-07 Bishal Santra , Sakya Basak , Abhinandan De , Manish Gupta , Pawan Goyal

Multimodal large language models (MLLMs) have shown remarkable performance in vision-language tasks. However, existing MLLMs are primarily trained on generic datasets, limiting their ability to reason on domain-specific visual cues such as…

Computer Vision and Pattern Recognition · Computer Science 2025-07-15 Hatef Otroshi Shahreza , Sébastien Marcel

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…

Machine Learning · Computer Science 2023-01-04 Lirong Wu , Yufei Huang , Haitao Lin , Stan Z. Li

Prompt engineering has emerged as an indispensable technique for extending the capabilities of large language models (LLMs) and vision-language models (VLMs). This approach leverages task-specific instructions, known as prompts, to enhance…

Artificial Intelligence · Computer Science 2025-03-18 Pranab Sahoo , Ayush Kumar Singh , Sriparna Saha , Vinija Jain , Samrat Mondal , Aman Chadha

This paper presents a comprehensive and practical guide for practitioners and end-users working with Large Language Models (LLMs) in their downstream natural language processing (NLP) tasks. We provide discussions and insights into the…

Computation and Language · Computer Science 2023-04-28 Jingfeng Yang , Hongye Jin , Ruixiang Tang , Xiaotian Han , Qizhang Feng , Haoming Jiang , Bing Yin , Xia Hu

This paper investigates the performance of the Large Language Models (LLMs) ChatGPT-3.5 and GPT-4 in solving introductory programming tasks. Based on the performance, implications for didactic scenarios and assessment formats utilizing LLMs…

Software Engineering · Computer Science 2023-08-21 Natalie Kiesler , Daniel Schiffner

Penetration testing, a crucial industrial practice for ensuring system security, has traditionally resisted automation due to the extensive expertise required by human professionals. Large Language Models (LLMs) have shown significant…

Software Engineering · Computer Science 2024-06-04 Gelei Deng , Yi Liu , Víctor Mayoral-Vilches , Peng Liu , Yuekang Li , Yuan Xu , Tianwei Zhang , Yang Liu , Martin Pinzger , Stefan Rass

Deciphering the function of unseen protein sequences is a fundamental challenge with broad scientific impact, yet most existing methods depend on task-specific adapters or large-scale supervised fine-tuning. We introduce the…

Machine Learning · Computer Science 2025-10-14 Xinhui Chen , Zuchao Li , Mengqi Gao , Yufeng Zhang , Chak Tou Leong , Haoyang Li , Jiaqi Chen

Large Language Models (LLMs) recently demonstrated capabilities for generating source code in common programming languages. Additionally, commercial products such as ChatGPT 4 started to provide code interpreters, allowing for the automatic…

Software Engineering · Computer Science 2023-11-15 Felix Härer