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

Challenges of Big Data Analysis

Big Data bring new opportunities to modern society and challenges to data scientists. On one hand, Big Data hold great promises for discovering subtle population patterns and heterogeneities that are not possible with small-scale data. On the other hand, the massive sample size and high dimensionality of Big Data introduce unique computational and statistical challenges, including scalability and storage bottleneck, noise accumulation, spurious correlation, incidental endogeneity, and measurement errors. These challenges are distinguished and require new computational and statistical paradigm. This article give overviews on the salient features of Big Data and how these features impact on paradigm change on statistical and computational methods as well as computing architectures. We also provide various new perspectives on the Big Data analysis and computation. In particular, we emphasis on the viability of the sparsest solution in high-confidence set and point out that exogeneous assumptions in most statistical methods for Big Data can not be validated due to incidental endogeneity. They can lead to wrong statistical inferences and consequently wrong scientific conclusions

Joint & Progressive Learning from High-Dimensional Data for Multi-Label Classification

Despite the fact that nonlinear subspace learning techniques (e.g. manifold learning) have successfully applied to data representation, there is still room for improvement in explainability (explicit mapping), generalization (out-of-samples), and cost-effectiveness (linearization). To this end, a novel linearized subspace learning technique is developed in a joint and progressive way, called \textbf{j}oint and \textbf{p}rogressive \textbf{l}earning str\textbf{a}teg\textbf{y} (J-Play), with its application to multi-label classification. The J-Play learns high-level and semantically meaningful feature representation from high-dimensional data by 1) jointly performing multiple subspace learning and classification to find a latent subspace where samples are expected to be better classified; 2) progressively learning multi-coupled projections to linearly approach the optimal mapping bridging the original space with the most discriminative subspace; 3) locally embedding manifold structure in each learnable latent subspace. Extensive experiments are performed to demonstrate the superiority and effectiveness of the proposed method in comparison with previous state-of-the-art methods.Comment: accepted in ECCV 201