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 of outlier detection methodologies

Outlier detection has been used for centuries to detect and, where appropriate, remove anomalous observations from data. Outliers arise due to mechanical faults, changes in system behaviour, fraudulent behaviour, human error, instrument error or simply through natural deviations in populations. Their detection can identify system faults and fraud before they escalate with potentially catastrophic consequences. It can identify errors and remove their contaminating effect on the data set and as such to purify the data for processing. The original outlier detection methods were arbitrary but now, principled and systematic techniques are used, drawn from the full gamut of Computer Science and Statistics. In this paper, we introduce a survey of contemporary techniques for outlier detection. We identify their respective motivations and distinguish their advantages and disadvantages in a comparative review

From patterned response dependency to structured covariate dependency: categorical-pattern-matching

Data generated from a system of interest typically consists of measurements from an ensemble of subjects across multiple response and covariate features, and is naturally represented by one response-matrix against one covariate-matrix. Likely each of these two matrices simultaneously embraces heterogeneous data types: continuous, discrete and categorical. Here a matrix is used as a practical platform to ideally keep hidden dependency among/between subjects and features intact on its lattice. Response and covariate dependency is individually computed and expressed through mutliscale blocks via a newly developed computing paradigm named Data Mechanics. We propose a categorical pattern matching approach to establish causal linkages in a form of information flows from patterned response dependency to structured covariate dependency. The strength of an information flow is evaluated by applying the combinatorial information theory. This unified platform for system knowledge discovery is illustrated through five data sets. In each illustrative case, an information flow is demonstrated as an organization of discovered knowledge loci via emergent visible and readable heterogeneity. This unified approach fundamentally resolves many long standing issues, including statistical modeling, multiple response, renormalization and feature selections, in data analysis, but without involving man-made structures and distribution assumptions. The results reported here enhance the idea that linking patterns of response dependency to structures of covariate dependency is the true philosophical foundation underlying data-driven computing and learning in sciences.Comment: 32 pages, 10 figures, 3 box picture

Terrain classification for a quadruped robot

Using data retrieved from the Puppy II robot at the University of Zurich (UZH), we show that machine learning techniques with non-linearities and fading memory are effective for terrain classification, both supervised and unsupervised, even with a limited selection of input sensors. The results indicate that most information for terrain classification is found in the combination of tactile sensors and proprioceptive joint angle sensors. The classification error is small enough to have a robot adapt the gait to the terrain and hence move more robustly