A novel machine learning-based workflow to capture intra-patient heterogeneity through transcriptional multi-label characterization and clinically relevant classification

Objectives: Patient classification into specific molecular subtypes is paramount in biomedical research and clinical practice to face complex, heterogeneous diseases. Existing methods, especially for gene expression-based cancer subtyping, often simplify patient molecular portraits, neglecting the potential co-occurrence of traits from multiple subtypes. Yet, recognizing intra-sample heterogeneity is essential for more precise patient characterization and improved personalized treatments. Methods: We developed a novel computational workflow, named MULTI-STAR, which addresses current limitations and provides tailored solutions for reliable multi-label patient subtyping. MULTI-STAR uses state-of-the-art subtyping methods to obtain promising machine learning-based multi-label classifiers, leveraging gene expression profiles. It modifies standard single-label similarity-based techniques to obtain multi-label patient characterizations. Then, it employs these characterizations to train single-sample predictors using different multi-label strategies and find the best-performing classifiers. Results: MULTI-STAR classifiers offer advanced multi-label recognition of all the subtypes contributing to the molecular and clinical traits of a patient, also distinguishing the primary from the additional relevant secondary subtype(s). The efficacy was demonstrated by developing multi-label solutions for breast and colorectal cancer subtyping that outperform existing methods in terms of prognostic value, primarily for overall survival predictions, and ability to work on a single sample at a time, as required in clinical practice. Conclusions: This work emphasizes the importance of moving to multi-label subtyping to capture all the molecular traits of individual patients, considering also previously overlooked secondary assignments and paving the way for improved clinical decision-making processes in diverse heterogeneous disease contexts. Indeed, MULTI-STAR novel, reproducible and generalizable approach provides comprehensive representations of patient inner heterogeneity and clinically relevant insights, contributing to precision medicine and personalized treatments.