Artificial intelligence algorithms drive the deciphering of traditional Chinese medicine by analyzing the chemicalome, targetome, and bioactivome

Artificial intelligence (AI) is reshaping the research paradigm of traditional Chinese medicine (TCM) in a profound way. This review offers a systematic account of how AI algorithms propel the modernization of TCM through the integrated analysis of three core concepts: the chemicalome, referring to the collection of in vitro and in vivo chemical constituents derived from TCM; the targetome, defined as the set of biological macromolecules that engage in interactions with TCM components; and the bioactivome, signifying the range of integrated biological activities and phenotypic outcomes induced by TCM interventions. First, it illustrates how AI enables comprehensive characterization of complex in vitro and in vivo chemicalomes by revolutionizing mass spectrometry analysis and metabolite identification techniques. Next, it examines how AI works in conjunction with experimental technologies to systematically predict the targetome and validate these predictions. Furthermore, the review clarifies how AI deciphers the bioactivome arising from TCM interventions and uncovers mechanisms through the integration of multi-omics datasets. Finally, it explores methodologies for establishing comprehensive interconnections among the chemicalome, targetome, and bioactivome. This analytical framework demonstrates that AI functions not just as a tool to enhance research efficiency, but also as a foundational methodology capable of systematically decoding TCM and linking traditional wisdom with modern science.