A deep matrix factorization method for learning attribute representations

Semi-Non-negative Matrix Factorization is a technique that learns a low-dimensional representation of a dataset that lends itself to a clustering interpretation. It is possible that the mapping between this new representation and our original data matrix contains rather complex hierarchical information with implicit lower-level hidden attributes, that classical one level clustering methodologies can not interpret. In this work we propose a novel model, Deep Semi-NMF, that is able to learn such hidden representations that allow themselves to an interpretation of clustering according to different, unknown attributes of a given dataset. We also present a semi-supervised version of the algorithm, named Deep WSF, that allows the use of (partial) prior information for each of the known attributes of a dataset, that allows the model to be used on datasets with mixed attribute knowledge. Finally, we show that our models are able to learn low-dimensional representations that are better suited for clustering, but also classification, outperforming Semi-Non-negative Matrix Factorization, but also other state-of-the-art methodologies variants.Comment: Submitted to TPAMI (16-Mar-2015

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues