Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping

Interpretation of allelic copy measurements at polymorphic markers in cancer samples presents distinctive challenges and opportunities. Due to frequent gross chromosomal alterations occurring in cancer (aneuploidy), many genomic regions are present at homologous-allele imbalance. Within such regions, the unequal contribution of alleles at heterozygous markers allows for direct phasing of the haplotype derived from each individual parent. In addition, genome-wide estimates of homologue specific copy- ratios (HSCRs) are important for interpretation of the cancer genome in terms of fixed integral copy-numbers. We describe HAPSEG, a probabilistic method to interpret bi- allelic marker data in cancer samples. HAPSEG operates by partitioning the genome into segments of distinct copy number and modeling the four distinct genotypes in each segment. We describe general methods for fitting these models to data which are suit- able for both SNP microarrays and massively parallel sequencing data. In addition, we demonstrate a specially tailored error-model for interpretation of systematic variations arising in microarray platforms. The ability to directly determine haplotypes from cancer samples represents an opportunity to expand reference panels of phased chromosomes, which may have general interest in various population genetic applications. In addition, this property may be exploited to interrogate the relationship between germline risk and cancer phenotype with greater sensitivity than is possible using unphased genotype. Finally, we exploit the statistical dependency of phased genotypes to enable the fitting of more elaborate sample-level error-model parameters, allowing more accurate estimation of HSCRs in cancer samples

Deep Neural Networks for ECG-Based Pulse Detection during Out-of-Hospital Cardiac Arrest

The automatic detection of pulse during out-of-hospital cardiac arrest (OHCA) is necessary for the early recognition of the arrest and the detection of return of spontaneous circulation (end of the arrest). The only signal available in every single defibrillator and valid for the detection of pulse is the electrocardiogram (ECG). In this study we propose two deep neural network (DNN) architectures to detect pulse using short ECG segments (5 s), i.e., to classify the rhythm into pulseless electrical activity (PEA) or pulse-generating rhythm (PR). A total of 3914 5-s ECG segments, 2372 PR and 1542 PEA, were extracted from 279 OHCA episodes. Data were partitioned patient-wise into training (80%) and test (20%) sets. The first DNN architecture was a fully convolutional neural network, and the second architecture added a recurrent layer to learn temporal dependencies. Both DNN architectures were tuned using Bayesian optimization, and the results for the test set were compared to state-of-the art PR/PEA discrimination algorithms based on machine learning and hand crafted features. The PR/PEA classifiers were evaluated in terms of sensitivity (Se) for PR, specificity (Sp) for PEA, and the balanced accuracy (BAC), the average of Se and Sp. The Se/Sp/BAC of the DNN architectures were 94.1%/92.9%/93.5% for the first one, and 95.5%/91.6%/93.5% for the second one. Both architectures improved the performance of state of the art methods by more than 1.5 points in BAC.This work was supported by: The Spanish Ministerio de Economía y Competitividad, TEC2015-64678-R, jointly with the Fondo Europeo de Desarrollo Regional (FEDER), UPV/EHU via GIU17/031 and the Basque Government through the grant PRE_2018_2_0260

The group fused Lasso for multiple change-point detection

We present the group fused Lasso for detection of multiple change-points shared by a set of co-occurring one-dimensional signals. Change-points are detected by approximating the original signals with a constraint on the multidimensional total variation, leading to piecewise-constant approximations. Fast algorithms are proposed to solve the resulting optimization problems, either exactly or approximately. Conditions are given for consistency of both algorithms as the number of signals increases, and empirical evidence is provided to support the results on simulated and array comparative genomic hybridization data

Current Challenges and Visions in Music Recommender Systems Research

Music recommender systems (MRS) have experienced a boom in recent years, thanks to the emergence and success of online streaming services, which nowadays make available almost all music in the world at the user's fingertip. While today's MRS considerably help users to find interesting music in these huge catalogs, MRS research is still facing substantial challenges. In particular when it comes to build, incorporate, and evaluate recommendation strategies that integrate information beyond simple user--item interactions or content-based descriptors, but dig deep into the very essence of listener needs, preferences, and intentions, MRS research becomes a big endeavor and related publications quite sparse. The purpose of this trends and survey article is twofold. We first identify and shed light on what we believe are the most pressing challenges MRS research is facing, from both academic and industry perspectives. We review the state of the art towards solving these challenges and discuss its limitations. Second, we detail possible future directions and visions we contemplate for the further evolution of the field. The article should therefore serve two purposes: giving the interested reader an overview of current challenges in MRS research and providing guidance for young researchers by identifying interesting, yet under-researched, directions in the field

