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

Stacking-Based Deep Neural Network: Deep Analytic Network for Pattern Classification

Stacking-based deep neural network (S-DNN) is aggregated with pluralities of basic learning modules, one after another, to synthesize a deep neural network (DNN) alternative for pattern classification. Contrary to the DNNs trained end to end by backpropagation (BP), each S-DNN layer, i.e., a self-learnable module, is to be trained decisively and independently without BP intervention. In this paper, a ridge regression-based S-DNN, dubbed deep analytic network (DAN), along with its kernelization (K-DAN), are devised for multilayer feature re-learning from the pre-extracted baseline features and the structured features. Our theoretical formulation demonstrates that DAN/K-DAN re-learn by perturbing the intra/inter-class variations, apart from diminishing the prediction errors. We scrutinize the DAN/K-DAN performance for pattern classification on datasets of varying domains - faces, handwritten digits, generic objects, to name a few. Unlike the typical BP-optimized DNNs to be trained from gigantic datasets by GPU, we disclose that DAN/K-DAN are trainable using only CPU even for small-scale training sets. Our experimental results disclose that DAN/K-DAN outperform the present S-DNNs and also the BP-trained DNNs, including multiplayer perceptron, deep belief network, etc., without data augmentation applied.Comment: 14 pages, 7 figures, 11 table