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

Mean field variational Bayesian inference for support vector machine classification

A mean field variational Bayes approach to support vector machines (SVMs) using the latent variable representation on Polson & Scott (2012) is presented. This representation allows circumvention of many of the shortcomings associated with classical SVMs including automatic penalty parameter selection, the ability to handle dependent samples, missing data and variable selection. We demonstrate on simulated and real datasets that our approach is easily extendable to non-standard situations and outperforms the classical SVM approach whilst remaining computationally efficient.Comment: 18 pages, 4 figure

Unsupervised Representation Learning with Minimax Distance Measures

We investigate the use of Minimax distances to extract in a nonparametric way the features that capture the unknown underlying patterns and structures in the data. We develop a general-purpose and computationally efficient framework to employ Minimax distances with many machine learning methods that perform on numerical data. We study both computing the pairwise Minimax distances for all pairs of objects and as well as computing the Minimax distances of all the objects to/from a fixed (test) object. We first efficiently compute the pairwise Minimax distances between the objects, using the equivalence of Minimax distances over a graph and over a minimum spanning tree constructed on that. Then, we perform an embedding of the pairwise Minimax distances into a new vector space, such that their squared Euclidean distances in the new space equal to the pairwise Minimax distances in the original space. We also study the case of having multiple pairwise Minimax matrices, instead of a single one. Thereby, we propose an embedding via first summing up the centered matrices and then performing an eigenvalue decomposition to obtain the relevant features. In the following, we study computing Minimax distances from a fixed (test) object which can be used for instance in K-nearest neighbor search. Similar to the case of all-pair pairwise Minimax distances, we develop an efficient and general-purpose algorithm that is applicable with any arbitrary base distance measure. Moreover, we investigate in detail the edges selected by the Minimax distances and thereby explore the ability of Minimax distances in detecting outlier objects. Finally, for each setting, we perform several experiments to demonstrate the effectiveness of our framework.Comment: 32 page

Deep Generative Models for Reject Inference in Credit Scoring

Credit scoring models based on accepted applications may be biased and their consequences can have a statistical and economic impact. Reject inference is the process of attempting to infer the creditworthiness status of the rejected applications. In this research, we use deep generative models to develop two new semi-supervised Bayesian models for reject inference in credit scoring, in which we model the data generating process to be dependent on a Gaussian mixture. The goal is to improve the classification accuracy in credit scoring models by adding reject applications. Our proposed models infer the unknown creditworthiness of the rejected applications by exact enumeration of the two possible outcomes of the loan (default or non-default). The efficient stochastic gradient optimization technique used in deep generative models makes our models suitable for large data sets. Finally, the experiments in this research show that our proposed models perform better than classical and alternative machine learning models for reject inference in credit scoring