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Artificial intelligence (AI) has played an increasingly important role in chemical research. However, most models currently used in chemistry are specialist models that require training and tuning for specific tasks. A more generic and…

Computation and Language · Computer Science 2025-07-03 Zihan Zhao , Da Ma , Lu Chen , Liangtai Sun , Zihao Li , Yi Xia , Bo Chen , Hongshen Xu , Zichen Zhu , Su Zhu , Shuai Fan , Guodong Shen , Kai Yu , Xin Chen

Rapid developments of AI tools are expected to offer unprecedented assistance to the research of natural science including chemistry. However, neither existing unimodal task-specific specialist models nor emerging general large multimodal…

Machine Learning · Computer Science 2025-01-03 Zihan Zhao , Bo Chen , Jingpiao Li , Lu Chen , Liyang Wen , Pengyu Wang , Zichen Zhu , Danyang Zhang , Ziping Wan , Yansi Li , Zhongyang Dai , Xin Chen , Kai Yu

Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction…

Machine Learning · Computer Science 2024-08-21 Yifei Yang , Runhan Shi , Zuchao Li , Shu Jiang , Bao-Liang Lu , Yang Yang , Hai Zhao

Large language models (LLMs) have made impressive progress in chemistry applications. However, the community lacks an LLM specifically designed for chemistry. The main challenges are two-fold: firstly, most chemical data and scientific…

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs…

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose…

Machine Learning · Computer Science 2025-08-05 Qian Tan , Dongzhan Zhou , Peng Xia , Wanhao Liu , Wanli Ouyang , Lei Bai , Yuqiang Li , Tianfan Fu

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of…

Machine Learning · Computer Science 2025-07-18 Eduardo Soares , Victor Shirasuna , Emilio Vital Brazil , Renato Cerqueira , Dmitry Zubarev , Kristin Schmidt

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning…

Atomized chemical knowledge, such as functional group information of molecules and reactions, plays a pivotal intermediate role in the reasoning process that connects molecular structures with their properties and reactivities. While large…

Computational Engineering, Finance, and Science · Computer Science 2026-04-15 Zihan Zhao , Ziping Wan , Lu Chen , Xuanze Lin , Shiyang Yu , Situo Zhang , Da Ma , Zichen Zhu , Danyang Zhang , Huayang Wang , Zhongyang Dai , Liyang Wen , Bo Chen , Xin Chen , Kai Yu

Large language models have revolutionized artificial intelligence by enabling large, generalizable models trained through self-supervision. This paradigm has inspired the development of scientific foundation models (FMs). However, applying…

Foundation models (FMs) are catalyzing a transformative shift in materials science (MatSci) by enabling scalable, general-purpose, and multimodal AI systems for scientific discovery. Unlike traditional machine learning models, which are…

Machine Learning · Computer Science 2025-06-27 Minh-Hao Van , Prateek Verma , Chen Zhao , Xintao Wu

Chemical synthesis, as a foundational methodology in the creation of transformative molecules, exerts substantial influence across diverse sectors from life sciences to materials and energy. Current chemical synthesis practices emphasize…

Molecular property prediction and generative design via deep learning models has been the subject of intense research given its potential to accelerate development of new, high-performance materials. More recently, these workflows have been…

Artificial Intelligence · Computer Science 2024-12-16 Nathaniel H. Park , Tiffany J. Callahan , James L. Hedrick , Tim Erdmann , Sara Capponi

Accurate molecular property prediction is central to drug discovery, catalysis, and process design, yet real-world applications are often limited by small datasets. Molecular foundation models provide a promising direction by learning…

Machine Learning · Computer Science 2026-04-21 Karim K. Ben Hicham , Jan G. Rittig , Martin Grohe , Alexander Mitsos

Recent advances in large language models (LLMs) have demonstrated transformative potential across diverse fields. While LLMs have been applied to molecular simplified molecular input line entry system (SMILES) in computer-aided synthesis…

Machine Learning · Computer Science 2026-01-07 Kenan Li , Yijian Zhang , Jin Wang , Haipeng Gan , Zeying Sun , Xiaoguang Lei , Hao Dong

We introduce ChemPro, a progressive benchmark with 4100 natural language question-answer pairs in Chemistry, across 4 coherent sections of difficulty designed to assess the proficiency of Large Language Models (LLMs) in a broad spectrum of…

Computation and Language · Computer Science 2026-04-22 Aaditya Baranwal , Shruti Vyas

The advancement and extensive application of large language models (LLMs) have been remarkable, including their use in scientific research assistance. However, these models often generate scientifically incorrect or unsafe responses, and in…

Computation and Language · Computer Science 2024-11-28 Haochen Zhao , Xiangru Tang , Ziran Yang , Xiao Han , Xuanzhi Feng , Yueqing Fan , Senhao Cheng , Di Jin , Yilun Zhao , Arman Cohan , Mark Gerstein

Natural products, as metabolites from microorganisms, animals, or plants, exhibit diverse biological activities, making them crucial for drug discovery. Nowadays, existing deep learning methods for natural products research primarily rely…

Quantitative Methods · Quantitative Biology 2026-05-11 Yuheng Ding , Bo Qiang , Shaoning Li , Yiran Zhou , Jie Yu , Qi Li , Cheng Shi , Liangren Zhang , Yusong Wang , Nanning Zheng , Zhenming Liu

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address…

Large Language Models (LLMs) have achieved remarkable success and have been applied across various scientific fields, including chemistry. However, many chemical tasks require the processing of visual information, which cannot be…

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