Integrating Multi-Omics Using Bayesian Ridge Regression with Iterative Similarity Bagging

Abstract

Cancer research has increasingly utilized multi-omics analysis in recent decades to obtain biomolecular information from multiple layers, thereby gaining a better understanding of complex biological systems. However, the curse of dimensionality is one of the most significant challenges when handling omics or biological data. Additionally, integrating multi-omics by transforming different omics types into a new representation can reduce a model’s interpretability, as the extracted features may lose the biological context. This paper proposes Iterative Similarity Bagging (ISB), assisted by Bayesian Ridge Regression (BRR). BRR serves as a domain-oriented supervised feature selection method, choosing essential features by calculating the coefficients for each feature. Despite this, the BRR output datasets contain many features, leading to complexity and high dimensionality. To address this, ISB was introduced to dynamically reduce dimensionality and complexity without losing the biological integrity of the omics data, which often occurs with transformation-based integration approaches. The evaluation measures employed were Root Mean Square Error (RMSE), the Pearson Correlation Coefficient (PCC), and the coefficient of determination (R2). The results demonstrate that the proposed method outperforms some current models in terms of regression performance, achieving an RMSE of 0.12, a PCC of 0.879, and an R2 of 0.77 for the CCLE. For the GDSC, it achieved an RMSE of 0.029, a PCC of 0.90, and an R2 of 0.80.