M$^{3}$-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery

• URL: http://arxiv.org/abs/2412.06847v2
• Date: Sun, 16 Mar 2025 12:37:49 GMT
• Title: M$^{3}$-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery
• Authors: Siyuan Guo, Lexuan Wang, Chang Jin, Jinxian Wang, Han Peng, Huayang Shi, Wengen Li, Jihong Guan, Shuigeng Zhou,
• Abstract summary: M$3$-20M is 71 times more in the number of molecules than the largest existing dataset.<n>This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions.
• Score: 23.60901496004578
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: This paper introduces M$^{3}$-20M, a large-scale Multi-Modal Molecule dataset that contains over 20 million molecules, with the data mainly being integrated from existing databases and partially generated by large language models. Designed to support AI-driven drug design and discovery, M$^{3}$-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit the training or fine-tuning of models, including large language models for drug design and discovery tasks. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M$^{3}$-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, GPT-4, and Llama3-8b. Our experimental results show that M$^{3}$-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than existing single-modal datasets, which validates the value and potential of M$^{3}$-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

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