Bayesian detection of piecewise linear trends in replicated time-series with application to growth data modelling

We consider the situation where a temporal process is composed of contiguous segments with differing slopes and replicated noise-corrupted time series measurements are observed. The unknown mean of the data generating process is modelled as a piecewise linear function of time with an unknown number of change-points. We develop a Bayesian approach to infer the joint posterior distribution of the number and position of change-points as well as the unknown mean parameters. A-priori, the proposed model uses an overfitting number of mean parameters but, conditionally on a set of change-points, only a subset of them influences the likelihood. An exponentially decreasing prior distribution on the number of change-points gives rise to a posterior distribution concentrating on sparse representations of the underlying sequence. A Metropolis-Hastings Markov chain Monte Carlo (MCMC) sampler is constructed for approximating the posterior distribution. Our method is benchmarked using simulated data and is applied to uncover differences in the dynamics of fungal growth from imaging time course data collected from different strains. The source code is available on CRAN.Comment: Accepted to International Journal of Biostatistic

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

<p>Abstract</p> <p>Background</p> <p>High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH) analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses.</p> <p>Results</p> <p>We propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances.</p> <p>Conclusions</p> <p>TumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH) in the tumor from allelic signals of Affymetrix or Illumina origin. We also conclude that high-precision allelic estimates can be obtained from a single pair of tumor-normal hybridizations, if TumorBoost is combined with single-array preprocessing methods such as (allele-specific) CRMA v2 for Affymetrix or BeadStudio's (proprietary) XY-normalization method for Illumina. A bounded-memory implementation is available in the open-source and cross-platform R package <it>aroma.cn</it>, which is part of the Aroma Project (<url>http://www.aroma-project.org/</url>).</p

A Kernel Multiple Change-point Algorithm via Model Selection

International audienceWe tackle the change-point problem with data belonging to a general set. We build a penalty for choosing the number of change-points in the kernel-based method of Harchaoui and Cappé (2007). This penalty generalizes the one proposed by Lebarbier (2005) for one-dimensional signals. We prove a non-asymptotic oracle inequality for the proposed method, thanks to a new concentration result for some function of Hilbert-space valued random variables. Experiments on synthetic data illustrate the accuracy of our method, showing that it can detect changes in the whole distribution of data, even when the mean and variance are constant

Joint segmentation of multivariate Gaussian processes using mixed linear models

The joint segmentation of multiple series is considered. A mixed linear model is used to account for both covariates and correlations between signals. An estimation algorithm based on EM which involves a new dynamic programming strategy for the segmentation step is proposed. The computational efficiency of this procedure is shown and its performance is assessed through simulation experiments. Applications are presented in the field of climatic data analysis. (C) 2010 Elsevier B.V. All rights reserved

Joint segmentation of multivariate Gaussian processes using mixed linear models

International audienceWe consider the joint segmentation of multiple series. We use a mixed linear model to account for both covariates and correlations between signals. We propose an estimation algorithm based on EM which involves dynamic programming for the segmentation step. We show the computational e±ciency of this procedure. An application to microarray CGH profiles from multiple patients is presented