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.

Nonparametric Bayesian sparse factor models with application to gene expression modeling

A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data $\mathbf{Y}$ is modeled as a linear superposition, $\mathbf{G}$, of a potentially infinite number of hidden factors, $\mathbf{X}$. The Indian Buffet Process (IBP) is used as a prior on $\mathbf{G}$ to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated data sets based on a known sparse connectivity matrix for E. Coli, and on three biological data sets of increasing complexity.

Real time feature-based facial tracking using Lie algebras

We have developed a novel human facial tracking system that operates in real time at a video frame rate without needing any special hardware. The approach is based on the use of Lie algebra, and uses three-dimensional feature points on the targeted human face. It is assumed that the roughly estimated facial model (relative coordinates of the three-dimensional feature points) is known. First, the initial feature positions of the face are determined using a model fitting technique. Then, the tracking is operated by the following sequence: (1) capture the new video frame and render feature points to the image plane; (2) search for new positions of the feature points on the image plane; (3) get the Euclidean matrix from the moving vector and the three-dimensional information for the points; and (4) rotate and translate the feature points by using the Euclidean matrix, and render the new points on the image plane. The key algorithm of this tracker is to estimate the Euclidean matrix by using a least square technique based on Lie algebra. The resulting tracker performed very well on the task of tracking a human face.