Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

We analyze the betweenness centrality (BC) of nodes in large complex networks. In general, the BC is increasing with connectivity as a power law with an exponent $\eta$. We find that for trees or networks with a small loop density $\eta=2$ while a larger density of loops leads to $\eta<2$. For scale-free networks characterized by an exponent $\gamma$ which describes the connectivity distribution decay, the BC is also distributed according to a power law with a non universal exponent $\delta$. We show that this exponent $\delta$ must satisfy the exact bound $\delta\geq (\gamma+1)/2$. If the scale free network is a tree, then we have the equality $\delta=(\gamma+1)/2$.

Betweenness Centrality in Large Complex Networks

One of the most powerful tools to assess the dynamical characteristics of time series is entropy. Sample entropy (SE), though powerful, is not fast enough, especially for long signals. Permutation entropy (PE), as a broadly used irregularity indicator, considers only the order of the amplitude values and hence some information regarding the amplitudes may be discarded. To tackle these problems, we introduce a new method, termed dispersion entropy (DE), to quantify the regularity of time series. We gain insight into the dependency of DE on several straightforward signal-processing concepts via a set of synthetic time series. The results show that DE, unlike PE, can detect the noise bandwidth and simultaneous frequency and amplitude change. We also employ DE to three publicly available real datasets. The simulations on real-valued signals show that the DE method considerably outperforms PE to discriminate different groups of each dataset. In addition, the computation time of DE is significantly less than that of SE and PE.

Dispersion Entropy: A Measure for Time-Series Analysis

In this paper we present a review of the most current avenues of research into Kinect-based elderly care and stroke rehabilitation systems to provide an overview of the state of the art, limitations, and issues of concern as well as suggestions for future work in this direction. The central purpose of this review was to collect all relevant study information into one place in order to support and guide current research as well as inform researchers planning to embark on similar studies or applications. The paper is structured into three main sections, each one presenting a review of the literature for a specific topic. Elderly Care section is comprised of two subsections: Fall detection and Fall risk reduction. Stroke Rehabilitation section contains studies grouped under Evaluation of Kinect’s spatial accuracy, and Kinect-based rehabilitation methods. The third section, Serious and exercise games, contains studies that are indirectly related to the first two sections and present a complete system for elderly care or stroke rehabilitation in a Kinect-based game format. Each of the three main sections conclude with a discussion of limitations of Kinect in its respective applications. The paper concludes with overall remarks regarding use of Kinect in elderly care and stroke rehabilitation applications and suggestions for future work. A concise summary with significant findings and subject demographics (when applicable) of each study included in the review is also provided in table format.

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Systematic review of Kinect applications in elderly care and stroke rehabilitation

Permutation entropy (PE) has been recently suggested as a novel measure to characterize the complexity of nonlinear time series. In this paper, we propose a simple method to address some of PE's limitations, mainly its inability to differentiate between distinct patterns of a certain motif and the sensitivity of patterns close to the noise floor. The method relies on the fact that patterns may be too disparate in amplitudes and variances and proceeds by assigning weights for each extracted vector when computing the relative frequencies associated with every motif. Simulations were conducted over synthetic and real data for a weighting scheme inspired by the variance of each pattern. Results show better robustness and stability in the presence of higher levels of noise, in addition to a distinctive ability to extract complexity information from data with spiky features or having abrupt changes in magnitude.

Weighted-permutation entropy: a complexity measure for time series incorporating amplitude information.

