A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Novel applications of BEM based Poisson level set approach

Accurate and efficient computation of the distance function d for a given domain is important for many areas of numerical modeling. Partial differential (e.g. HamiltonJacobi type) equation based distance function algorithms have desirable computational efficiency and accuracy. In this study, as an alternative, a Poisson equation based level set (distance function) is considered and solved using the meshless boundary element method (BEM). The application of this for shape topology analysis, including the medial axis for domain decomposition, geometric de-featuring and other aspects of numerical modeling is assessed. © 2011 Elsevier Ltd. All rights reserved.

Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

From subspace learning to distance learning: A geometrical optimization approach

In this paper, we adopt a differential-geometry viewpoint to tackle the problem of learning a distance online. As this problem can be cast into the estimation of a fixed-rank positive semidefinite (PSD) matrix, we develop algorithms that exploits the rich geometry structure of the set of fixed-rank PSD matrices. We propose a method which separately updates the subspace of the matrix and its projection onto that subspace. A proper weighting of the two iterations enables to continuously interpolate between the problem of learning a subspace and learning a distance when the subspace is fixed. © 2009 IEEE.

A perturbation approach to the stabilization of nonlinear cascade systems with time-delay

The effect of bounded input perturbations on the stability of nonlinear globally asymptotically stable delay differential equations is analyzed. We investigate under which conditions global stability is preserved and if not, whether semi-global stabilization is possible by controlling the size or shape of the perturbation. These results are used to study the stabilization of partially linear cascade systems with partial state feedback.