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The integration of Large Language Models (LLMs) into the drug discovery and development field marks a significant paradigm shift, offering novel methodologies for understanding disease mechanisms, facilitating drug discovery, and optimizing…

Quantitative Methods · Quantitative Biology 2024-09-10 Yizhen Zheng , Huan Yee Koh , Maddie Yang , Li Li , Lauren T. May , Geoffrey I. Webb , Shirui Pan , George Church

The discovery of novel small molecule drugs remains a critical scientific challenge with far-reaching implications for treating diseases and advancing human health. Traditional drug development--especially for small molecule…

Biomolecules · Quantitative Biology 2025-04-01 Bowen Gao , Yanwen Huang , Yiqiao Liu , Wenxuan Xie , Wei-Ying Ma , Ya-Qin Zhang , Yanyan Lan

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

Large language models (LLMs) integrated with autonomous agents hold significant potential for advancing scientific discovery through automated reasoning and task execution. However, applying LLM agents to drug discovery is still constrained…

Artificial Intelligence · Computer Science 2025-07-29 Kun Li , Zhennan Wu , Shoupeng Wang , Jia Wu , Shirui Pan , Wenbin Hu

We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the…

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Machine Learning · Computer Science 2025-05-23 Ziqing Wang , Kexin Zhang , Zihan Zhao , Yibo Wen , Abhishek Pandey , Han Liu , Kaize Ding

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

Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug…

Quantitative Methods · Quantitative Biology 2024-01-22 Geyan Ye , Xibao Cai , Houtim Lai , Xing Wang , Junhong Huang , Longyue Wang , Wei Liu , Xiangxiang Zeng

Large Language Models (LLMs) have recently demonstrated remarkable performance in general tasks across various fields. However, their effectiveness within specific domains such as drug development remains challenges. To solve these…

Artificial Intelligence · Computer Science 2024-10-16 Tengfei Ma , Xuan Lin , Tianle Li , Chaoyi Li , Long Chen , Peng Zhou , Xibao Cai , Xinyu Yang , Daojian Zeng , Dongsheng Cao , Xiangxiang Zeng

Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties…

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models…

Chemical Physics · Physics 2024-10-22 Nikita Janakarajan , Tim Erdmann , Sarath Swaminathan , Teodoro Laino , Jannis Born

The rapid advancement of Large Language Models (LLMs) has revolutionized various sectors by automating routine tasks, marking a step toward the realization of Artificial General Intelligence (AGI). However, they still struggle to…

Machine Learning · Computer Science 2024-02-21 Zihao Tang , Zheqi Lv , Shengyu Zhang , Fei Wu , Kun Kuang

Graph Machine Learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets…

The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…

Atomic Physics · Physics 2025-05-20 Adarsh Singh

The drug development process necessitates that pharmacologists undertake various tasks, such as reviewing literature, formulating hypotheses, designing experiments, and interpreting results. Each stage requires accessing and querying vast…

Computation and Language · Computer Science 2023-08-01 Hong Lu , Chuan Li , Yinheng Li , Jie Zhao

Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Biomolecules · Quantitative Biology 2024-05-14 Xianggen Liu , Yan Guo , Haoran Li , Jin Liu , Shudong Huang , Bowen Ke , Jiancheng Lv

This paper explores the advancements and applications of large-scale models in the medical field, with a particular focus on Medical Large Models (MedLMs). These models, encompassing Large Language Models (LLMs), Vision Models, 3D Large…

Artificial Intelligence · Computer Science 2025-10-08 YunHe Su , Zhengyang Lu , Junhui Liu , Ke Pang , Haoran Dai , Sa Liu , Yuxin Jia , Lujia Ge , Jing-min Yang

Discovering the governing equations of dynamical systems is a central problem across many scientific disciplines. As experimental data become increasingly available, automated equation discovery methods offer a promising data-driven…

Machine Learning · Computer Science 2026-04-07 Amirmohammad Ziaei Bideh , Jonathan Gryak

The recommendation of medication is a vital aspect of intelligent healthcare systems, as it involves prescribing the most suitable drugs based on a patient's specific health needs. Unfortunately, many sophisticated models currently in use…

Information Retrieval · Computer Science 2025-01-28 Qidong Liu , Xian Wu , Xiangyu Zhao , Yuanshao Zhu , Zijian Zhang , Feng Tian , Yefeng Zheng

One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability of the model building and evaluation process. With this in mind, we have developed an end-to-end…

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