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. Phenotype and outcome prediction using sets of selected biomarkers are well-established prediction tasks in the context of computational biology, including different prediction problems ranging from the response to a specific drug 1,2 , diagnosis and prognosis 3-5 , classification of cancer subtypes 6 , outcome and recurrence prediction 7-9 and other related prediction problems 10. State-of-the-art methods for these problems are largely based on inductive supervised models that use sets of selected biomarkers, usually represented as vectors, to predict the phenotype or outcome of interest (see, e.g. 11-13), without taking into account the relationships between individuals. Several works proposed "network-based" methods by constructing graphs of patients, in order to discover the underlying structure of the data (e.g. discovery of subtypes of diseases, clinical stratification of patients) 14-17. These methods mainly used unsupervised approaches and hence have been not specifically designed and are not appropriate for phenotype/outcome prediction problems. Recently a few works proposed semi-supervised "network-based" approaches for the prediction of the phenotype/outcome of patients, on the basis of their bio-molecular profiles (e.g. gene expression of genotypic profiles) 18,19 , including also methods able to integrate multiple sources of omics data 20 , and methods based on Supervised Random Walks 21 , specifically modified for the classification of tumors 22. In this work, we introduce a novel network-based method for modeling in the "patient space". In this context the nodes of the network represent patients through an n-dimensional set of biomarker values (e.g. a set of gene expression values), and edges represent similarities between the biomarkers of a pair of patients. Hence, this "patient-space" differs from the classical "biomarker-space", where nodes represent biomarkers and edges similarities between biomarkers and not between patients 23,24...