2023/06/21 by Zheni Zeng, Bangchen Yin, Zeng, Zheni +17
Arts and Humanities · Computer Science · Materials Science · #Academic Writing and Publishing #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #Computation and Language (cs.CL) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning in Materials Science
paper · pdf · doi:10.48550/arxiv.2306.11976
openalex publication_date 2023/06/21 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 mining, etc.) are of great significance while having a high technical threshold. Bridging the molecule expressions in natural language and chemical language can not only hugely improve the interpretability and reduce the operation difficulty of these tasks, but also fuse the chemical knowledge scattered in complementary materials for a deeper comprehension of molecules. Based on these benefits, we propose the conversational molecular design, a novel task adopting natural language for describing and editing target molecules. To better accomplish this task, we design ChatMol, a knowledgeable and versatile generative pre-trained model, enhanced by injecting experimental property information, molecular spatial knowledge, and the associations between natural and chemical languages into it. Several typical solutions including large language models (e.g., ChatGPT) are evaluated, proving the challenge of conversational molecular design and the effectiveness of our knowledge enhancement method. Case observations and analysis are conducted to provide directions for further exploration of natural-language interaction in molecular discovery.