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 linear approach for sparse coding by a two-layer neural network

Many approaches to transform classification problems from non-linear to linear by feature transformation have been recently presented in the literature. These notably include sparse coding methods and deep neural networks. However, many of these approaches require the repeated application of a learning process upon the presentation of unseen data input vectors, or else involve the use of large numbers of parameters and hyper-parameters, which must be chosen through cross-validation, thus increasing running time dramatically. In this paper, we propose and experimentally investigate a new approach for the purpose of overcoming limitations of both kinds. The proposed approach makes use of a linear auto-associative network (called SCNN) with just one hidden layer. The combination of this architecture with a specific error function to be minimized enables one to learn a linear encoder computing a sparse code which turns out to be as similar as possible to the sparse coding that one obtains by re-training the neural network. Importantly, the linearity of SCNN and the choice of the error function allow one to achieve reduced running time in the learning phase. The proposed architecture is evaluated on the basis of two standard machine learning tasks. Its performances are compared with those of recently proposed non-linear auto-associative neural networks. The overall results suggest that linear encoders can be profitably used to obtain sparse data representations in the context of machine learning problems, provided that an appropriate error function is used during the learning phase

A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community

In recent years, deep learning (DL), a re-branding of neural networks (NNs), has risen to the top in numerous areas, namely computer vision (CV), speech recognition, natural language processing, etc. Whereas remote sensing (RS) possesses a number of unique challenges, primarily related to sensors and applications, inevitably RS draws from many of the same theories as CV; e.g., statistics, fusion, and machine learning, to name a few. This means that the RS community should be aware of, if not at the leading edge of, of advancements like DL. Herein, we provide the most comprehensive survey of state-of-the-art RS DL research. We also review recent new developments in the DL field that can be used in DL for RS. Namely, we focus on theories, tools and challenges for the RS community. Specifically, we focus on unsolved challenges and opportunities as it relates to (i) inadequate data sets, (ii) human-understandable solutions for modelling physical phenomena, (iii) Big Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and learning algorithms for spectral, spatial and temporal data, (vi) transfer learning, (vii) an improved theoretical understanding of DL systems, (viii) high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote Sensin