Localization of adaptive variants in human genomes using averaged one-dependence estimation.

Statistical methods for identifying adaptive mutations from population genetic data face several obstacles: assessing the significance of genomic outliers, integrating correlated measures of selection into one analytic framework, and distinguishing adaptive variants from hitchhiking neutral variants. Here, we introduce SWIF(r), a probabilistic method that detects selective sweeps by learning the distributions of multiple selection statistics under different evolutionary scenarios and calculating the posterior probability of a sweep at each genomic site. SWIF(r) is trained using simulations from a user-specified demographic model and explicitly models the joint distributions of selection statistics, thereby increasing its power to both identify regions undergoing sweeps and localize adaptive mutations. Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity. SWIF(r) provides a transparent probabilistic framework for localizing beneficial mutations that is extensible to a variety of evolutionary scenarios

Bayesian semiparametric analysis for two-phase studies of gene-environment interaction

The two-phase sampling design is a cost-efficient way of collecting expensive covariate information on a judiciously selected subsample. It is natural to apply such a strategy for collecting genetic data in a subsample enriched for exposure to environmental factors for gene-environment interaction (G x E) analysis. In this paper, we consider two-phase studies of G x E interaction where phase I data are available on exposure, covariates and disease status. Stratified sampling is done to prioritize individuals for genotyping at phase II conditional on disease and exposure. We consider a Bayesian analysis based on the joint retrospective likelihood of phases I and II data. We address several important statistical issues: (i) we consider a model with multiple genes, environmental factors and their pairwise interactions. We employ a Bayesian variable selection algorithm to reduce the dimensionality of this potentially high-dimensional model; (ii) we use the assumption of gene-gene and gene-environment independence to trade off between bias and efficiency for estimating the interaction parameters through use of hierarchical priors reflecting this assumption; (iii) we posit a flexible model for the joint distribution of the phase I categorical variables using the nonparametric Bayes construction of Dunson and Xing [J. Amer. Statist. Assoc. 104 (2009) 1042-1051].Comment: Published in at http://dx.doi.org/10.1214/12-AOAS599 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Leak localization in water distribution networks using pressure and data-driven classifier approach

Leaks in water distribution networks (WDNs) are one of the main reasons for water loss during fluid transportation. Considering the worldwide problem of water scarcity, added to the challenges that a growing population brings, minimizing water losses through leak detection and localization, timely and efficiently using advanced techniques is an urgent humanitarian need. There are numerous methods being used to localize water leaks in WDNs through constructing hydraulic models or analyzing flow/pressure deviations between the observed data and the estimated values. However, from the application perspective, it is very practical to implement an approach which does not rely too much on measurements and complex models with reasonable computation demand. Under this context, this paper presents a novel method for leak localization which uses a data-driven approach based on limit pressure measurements in WDNs with two stages included: (1) Two different machine learning classifiers based on linear discriminant analysis (LDA) and neural networks (NNET) are developed to determine the probabilities of each node having a leak inside a WDN; (2) Bayesian temporal reasoning is applied afterwards to rescale the probabilities of each possible leak location at each time step after a leak is detected, with the aim of improving the localization accuracy. As an initial illustration, the hypothetical benchmark Hanoi district metered area (DMA) is used as the case study to test the performance of the proposed approach. Using the fitting accuracy and average topological distance (ATD) as performance indicators, the preliminary results reaches more than 80% accuracy in the best cases.Peer ReviewedPostprint (published version

Fast human motion prediction for human-robot collaboration with wearable interfaces

In this paper, we aim at improving human motion prediction during human-robot collaboration in industrial facilities by exploiting contributions from both physical and physiological signals. Improved human-machine collaboration could prove useful in several areas, while it is crucial for interacting robots to understand human movement as soon as possible to avoid accidents and injuries. In this perspective, we propose a novel human-robot interface capable to anticipate the user intention while performing reaching movements on a working bench in order to plan the action of a collaborative robot. The proposed interface can find many applications in the Industry 4.0 framework, where autonomous and collaborative robots will be an essential part of innovative facilities. A motion intention prediction and a motion direction prediction levels have been developed to improve detection speed and accuracy. A Gaussian Mixture Model (GMM) has been trained with IMU and EMG data following an evidence accumulation approach to predict reaching direction. Novel dynamic stopping criteria have been proposed to flexibly adjust the trade-off between early anticipation and accuracy according to the application. The output of the two predictors has been used as external inputs to a Finite State Machine (FSM) to control the behaviour of a physical robot according to user's action or inaction. Results show that our system outperforms previous methods, achieving a real-time classification accuracy of $94.3\pm2.9\%$ after $160.0msec\pm80.0msec$ from movement onset

A Comparative Study for 2D and 3D Computer-aided Diagnosis Methods for Solitary Pulmonary Nodules

Many computer-aided diagnosis (CAD) methods, including 2D and 3D approaches, have been proposed for solitary pulmonary nodules (SPNs). However, the detection and diagnosis of SPNs remain challenging in many clinical circumstances. One goal of this work is to investigate the relative diagnostic accuracy of 2D and 3D methods. An additional goal is to develop a two-stage approach that combines the simplicity of 2D and the accuracy of 3D methods. The experimental results show statistically significant differences between the diagnostic accuracy of 2D and 3D methods. The results also show that with a very minor drop in diagnostic performance the two-stage approach can significantly reduce the number of nodules needed to be processed by the 3D method, streamlining the computational demand