Application of Transformers in Cheminformatics

• Published in: Journal of chemical information and modeling 2024-06, Vol.64 (11), p.4392-4409
• Main Authors: Luong, Kha-Dinh, Singh, Ambuj
• Format: Article
• Language: English
• Subjects: Computation; Computer vision; Machine learning; Natural language processing; Representations; Review; Task complexity
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.3c02070

By accelerating time-consuming processes with high efficiency, computing has become an essential part of many modern chemical pipelines. Machine learning is a class of computing methods that can discover patterns within chemical data and utilize this knowledge for a wide variety of downstream tasks, such as property prediction or substance generation. The complex and diverse chemical space requires complex machine learning architectures with great learning power. Recently, learning models based on transformer architectures have revolutionized multiple domains of machine learning, including natural language processing and computer vision. Naturally, there have been ongoing endeavors in adopting these techniques to the chemical domain, resulting in a surge of publications within a short period. The diversity of chemical structures, use cases, and learning models necessitate a comprehensive summarization of existing works. In this paper, we review recent innovations in adapting transformers to solve learning problems in chemistry. Because chemical data is diverse and complex, we structure our discussion based on chemical representations. Specifically, we highlight the strengths and weaknesses of each representation, the current progress of adapting transformer architectures, and future directions.