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Large language models have made remarkable progress in the field of molecular science, particularly in understanding and generating functional small molecules. This success is largely attributed to the effectiveness of molecular…

Biomolecules · Quantitative Biology 2025-03-14 Zicheng Ma , Chuanliu Fan , Zhicong Wang , Zhenyu Chen , Xiaohan Lin , Yanheng Li , Shihao Feng , Jun Zhang , Ziqiang Cao , Yi Qin Gao

Large Language Models (LLMs) possess human-level cognitive and decision-making capabilities, making them a key technology for 6G. However, applying LLMs to the communication domain faces three major challenges: 1) Inadequate communication…

Information Theory · Computer Science 2025-02-27 Feibo Jiang , Wanyun Zhu , Li Dong , Kezhi Wang , Kun Yang , Cunhua Pan , Octavia A. Dobre

The proliferation of complex structured data in hybrid sources, such as PDF documents and web pages, presents unique challenges for current Large Language Models (LLMs) and Multi-modal Large Language Models (MLLMs) in providing accurate…

Information Retrieval · Computer Science 2025-08-22 Shivani Upadhyay , Messiah Ataey , Syed Shariyar Murtaza , Yifan Nie , Jimmy Lin

Language is essentially a complex, intricate system of human expressions governed by grammatical rules. It poses a significant challenge to develop capable AI algorithms for comprehending and grasping a language. As a major approach,…

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial…

Computation and Language · Computer Science 2023-10-17 Markus J. Buehler

Protein language models (PLMs) learn probability distributions over natural protein sequences. By learning from hundreds of millions of natural protein sequences, protein understanding and design capabilities emerge. Recent works have shown…

Quantitative Methods · Quantitative Biology 2026-02-27 Timothy Fei Truong , Tristan Bepler

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

Significant progress has been made in advancing large multimodal conversational models (LMMs), capitalizing on vast repositories of image-text data available online. Despite this progress, these models often encounter substantial domain…

Computer Vision and Pattern Recognition · Computer Science 2025-01-10 Muhammad Awais , Ali Husain Salem Abdulla Alharthi , Amandeep Kumar , Hisham Cholakkal , Rao Muhammad Anwer

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs…

Machine Learning · Computer Science 2024-09-25 Tianyu Liu , Yijia Xiao , Xiao Luo , Hua Xu , W. Jim Zheng , Hongyu Zhao

Studying protein mutations within amino acid sequences holds tremendous significance in life sciences. Protein language models (PLMs) have demonstrated strong capabilities in broad biological applications. However, due to architectural…

Machine Learning · Computer Science 2024-10-31 Yizhen Luo , Zikun Nie , Massimo Hong , Suyuan Zhao , Hao Zhou , Zaiqing Nie

Large Language Models (LLMs), typified by OpenAI's GPT, have marked a significant advancement in artificial intelligence. Trained on vast amounts of text data, LLMs are capable of understanding and generating human-like text across a…

Artificial Intelligence · Computer Science 2024-10-29 Haochen Zhang , Yuyang Dong , Chuan Xiao , Masafumi Oyamada

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

Biomolecules · Quantitative Biology 2026-05-28 Dan Kalifa , Uriel Singer , Kira Radinsky

Protein language models (PLMs) have emerged as powerful tools to detect complex patterns of protein sequences. However, the capability of PLMs to fully capture information on protein sequences might be limited by focusing on single…

Machine Learning · Computer Science 2025-05-27 Hazem Alsamkary , Mohamed Elshaffei , Mohamed Elkerdawy , Ahmed Elnaggar

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches…

Multimodal Large Language Models (MLLMs) show promise for medical applications, yet progress in dermatology lags due to limited training data, narrow task coverage, and lack of clinically-grounded supervision that mirrors expert diagnostic…

Computation and Language · Computer Science 2026-01-06 Jinghan Ru , Siyuan Yan , Yuguo Yin , Yuexian Zou , Zongyuan Ge

Predicting protein stability changes induced by single-point mutations has been a persistent challenge over the years, attracting immense interest from numerous researchers. The ability to precisely predict protein thermostability is…

Biomolecules · Quantitative Biology 2023-12-08 Yijie Zhang , Zhangyang Gao , Cheng Tan , Stan Z. Li

Protein language models (pLMs) produce per-residue representations that capture evolutionary and structural information, yet their mean-pooled sequence embeddings are not explicitly trained to reflect functional, evolutionary or structural…

Machine Learning · Computer Science 2026-05-11 Dan Ofer , Oriel Perets , Michal Linial , Nadav Rappoport

Protein language models (PLMs) learn contextual representations from protein sequences and are profoundly impacting various scientific disciplines spanning protein design, drug discovery, and structural predictions. One particular research…

Quantitative Methods · Quantitative Biology 2024-02-07 Andreas Dounas , Tudor-Stefan Cotet , Alexander Yermanos

The emergence of Multimodal Large Language Models (MLLMs) has revolutionized image understanding by bridging textual and visual modalities. However, these models often struggle with capturing fine-grained semantic information, such as the…

Computer Vision and Pattern Recognition · Computer Science 2025-07-16 Jie Yang , Wang Zeng , Sheng Jin , Lumin Xu , Wentao Liu , Chen Qian , Zhen Li , Ruimao Zhang

This paper presents a comprehensive survey of ChatGPT-related (GPT-3.5 and GPT-4) research, state-of-the-art large language models (LLM) from the GPT series, and their prospective applications across diverse domains. Indeed, key innovations…