Although neuropsychiatric (NP) disorders are among the top causes of disability worldwide with enormous financial costs, they can still be viewed as part of the most complex disorders that are of unknown etiology and incomprehensible pathophysiology. The complexity of NP disorders arises from their etiologic heterogeneity and the concurrent influence of environmental and genetic factors. In addition, the absence of rigid boundaries between the normal and diseased state, the remarkable overlap of symptoms among conditions, the high inter-individual and inter-population variations, and the absence of discriminative molecular and/or imaging biomarkers for these diseases makes difficult an accurate diagnosis. Along with the complexity of NP disorders, the practice of psychiatry suffers from a “top-down” method that relied on symptom checklists. Although checklist diagnoses cost less in terms of time and money, they are less accurate than a comprehensive assessment. Thus, reliable and objective diagnostic tools such as biomarkers are needed that can detect and discriminate among NP disorders. The real promise in understanding the pathophysiology of NP disorders lies in bringing back psychiatry to its biological basis in a systemic approach which is needed given the NP disorders’ complexity to understand their normal functioning and response to perturbation. This approach is implemented in the systems biology discipline that enables the discovery of disease-specific NP biomarkers for diagnosis and therapeutics. Systems biology involves the use of sophisticated computer software “omics”-based discovery tools and advanced performance computational techniques in order to understand the behavior of biological systems and identify diagnostic and prognostic biomarkers specific for NP disorders together with new targets of therapeutics. In this review, we try to shed light on the need of systems biology, bioinformatics and biomarkers in neuropsychiatry, and illustrate how the kn

/pdf/systems-biology-bioinformatics-and-biomarkers-in-3l1t12c3zp.pdf

Systems biology, bioinformatics, and biomarkers in neuropsychiatry.

The exquisite human ability to perceive facial features has been explained by the activity of neurons particularly responsive to faces, found in the fusiform gyrus and the anterior part of the superior temporal sulcus. This study hypothesizes and demonstrates that it is possible to automatically discriminate face processing from processing of a simple control stimulus based on processed EEGs in an online fashion with high temporal resolution using measures of statistical dependence applied on steady-state visual evoked potentials. Correlation, mutual information, and a novel measure of association, referred to as generalized measure of association (GMA), were applied on filtered current source density data. Dependences between channel locations were assessed for two separate conditions elicited by distinct pictures (a face and a Gabor grating) flickering at a rate of 17.5 Hz. Filter settings were chosen to minimize the distortion produced by bandpassing parameters on dependence estimation. Statistical analysis was performed for automated stimulus classification using the Kolmogorov-Smirnov test. Results show active regions in the occipito-parietal part of the brain for both conditions with a greater dependence between occipital and inferotemporal sites for the face stimulus. GMA achieved a higher performance in discriminating the two conditions. Because no additional face-like stimuli were examined, this study established a basic difference between one particular face and one nonface stimulus. Future work may use additional stimuli and experimental manipulations to determine the specificity of the current connectivity results.

/pdf/quantifying-cognitive-state-from-eeg-using-dependence-ddvnx6d8d3.pdf

Quantifying Cognitive State From EEG Using Dependence Measures

The purpose of this paper is two-fold: first, to propose a modification to the generalized measure of association (GMA) framework that reduces the effect of temporal structure in time series; second, to assess the reliability of using association methods to capture dependence between pairs of EEG channels using their time series or envelopes. To achieve the first goal, the GMA algorithm was updated so as to minimize the effect of the correlation inherent in the time structure. The reliability of the modified scheme was then assessed on both synthetic and real data. Synthetic data was generated from a Clayton copula, for which null hypotheses of uncorrelatedness were constructed for the signal. The signal was processed such that the envelope emulated important characteristics of experimental EEG data. Results show that the modified GMA procedure can capture pairwise dependence between generated signals as well as their envelopes with good statistical power. Furthermore, applying GMA and Kendall's tau to quantify dependence using the extracted envelopes of processed EEG data concords with previous findings using the signal itself.

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An Association Framework to Analyze Dependence Structure in Time Series

/pdf/engineering-in-medicine-and-biology-society-embc-2012-annual-14bwtbsyoh.pdf

Bilal H. Fadlallah

Papers

Weighted-permutation entropy: a complexity measure for time series incorporating amplitude information.

Systems biology, bioinformatics, and biomarkers in neuropsychiatry.

Quantifying Cognitive State From EEG Using Dependence Measures

An Association Framework to Analyze Dependence Structure in Time Series

Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE