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International initiatives such as the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), Cancer Genome Atlas (TCGA), and the International Cancer Genome Consortium (ICGC) are collecting multiple data sets at different genome-scales with the aim to identify novel cancer bio-markers and predict patient survival. To analyse such data, several machine learning, bioinformatics and statistical methods have been applied, among them neural networks such as autoencoders. Although these models provide a good statistical learning framework to analyse multi-omic and/or clinical data, there is a distinct lack of work on how to integrate diverse patient data and identify the optimal design best suited to the available data. In this paper, we investigate several autoencoder architectures that integrate a variety of cancer patient data types (e.g., multi-omics and clinical data). We perform extensive analyses of these approaches and provide a clear methodological and computational framework for designing systems that enable clinicians to investigate cancer traits and translate the results into clinical applications. We demonstrate how these networks can be designed, built and, in particular, applied to tasks of integrative analyses of heterogeneous breast cancer data. The results show that these approaches yield relevant data representations that, in turn, lead to accurate and stable diagnosis.

Research in psychology about reasoning has often been restricted to relatively inexpressive statements involving quantifiers (e.g. syllogisms). This is limited to situations that typically do not arise in practical settings, like ontology engineering. In order to provide an analysis of inference, we focus on reasoning tasks presented in external graphic representations where statements correspond to those involving multiple quantifiers and unary and binary relations. Our experiment measured participants’ performance when reasoning with two notations. The first notation used topological constraints to convey information via node-link diagrams (i.e. graphs). The second used topological and spatial constraints to convey information (Euler diagrams with additional graph-like syntax). We found that topo-spatial representations were more effective for inferences than topological representations alone. Reasoning with statements involving multiple quantifiers was harder than reasoning with single quantifiers in topological representations, but not in topo-spatial representations. These findings are compared to those in sentential reasoning tasks.