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

KCRC-LCD: Discriminative Kernel Collaborative Representation with Locality Constrained Dictionary for Visual Categorization

We consider the image classification problem via kernel collaborative representation classification with locality constrained dictionary (KCRC-LCD). Specifically, we propose a kernel collaborative representation classification (KCRC) approach in which kernel method is used to improve the discrimination ability of collaborative representation classification (CRC). We then measure the similarities between the query and atoms in the global dictionary in order to construct a locality constrained dictionary (LCD) for KCRC. In addition, we discuss several similarity measure approaches in LCD and further present a simple yet effective unified similarity measure whose superiority is validated in experiments. There are several appealing aspects associated with LCD. First, LCD can be nicely incorporated under the framework of KCRC. The LCD similarity measure can be kernelized under KCRC, which theoretically links CRC and LCD under the kernel method. Second, KCRC-LCD becomes more scalable to both the training set size and the feature dimension. Example shows that KCRC is able to perfectly classify data with certain distribution, while conventional CRC fails completely. Comprehensive experiments on many public datasets also show that KCRC-LCD is a robust discriminative classifier with both excellent performance and good scalability, being comparable or outperforming many other state-of-the-art approaches