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Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical…

Computational Engineering, Finance, and Science · Computer Science 2025-10-23 Weida Wang , Benteng Chen , Di Zhang , Wanhao Liu , Shuchen Pu , Ben Gao , Jin Zeng , Xiaoyong Wei , Tianshu Yu , Shuzhou Sun , Tianfan Fu , Wanli Ouyang , Lei Bai , Jiatong Li , Zifu Wang , Yuqiang Li , Shufei Zhang

Applications of machine learning in chemistry are often limited by the scarcity and expense of labeled data, restricting traditional supervised methods. In this work, we introduce a framework for molecular reasoning using general-purpose…

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

While Vision-Language Models (VLMs) have demonstrated significant potential in chemical visual understanding, current models are predominantly optimized for direct visual question-answering tasks. This paradigm often results in "black-box"…

Computation and Language · Computer Science 2026-04-09 Xuanle Zhao , Xinyuan Cai , Xiang Cheng , Xiuyi Chen , Bo Xu

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug…

Artificial Intelligence · Computer Science 2026-01-08 Hao Li , He Cao , Bin Feng , Yanjun Shao , Xiangru Tang , Zhiyuan Yan , Li Yuan , Yonghong Tian , Yu Li

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…

While automated chemical tools excel at specific tasks, they have struggled to capture the strategic thinking that characterizes expert chemical reasoning. Here we demonstrate that large language models (LLMs) can serve as powerful tools…

Artificial Intelligence · Computer Science 2025-07-25 Andres M Bran , Theo A Neukomm , Daniel P Armstrong , Zlatko Jončev , Philippe Schwaller

Large Language Models (LLMs) are widely used across various scenarios due to their exceptional reasoning capabilities and natural language understanding. While LLMs demonstrate strong performance in tasks involving mathematics and coding,…

Artificial Intelligence · Computer Science 2025-06-03 Xinyi Liu , Lipeng Ma , Yixuan Li , Weidong Yang , Qingyuan Zhou , Jiayi Song , Shuhao Li , Ben Fei

Retrosynthesis planning, essential in organic synthesis and drug discovery, has greatly benefited from recent AI-driven advancements. Nevertheless, existing methods frequently face limitations in both applicability and explainability.…

Computational Engineering, Finance, and Science · Computer Science 2025-07-24 Situo Zhang , Hanqi Li , Lu Chen , Zihan Zhao , Xuanze Lin , Zichen Zhu , Bo Chen , Xin Chen , Kai Yu

Despite the outstanding capabilities of large language models (LLMs), knowledge-intensive reasoning still remains a challenging task due to LLMs' limitations in compositional reasoning and the hallucination problem. A prevalent solution is…

Computation and Language · Computer Science 2025-09-29 Amy Xin , Jinxin Liu , Zijun Yao , Zhicheng Lee , Shulin Cao , Lei Hou , Juanzi Li

Chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) in natural language to perform complex reasoning. However, chemical reasoning is inherently continuous and structural, and forcing it into discrete…

Large Language Models (LLMs) excel in diverse areas, yet struggle with complex scientific reasoning, especially in the field of chemistry. Different from the simple chemistry tasks (e.g., molecule classification) addressed in previous…

Computation and Language · Computer Science 2024-02-12 Siru Ouyang , Zhuosheng Zhang , Bing Yan , Xuan Liu , Yejin Choi , Jiawei Han , Lianhui Qin

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling…

Computation and Language · Computer Science 2025-01-14 Xiangru Tang , Tianyu Hu , Muyang Ye , Yanjun Shao , Xunjian Yin , Siru Ouyang , Wangchunshu Zhou , Pan Lu , Zhuosheng Zhang , Yilun Zhao , Arman Cohan , Mark Gerstein

Large Language Models (LLMs) exhibit strong general reasoning but struggle in molecular science due to the lack of explicit chemical priors in standard string representations. Current solutions face a fundamental dilemma. Training-based…

Computation and Language · Computer Science 2025-12-23 Mingxu Zhang , Dazhong Shen , Qi Zhang , Ying Sun

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…

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…

Recent advancements in large language models (LLMs) have demonstrated strong potential for enabling domain-specific intelligence. In this work, we present our vision for building an AI-powered chemical brain, which frames chemical…

Artificial Intelligence · Computer Science 2026-01-12 Weichen Dai , Yezeng Chen , Zijie Dai , Yubo Liu , Zhijie Huang , Yixuan Pan , Baiyang Song , Chengli Zhong , Xinhe Li , Zeyu Wang , Zhuoying Feng , Yi Zhou

Large Language Models (LLMs) have shown outstanding performance across wide range of downstream tasks. This competency is attributed to their substantial parameter size and pre-training on extensive corpus. Moreover, LLMs have exhibited…

Computation and Language · Computer Science 2023-08-10 Yuhan Ma , Haiqi Jiang , Chenyou Fan

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

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
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