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

A Survey on Soft Subspace Clustering

Subspace clustering (SC) is a promising clustering technology to identify clusters based on their associations with subspaces in high dimensional spaces. SC can be classified into hard subspace clustering (HSC) and soft subspace clustering (SSC). While HSC algorithms have been extensively studied and well accepted by the scientific community, SSC algorithms are relatively new but gaining more attention in recent years due to better adaptability. In the paper, a comprehensive survey on existing SSC algorithms and the recent development are presented. The SSC algorithms are classified systematically into three main categories, namely, conventional SSC (CSSC), independent SSC (ISSC) and extended SSC (XSSC). The characteristics of these algorithms are highlighted and the potential future development of SSC is also discussed.Comment: This paper has been published in Information Sciences Journal in 201

Bandwidth selection for kernel estimation in mixed multi-dimensional spaces

Kernel estimation techniques, such as mean shift, suffer from one major drawback: the kernel bandwidth selection. The bandwidth can be fixed for all the data set or can vary at each points. Automatic bandwidth selection becomes a real challenge in case of multidimensional heterogeneous features. This paper presents a solution to this problem. It is an extension of \cite{Comaniciu03a} which was based on the fundamental property of normal distributions regarding the bias of the normalized density gradient. The selection is done iteratively for each type of features, by looking for the stability of local bandwidth estimates across a predefined range of bandwidths. A pseudo balloon mean shift filtering and partitioning are introduced. The validity of the method is demonstrated in the context of color image segmentation based on a 5-dimensional space

Brain image clustering by wavelet energy and CBSSO optimization algorithm

Previously, the diagnosis of brain abnormality was significantly important in the saving of social and hospital resources. Wavelet energy is known as an effective feature detection which has great efficiency in different utilities. This paper suggests a new method based on wavelet energy to automatically classify magnetic resonance imaging (MRI) brain images into two groups (normal and abnormal), utilizing support vector machine (SVM) classification based on chaotic binary shark smell optimization (CBSSO) to optimize the SVM weights. The results of the suggested CBSSO-based KSVM are compared favorably to several other methods in terms of better sensitivity and authenticity. The proposed CAD system can additionally be utilized to categorize the images with various pathological conditions, types, and illness modes