In bioinformatics it is often desirable to combine data from various measurement sources and thus structured feature vectors are to be analyzed that possess different intrinsic blocking characteristics (e.g., different patterns of missing values, observation noiselevels, effective intrinsic dimensionalities). We propose a new machine learning tool, heterogeneous component analysis (HCA), for feature extraction in order to better understand the factors that underlie such complex structured heterogeneous data. HCA is a linear block-wise sparse Bayesian PCA based not only on a probabilistic model with block-wise residual variance terms but also on a Bayesian treatment of a block-wise sparse factor-loading matrix. We study various algorithmsthat implement our HCA concept extracting sparse heterogeneous structure by obtaining common components for the blocks and specific components withineach block. Simulations on toy and bioinformatics data underline the usefulness of the proposed structured matrix factorization concept.

We introduce a hierarchical Bayesian model for the discovery of putative regulators from gene expression data only. The hierarchy incorporates the knowledge that there are just a few regulators that by themselves only regulate a handful of genes. This is implemented through a so-called spike-and-slab prior, a mixture of Gaussians with different widths, with mixing weights from a hierarchical Bernoulli model. For efficient inference we implemented expectation propagation. Running the model on a malaria parasite data set, we found four genes with significant homology to transcription factors in an amoebe, one RNA regulator and three genes of unknown function (out of the top ten genes considered).

We propose a method for reconstruction of human brain states directly from functional neuroimaging data. The method extends the traditional multivariate regression analysis of discretized fMRI data to the domain of stochastic functional measurements, facilitating evaluation of brain responses to naturalistic stimuli and boosting the power of functional imaging. The method searches for sets of voxel timecourses that optimize a multivariate functional linear model in terms of Rsquare-statistic. Population based incremental learning is used to search for spatially distributed voxel clusters, taking into account the variation in Haemodynamic lag across brain areas and among subjects by voxel-wise non-linear registration of stimuli to fMRI data. The method captures spatially distributed brain responses to naturalistic stimuli without attempting to localize function. Application of the method for prediction of naturalistic stimuli from new and unknown fMRI data shows that the approach is capable of identifying distributed clusters of brain locations that are highly predictive of a specific stimuli.

Gunnar Rätsch Friedrich Miescher Laboratory Max Planck Society Tübingen, Germany We present a novel boosting algorithm, called SoftBoost, designed for sets of binary labeledexamples that are not necessarily separable by convex combinations of base hypotheses. Our algorithm achieves robustness by capping the distributions onthe examples. Our update of the distribution is motivated by minimizing a relative entropy subject to the capping constraints and constraints on the edges of the obtained base hypotheses. The capping constraints imply a soft margin in the dual optimization problem. Our algorithm produces a convex combination of hypotheses whose soft margin is within δ of its maximum.

This contribution develops a theoretical framework that takes into account the effect of approximate optimization on learning algorithms. The analysis shows distinct tradeoffs for the case of small-scale and large-scale learning problems. Small-scale learning problems are subject to the usual approximation--estimation tradeoff. Large-scale learning problems are subject to a qualitatively different tradeoff involving the computational complexity of the underlying optimization algorithms in non-trivial ways.

Clustering is often formulated as a discrete optimization problem. The objective is to find, among all partitions of the data set, the best one according to some quality measure. However, in the statistical setting where we assume that the finite data set has been sampled from some underlying space, the goal is not to find the best partition of the given sample, but to approximate the true partition of the underlying space.We argue that the discrete optimization approach usually does not achieve this goal. As an alternative, we suggest the paradigm of "nearest neighbor clustering". Instead of selecting the best out of all partitions of the sample, it only considers partitions in some restricted function class. Using tools from statistical learning theory we prove that nearest neighbor clustering is statistically consistent. Moreover,its worst case complexity is polynomial by construction, and it can be implemented with small average case complexity using branch and bound.

Markov jump processes play an important role in a large number of application domains. However, realistic systems are analytically intractable and they have traditionally been analysed using simulation based techniques, which do not provide a framework for statistical inference. We propose a mean field approximation to perform posterior inference and parameter estimation. The approximation allows a practical solution to the inference problem, {while still retaining a good degree of accuracy.} We illustrate our approach on two biologically motivated systems.

When predicting class labels for objects within a relational database, it is often helpful to consider a model for relationships: this allows for information between class labels to be shared and to improve prediction performance. However, there are different ways by which objects can be related within a relational database. One traditional way corresponds to a Markov network structure: each existing relation is represented by an undirected edge. This encodes that, conditioned on input features, each object label is independent of other object labels given its neighbors in the graph. However, there is no reason why Markov networks should be the only representation of choice for symmetric dependence structures. Here we discuss the case when relationships are postulated to exist due to hidden common causes.We discuss how the resulting graphical model differs from Markov networks, and how it describes different types of real-world relational processes. A Bayesian nonparametric classification model is built upon this graphical representation andevaluated with several empirical studies.

Assessing similarity between features is a key step in object recognition and scene categorization tasks. We argue that knowledge on the distribution of distances generated by similarity functions is crucial in deciding whether features are similar or not. Intuitively one would expect that similarities between features could arise from any distribution. In this paper, we will derive the contrary, and report the theoretical result that $L_p$-norms --a class of commonly applied distance metrics-- from one feature vector to other vectors are Weibull-distributed if the feature values are correlated and non-identically distributed. Besides these assumptions being realistic for images, we experimentally show them to hold for various popular feature extraction algorithms, for a diverse range of images. This fundamental insight opens new directions in the assessment of feature similarity, with projected improvements in object and scene recognition algorithms. Erratum: The authors of paper have declared that they have become convinced that the reasoning in the reference is too simple as a proof of their claims. As a consequence, they withdraw their theorems.

Maximum entropy analysis of binary variables provides an elegant way for studying therole of pairwise correlations in neural populations. Unfortunately, these approaches suffer from their poor scalability to high dimensions. In sensory coding, however,high-dimensional data is ubiquitous. Here, we introduce a new approach using a near-maximum entropy model, that makes this type of analysis feasiblefor very high-dimensional data--the model parameters can be derived in closed form and sampling is easy. Therefore, our NearMaxEnt approach can serve as a tool for testing predictions from a pairwise maximum entropy model not only for low-dimensional marginals, but also for high dimensional measurements of more than thousand units. We demonstrate its usefulness by studying natural images with dichotomized pixel intensities. Our results indicate that the statistics of such higher-dimensional measurements exhibit additional structure that are not predicted by pairwise correlations, despite the fact that pairwise correlations explain thelower-dimensional marginal statistics surprisingly well up to the limit of dimensionality where estimation of the full joint distribution is feasible.