Multinomial Logistic Regression with Adaptive Regularization for Cancer Subtype Classification via Multi-omics Data

Background: Integrating multi-omics data for cancer classification brings complementary biological insights while also facing challenges such as data integration, gene grouping, and adaptive weight construction. Objective: This paper aims to address the challenges faced by the cancer subtype classification and gene screening based on multi-omics data. Methods: Multinomial logistic regression with adaptive regularization (MLRAR) was proposed by integrating DNA methylation, gene mutation, and RNA-seq information. A data preprocessing strategy that effectively utilizes multi-omics information was presented, and the local maximum quasiclique merging (lmQCM) algorithm was implemented to group genes. Biological pathway information was utilized to evaluate the significance of gene groups, while the significance of each gene within a group was evaluated by integrating mutation information, information theory, and methylation information. Results: Compared to MRlasso, MRGL, MSGL, MROGL, AMRSOGL, and AGLRMR, the proposed method yielded improvements in subtype classification accuracy of breast cancer by 2.6%, 2.9%, 3.5%, 2.3%, 2.0%, and 1.8%, respectively. In addition, MLRAR also achieved significant improvements in ovarian cancer by 8.2%, 5.0%, 6.8%, 5.2%, 12.7%, and 6.3%, respectively. Conclusion: The proposed method can effectively deal with data integration, gene grouping, and adaptive weight construction.