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 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.

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.

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.

Many real-world domains are relational in nature, consisting of a set of objects related to each other in complex ways. This paper focuses on predicting the existence and the type of links between entities in such domains. We apply the relational Markov network framework of Taskar et al. to define a joint probabilistic model over the entire link graph -- entity attributes and links. The application of the RMN algorithm to this task requires the definition of probabilistic patterns over subgraph structures. We apply this method to two new relational datasets, one involving university webpages, and the other a social network. We show that the collective classification approach of RMNs, and the introduction of subgraph patterns over link labels, provide significant improvements in accuracy over flat classification, which attempts to predict each link in isolation.

Eigenvoice speaker adaptation has been shown to be effective when only a small amount of adaptation data is available. At the heart of the method is principal component analysis (PCA) employed to find the most important eigenvoices. In this paper, we postulate that nonlinear PCA, in particular kernel PCA, may be even more effective. One major challenge is to map the feature-space eigenvoices back to the observation space so that the state observation likelihoods can be computed during the estimation of eigenvoice weights and subsequent decoding. Our solution is to compute kernel PCA using composite kernels, and we will call our new method kernel eigenvoice speaker adaptation. On the TIDIGITS corpus, we found that compared with a speaker-independent model, our kernel eigenvoice adaptation method can reduce the word error rate by 28-33% while the standard eigenvoice approach can only match the performance of the speaker-independent model.

We present and empirically test a novel approach for categorizing 3-D free form object shapes represented by range data. In contrast to traditional surface-signature based systems that use alignment to match specific objects, we adapted the newly introduced symbolic-signature representation to classify deformable shapes [10]. Our approach constructs an abstract description of shape classes using an ensemble of classifiers that learn object class parts and their corresponding geometrical relationships from a set of numeric and symbolic descriptors. We used our classification engine in a series of large scale discrimination experiments on two well-defined classes that share many common distinctive features. The experimental results suggest that our method outperforms traditional numeric signature-based methodologies.

We argue that K-means and deterministic annealing algorithms for geometric clustering can be derived from the more general Information Bottleneck approach. If we cluster the identities of data points to preserve information about their location, the set of optimal solutions is massively degenerate. But if we treat the equations that define the optimal solution as an iterative algorithm, then a set of "smooth" initial conditions selects solutions with the desired geometrical properties. In addition to conceptual unification, we argue that this approach can be more efficient and robust than classic algorithms.

We propose a method for sequential Bayesian kernel regression. As is the case for the popular Relevance Vector Machine (RVM) [10, 11], the method automatically identifies the number and locations of the kernels. Our algorithm overcomes some of the computational difficulties related to batch methods for kernel regression. It is non-iterative, and requires only a single pass over the data. It is thus applicable to truly sequential data sets and batch data sets alike. The algorithm is based on a generalisation of Importance Sampling, which allows the design of intuitively simple and efficient proposal distributions for the model parameters. Comparative results on two standard data sets show our algorithm to compare favourably with existing batch estimation strategies.