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

Evolutionary Learning of Fuzzy Rules for Regression

The objective of this PhD Thesis is to design Genetic Fuzzy Systems (GFS) that learn Fuzzy Rule Based Systems to solve regression problems in a general manner. Particularly, the aim is to obtain models with low complexity while maintaining high precision without using expert-knowledge about the problem to be solved. This means that the GFSs have to work with raw data, that is, without any preprocessing that help the learning process to solve a particular problem. This is of particular interest, when no knowledge about the input data is available or for a first approximation to the problem. Moreover, within this objective, GFSs have to cope with large scale problems, thus the algorithms have to scale with the data