We propose an unsupervised methodology using independent component analysis (ICA) to cluster genes from DNA microarray data. Based on an ICA mixture model of genomic expression patterns, linear and nonlinear ICA finds components that are specific to certain biological processes. Genes that exhibit significant up-regulation or down-regulation within each component are grouped into clusters. We test the statistical significance of enrichment of gene annotations within each cluster. ICA-based clustering outperformed other leading methods in constructing functionally coherent clusters on various datasets. This result supports our model of genomic expression data as composite effect of independent biological processes. Comparison of clustering performance among various ICA algorithms including a kernel-based nonlinear ICA algorithm shows that nonlinear ICA performed the best for small datasets and natural-gradient maximization-likelihood worked well for all the datasets.

Computer animated agents and robots bring a social dimension to human computer interaction and force us to think in new ways about how computers could be used in daily life. Face to face communication is a real-time process operating at a time scale of less than a second. In this paper we present progress on a perceptual primitive to automatically detect frontal faces in the video stream and code them with respect to 7 dimensions in real time: neutral, anger, disgust, fear, joy, sadness, surprise. The face finder employs a cascade of feature detectors trained with boosting techniques [13, 2]. The expression recognizer employs a novel combination of Adaboost and SVM's. The generalization performance to new subjects for a 7-way forced choice was 93.3% and 97% correct on two publicly available datasets. The outputs of the classifier change smoothly as a function of time, providing a potentially valuable representation to code facial expression dynamics in a fully automatic and unobtrusive manner. The system was deployed and evaluated for measuring spontaneous facial expressions in the field in an application for automatic assessment of human-robot interaction.

We present the software architecture of a robotic system for mapping abandoned mines. The software is capable of acquiring consistent 2D maps of large mines with many cycles, represented as Markov random £elds.

We propose a functional mixture model for simultaneous clustering and alignment of sets of curves measured on a discrete time grid. The model is specifically tailored to gene expression time course data. Each functional cluster center is a nonlinear combination of solutions of a simple linear differential equation that describes the change of individual mRNA levels when the synthesis and decay rates are constant. The mixture of continuous time parametric functional forms allows one to (a) account for the heterogeneity in the observed profiles, (b) align the profiles in time by estimating real-valued time shifts, (c) capture the synthesis and decay of mRNA in the course of an experiment, and (d) regularize noisy profiles by enforcing smoothness in the mean curves. We derive an EM algorithm for estimating the parameters of the model, and apply the proposed approach to the set of cycling genes in yeast. The experiments show consistent improvement in predictive power and within cluster variance compared to regular Gaussian mixtures.

Pairwise coupling is a popular multi-class classification method that combines together all pairwise comparisons for each pair of classes. This paper presents two approaches for obtaining class probabilities. Both methods can be reduced to linear systems and are easy to implement. We show conceptually and experimentally that the proposed approaches are more stable than two existing popular methods: voting and [3].

We attempt to understand visual classification in humans using both psychophysical and machine learning techniques. Frontal views of human faces were used for a gender classification task. Human subjects classified the faces and their gender judgment, reaction time and confidence rating were recorded. Several hyperplane learning algorithms were used on the same classification task using the Principal Components of the texture and shape representation of the faces. The classification performance of the learning algorithms was estimated using the face database with the true gender of the faces as labels, and also with the gender estimated by the subjects.

We present an analysis of concentration-of-expectation phenomena in layered Bayesian networks that use generalized linear models as the local conditional probabilities. This framework encompasses a wide variety of probability distributions, including both discrete and continuous random variables. We utilize ideas from large deviation analysis and the delta method to devise and evaluate a class of approximate inference algorithms for layered Bayesian networks that have superior asymptotic error bounds and very fast computation time.

Principal components analysis (PCA) is one of the most widely used techniques in machine learning and data mining. Minor components analysis (MCA) is less well known, but can also play an important role in the presence of constraints on the data distribution. In this paper we present a probabilistic model for "extreme components analysis" (XCA) which at the maximum likelihood solution extracts an optimal combination of principal and minor components. For a given number of components, the log-likelihood of the XCA model is guaranteed to be larger or equal than that of the probabilistic models for PCA and MCA. We describe an efficient algorithm to solve for the globally optimal solution. For log-convex spectra we prove that the solution consists of principal components only, while for log-concave spectra the solution consists of minor components. In general, the solution admits a combination of both. In experiments we explore the properties of XCA on some synthetic and real-world datasets.

The decision functions constructed by support vector machines (SVM's) usually depend only on a subset of the training set--the so-called support vectors. We derive asymptotically sharp lower and upper bounds on the number of support vectors for several standard types of SVM's. In particular, we show for the Gaussian RBF kernel that the fraction of support vectors tends to twice the Bayes risk for the L1-SVM, to the probability of noise for the L2-SVM, and to 1 for the LS-SVM.

The Google search engine has enjoyed huge success with its web page ranking algorithm, which exploits global, rather than local, hyperlink structure of the web using random walks. Here we propose a simple universal ranking algorithm for data lying in the Euclidean space, such as text or image data. The core idea of our method is to rank the data with respect to the intrinsic manifold structure collectively revealed by a great amount of data. Encouraging experimental results from synthetic, image, and text data illustrate the validity of our method.