Global gene network exploration based on explainable artificial intelligence approach

Abstract

In recent years, personalized gene regulatory networks have received significant attention, and interpretation of the multilayer networks has been a critical issue for a comprehensive understanding of gene regulatory systems. Although several statistical and machine learning approaches have been developed and applied to reveal sample-specific regulatory pathways, integrative understanding of the massive multilayer networks remains a challenge. To resolve this problem, we propose a novel artificial intelligence (AI) strategy for comprehensive gene regulatory network analysis. In our strategy, personalized gene networks corresponding specific clinical characteristic are constructed and the constructed network is considered as a second-order tensor. Then, an explainable AI method based on deep learning is applied to decompose the multilayer networks, thus we can reveal all-encompassing gene regulatory systems characterized by clinical features of patients. To evaluate the proposed methodology, we apply our method to the multilayer gene networks under varying conditions of an epithelial–mesenchymal transition (EMT) process. From the comprehensive analysis of multilayer networks, we identified novel markers, and the biological mechanisms of the identified genes and their reciprocal mechanisms are verified through the literature. Although any biological knowledge about the identified genes was not incorporated in our analysis, our data-driven approach based on AI approach provides biologically reliable results. Furthermore, the results provide crucial evidences to reveal biological mechanism related to various diseases, e.g., keratinocyte proliferation. The use of explainable AI method based on the tensor decomposition enables us to reveal global and novel mechanisms of gene regulatory system from the massive multiple networks, which cannot be demonstrated by existing methods. We expect that the proposed method provides a new insight into network biology and it will be a useful tool to integrative gene network analysis related complex architectures of diseases.