Challenges of Big Data Analysis

Big Data bring new opportunities to modern society and challenges to data scientists. On one hand, Big Data hold great promises for discovering subtle population patterns and heterogeneities that are not possible with small-scale data. On the other hand, the massive sample size and high dimensionality of Big Data introduce unique computational and statistical challenges, including scalability and storage bottleneck, noise accumulation, spurious correlation, incidental endogeneity, and measurement errors. These challenges are distinguished and require new computational and statistical paradigm. This article give overviews on the salient features of Big Data and how these features impact on paradigm change on statistical and computational methods as well as computing architectures. We also provide various new perspectives on the Big Data analysis and computation. In particular, we emphasis on the viability of the sparsest solution in high-confidence set and point out that exogeneous assumptions in most statistical methods for Big Data can not be validated due to incidental endogeneity. They can lead to wrong statistical inferences and consequently wrong scientific conclusions

Low Complexity Regularization of Linear Inverse Problems

Inverse problems and regularization theory is a central theme in contemporary signal processing, where the goal is to reconstruct an unknown signal from partial indirect, and possibly noisy, measurements of it. A now standard method for recovering the unknown signal is to solve a convex optimization problem that enforces some prior knowledge about its structure. This has proved efficient in many problems routinely encountered in imaging sciences, statistics and machine learning. This chapter delivers a review of recent advances in the field where the regularization prior promotes solutions conforming to some notion of simplicity/low-complexity. These priors encompass as popular examples sparsity and group sparsity (to capture the compressibility of natural signals and images), total variation and analysis sparsity (to promote piecewise regularity), and low-rank (as natural extension of sparsity to matrix-valued data). Our aim is to provide a unified treatment of all these regularizations under a single umbrella, namely the theory of partial smoothness. This framework is very general and accommodates all low-complexity regularizers just mentioned, as well as many others. Partial smoothness turns out to be the canonical way to encode low-dimensional models that can be linear spaces or more general smooth manifolds. This review is intended to serve as a one stop shop toward the understanding of the theoretical properties of the so-regularized solutions. It covers a large spectrum including: (i) recovery guarantees and stability to noise, both in terms of $\ell^2$-stability and model (manifold) identification; (ii) sensitivity analysis to perturbations of the parameters involved (in particular the observations), with applications to unbiased risk estimation ; (iii) convergence properties of the forward-backward proximal splitting scheme, that is particularly well suited to solve the corresponding large-scale regularized optimization problem

Training Echo State Networks with Regularization through Dimensionality Reduction

In this paper we introduce a new framework to train an Echo State Network to predict real valued time-series. The method consists in projecting the output of the internal layer of the network on a space with lower dimensionality, before training the output layer to learn the target task. Notably, we enforce a regularization constraint that leads to better generalization capabilities. We evaluate the performances of our approach on several benchmark tests, using different techniques to train the readout of the network, achieving superior predictive performance when using the proposed framework. Finally, we provide an insight on the effectiveness of the implemented mechanics through a visualization of the trajectory in the phase space and relying on the methodologies of nonlinear time-series analysis. By applying our method on well known chaotic systems, we provide evidence that the lower dimensional embedding retains the dynamical properties of the underlying system better than the full-dimensional internal states of the network

Hybrid Neural Network and Support Vector Machine Method for Optimization

System and method for optimization of a design associated with a response function, using a hybrid neural net and support vector machine (NN/SVM) analysis to minimize or maximize an objective function, optionally subject to one or more constraints. As a first example, the NN/SVM analysis is applied iteratively to design of an aerodynamic component, such as an airfoil shape, where the objective function measures deviation from a target pressure distribution on the perimeter of the aerodynamic component. As a second example, the NN/SVM analysis is applied to data classification of a sequence of data points in a multidimensional space. The NN/SVM analysis is also applied to data regression

Health Assessment and Life Prediction of cutting tools based on support vector regression.

International audienceThe integrity of machining tools is important to maintain a high level of surface quality. The wear of the tool can lead to poor surface quality of the workpiece and even to damage of the machine. Furthermore, in some applications such as aeronautics and precision engineering, it is preferable to change the tool earlier rather than to loose the workpiece because of its high price compared to the tool's one. Thus, to maintain a high quality of the manufactured pieces, it is necessary to assess and predict the level of wear of the cutting tool. This can be done by using condition monitoring and prognostics. The aim is then to estimate and predict the amount of wear and calculate the remaining useful life of the cutting tool. This paper presents a method for tool condition assessment and life prediction. The method is based on nonlinear feature reduction and support vector regression. The number of original features extracted from the monitoring signals is first reduced. These features are then used to learn nonlinear regression models to estimate and predict the level of wear. The method is applied on experimental data taken from a set of cuttings and simulation results are given. These results show that the proposed method is suitable for assessing the wear evolution of the cutting tools and predicting their remaining useful life. This information can then be used by the operators to take appropriate maintenance actions