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Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in…

Machine Learning · Computer Science 2025-10-03 Dongki Kim , Wonbin Lee , Sung Ju Hwang

Understanding and designing biomolecules, such as proteins and small molecules, is central to advancing drug discovery, synthetic biology and enzyme engineering. Recent breakthroughs in artificial intelligence have revolutionized…

Computation and Language · Computer Science 2025-07-28 Xiang Zhuang , Keyan Ding , Tianwen Lyu , Yinuo Jiang , Xiaotong Li , Zhuoyi Xiang , Zeyuan Wang , Ming Qin , Kehua Feng , Jike Wang , Qiang Zhang , Huajun Chen

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

Capturing molecular knowledge with representation learning approaches holds significant potential in vast scientific fields such as chemistry and life science. An effective and generalizable molecular representation is expected to capture…

Machine Learning · Computer Science 2024-06-17 Yizhen Luo , Kai Yang , Massimo Hong , Xing Yi Liu , Zikun Nie , Hao Zhou , Zaiqing Nie

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our…

Biomolecules · Quantitative Biology 2024-12-20 He Cao , Zijing Liu , Xingyu Lu , Yuan Yao , Yu Li

Large Language Models (LLMs) are central to the one-for-all intelligent paradigm, but they face a fundamental challenge when dealing with heterogeneous scientific data such as molecules: the inherent gap between discrete linguistic symbols…

Artificial Intelligence · Computer Science 2026-05-22 Yuxuan Chen , Changwei Lv , Yunduo Xiao , Zhongjing Du , Daquan Zhou , Yukun Yan , Zheni Zeng , Zhiyuan Liu

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…

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures,…

Machine Learning · Computer Science 2025-05-23 Yunhui Jang , Jaehyung Kim , Sungsoo Ahn

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…

Machine Learning · Computer Science 2025-10-21 Yingxu Wang , Kunyu Zhang , Jiaxin Huang , Nan Yin , Siwei Liu , Eran Segal

Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain…

Computer Vision and Pattern Recognition · Computer Science 2026-02-02 Khiem Le , Zhichun Guo , Kaiwen Dong , Xiaobao Huang , Bozhao Nan , Roshni Iyer , Xiangliang Zhang , Olaf Wiest , Wei Wang , Ting Hua , Nitesh V. Chawla

In the molecular domain, numerous studies have explored the use of multimodal large language models (LLMs) to construct a general-purpose, multi-task molecular model. However, these efforts are still far from achieving a truly universal…

Machine Learning · Computer Science 2025-10-31 Chengxin Hu , Hao Li , Yihe Yuan , Zezheng Song , Chenyang Zhao , Haixin Wang

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

Large language models (LLMs) are playing an increasingly important role in scientific research, yet there remains a lack of comprehensive benchmarks to evaluate the breadth and depth of scientific knowledge embedded in these models. To…

Computation and Language · Computer Science 2025-10-08 Kehua Feng , Xinyi Shen , Weijie Wang , Xiang Zhuang , Yuqi Tang , Qiang Zhang , Keyan Ding

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as…

Quantitative Methods · Quantitative Biology 2024-03-05 Yin Fang , Xiaozhuan Liang , Ningyu Zhang , Kangwei Liu , Rui Huang , Zhuo Chen , Xiaohui Fan , Huajun Chen

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

Natural language is expected to be a key medium for various human-machine interactions in the era of large language models. When it comes to the biochemistry field, a series of tasks around molecules (e.g., property prediction, molecule…

Computation and Language · Computer Science 2023-06-22 Zheni Zeng , Bangchen Yin , Shipeng Wang , Jiarui Liu , Cheng Yang , Haishen Yao , Xingzhi Sun , Maosong Sun , Guotong Xie , Zhiyuan Liu

Human expertise in chemistry and biomedicine relies on contextual molecular understanding, a capability that large language models (LLMs) can extend through fine-grained alignment between molecular structures and text. Recent multimodal…

Computation and Language · Computer Science 2025-03-10 Sumin Ha , Jun Hyeong Kim , Yinhua Piao , Sun Kim

Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it…

Artificial Intelligence · Computer Science 2025-12-12 Chenyang Zuo , Siqi Fan , Zaiqing Nie

Large language models have made significant strides in natural language processing, enabling innovative applications in molecular science by processing textual representations of molecules. However, most existing language models cannot…

Machine Learning · Computer Science 2024-02-07 Pengfei Liu , Yiming Ren , Jun Tao , Zhixiang Ren

Deep learning has significantly advanced molecular modeling and design, enabling efficient understanding and discovery of novel molecules. In particular, large language models (LLMs) introduce a fresh research paradigm to tackle scientific…

Machine Learning · Computer Science 2025-01-06 Pengfei Liu , Jun Tao , Zhixiang Ren
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