3D IntelliGenes: AI/ML application using multi-omics data for biomarker discovery and disease prediction with multi-dimensional visualization

Abstract

Background: The cutting-edge artificial intelligence (AI) and machine learning (ML) techniques have proven effective at uncovering elucidative knowledge on disease-causing biomarkers and the biological underpinnings of a plethora of human diseases. However, the high-dimensional nature of multi-omics data presents numerous challenges in its effective presentation, annotation, and interpretation. Traditional 2D visualizations often fall short in capturing the intricate relationships between multi-omics features, hindering our ability to identify meaningful correlations. Methods: In this study, we focused on addressing such challenges by developing an innovative solution to better visualize results produced by AI/ML approaches on integrated clinical and multi-omics data for novel biomarker discovery and predictive analysis. We present an advanced version of our earlier published software with intuitive and interactive visualizations of multi-omics data in multi-dimensions i.e., 3D IntelliGenes, which offers deeper insights, most importantly by capturing greater variability in the patient data by understanding both linear and non-linear structures, evaluating AI/ML model performance, and delineating the joint impact of biomarkers on the corresponding disease states. Results: The overall functionality of 3D IntelliGenes is divided into two modules, data clustering and feature plotting. The data clustering module creates configurable 3D scatter plots to visualize the structure-preserving distribution of disease states, AI/ML classifier bias in the form of type I/II errors, and patient similarity through a robust density-driven clustering algorithm. Whereas the feature plotting module supports the joint analysis of pairs of multi-omics features to analyze the interdependence and discriminative power of co-expressed biomarkers. Conclusion: We report evaluated performance of 3D IntelliGenes using diverse cohorts of patients with cardiovascular and other diseases.