Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel network-based approach named Patient-Net (P-Net) in which biomolecular profiles of patients are modeled in a graph-structured space that represents gene expression relationships between patients. Then a kernel-based semi-supervised transductive algorithm is applied to the graph to explore the overall topology of the graph and to predict the phenotype/clinical outcome of patients. Experimental tests involving several publicly available datasets of patients afflicted with pancreatic, breast, colon and colorectal cancer show that our proposed method is competitive with state-of-the-art supervised and semi-supervised predictive systems. Importantly, P-Net also provides interpretable models that can be easily visualized to gain clues about the relationships between patients, and to formulate hypotheses about their stratification.
Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction / J. Gliozzo, P. Perlasca, M. Mesiti, E. Casiraghi, V. Vallacchi, E. Vergani, M. Frasca, G. Grossi, A. Petrini, M. Re, A. Paccanaro, G. Valentini. - In: SCIENTIFIC REPORTS. - ISSN 2045-2322. - 10:1(2020), pp. 3612.1-3612.15.
|Titolo:||Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction|
VALENTINI, GIORGIO (Corresponding)
|Parole Chiave:||graph-based learning; semi-supervised learning; outcome prediction; network medicine; machine learning; precision medicine|
|Settore Scientifico Disciplinare:||Settore INF/01 - Informatica|
Settore ING-INF/05 - Sistemi di Elaborazione delle Informazioni
|Data di pubblicazione:||2020|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1038/s41598-020-60235-8|
|Appare nelle tipologie:||01 - Articolo su periodico|