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 noise levels, 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 algorithms that implement our HCA concept extracting sparse heterogeneous structure by obtaining common components for the blocks and specific components within each block. Simulations on toy and bioinformatics data underline the usefulness of the proposed structured matrix factorization concept.

We extend position and phase-shift tuning, concepts already well established in the disparity energy neuron literature, to motion energy neurons. We show that Reichardt-like detectors can be considered examples of position tuning, and that motion energy filters whose complex valued spatiotemporal receptive fields are space-time separable can be considered examples of phase tuning. By combining these two types of detectors, we obtain an architecture for constructing motion energy neurons whose center frequencies can be adjusted by both phase and position shifts. Similar to recently described neurons in the primary visual cortex, these new motion energy neurons exhibit tuning that is between purely spacetime separable and purely speed tuned. We propose a functional role for this intermediate level of tuning by demonstrating that comparisons between pairs of these motion energy neurons can reliably discriminate between inputs whose velocities lie above or below a given reference velocity.

Point-based algorithms have been surprisingly successful in computing approximately optimalsolutions for partially observable Markov decision processes (POMDPs) in high dimensional belief spaces. In this work, we seek to understand the belief-space properties that allow some POMDP problems to be approximated efficiently and thus help to explain the point-based algorithms' success often observed inthe experiments. We show that an approximately optimal POMDP solution can be computed in time polynomial in the covering number of a reachable belief space, which is the subset of the belief space reachable from a given belief point. We also show that under the weaker condition of having a small covering number for an optimal reachable space, which is the subset of the belief space reachable under an optimal policy, computing an approximately optimal solution is NPhard. However, given a suitable set of points that "cover" an optimal reachable spacewell, an approximate solution can be computed in polynomial time. The covering number highlights several interesting properties that reduce the complexity ofPOMDP planning in practice, e.g., fully observed state variables, beliefs with sparse support, smooth beliefs, and circulant state-transition matrices.

We propose a new measure of conditional dependence of random variables, based on normalized cross-covariance operators on reproducing kernel Hilbert spaces. Unlike previous kernel dependence measures, the proposed criterion does not depend on the choice of kernel in the limit of infinite data, for a wide class of kernels. At the same time, it has a straightforward empirical estimate with good convergence behaviour. We discuss the theoretical properties of the measure, and demonstrate its application in experiments.

Brain-Computer Interfaces can suffer from a large variance of the subject conditions within and across sessions. For example vigilance fluctuations in the individual, variable task involvement, workload etc. alter the characteristics of EEG signals and thus challenge a stable BCI operation. In the present work we aim to define features based on a variant of the common spatial patterns (CSP) algorithm that are constructed invariant with respect to such nonstationarities. We enforce invariance properties by adding terms to the denominator of a Rayleigh coefficient representation of CSP such as disturbance covariance matrices from fluctuations in visual processing. In this manner physiological prior knowledge can be used to shape the classification engine for BCI. As a proof of concept we present a BCI classifier that is robust to changes in the level of parietal α -activity. In other words, the EEG decoding still works when there are lapses in vigilance.

Rosetta is one of the leading algorithms for protein structure prediction today. It is a Monte Carlo energy minimization method requiring many random restarts to find structures with low energy. In this paper we present a resampling technique for structure prediction of small alpha/beta proteins using Rosetta. From an initial round of Rosetta sampling, we learn properties of the energy landscape that guide a subsequent round of sampling toward lower-energy structures. Rather than attempt to fit the full energy landscape, we use feature selection methods--both L1-regularized linear regression and decision trees--to identify structural features that give rise to low energy. We then enrich these structural features in the second sampling round. Results are presented across a benchmark set of nine small alpha/beta proteins demonstrating that our methods seldom impair, and frequently improve, Rosetta's performance.

Although kernel measures of independence have been widely applied in machine learning (notably in kernel ICA), there is as yet no method to determine whether they have detected statistically significant dependence. We provide a novel test of the independence hypothesis for one particular kernel independence measure, the Hilbert-Schmidt independence criterion (HSIC).

A wide variety of Dirichlet-multinomial'topic' models have found interesting applications in recent years. While Gibbs sampling remains an important method of inference in such models, variational techniques have certain advantages such as easy assessment of convergence, easy optimization without the need to maintain detailed balance, a bound on the marginal likelihood, and sidestepping of issues with topic-identifiability. The most accurate variational technique thus far, namely collapsed variational latent Dirichlet allocation, did not deal with model selection nor did it include inference for hyperparameters. We address both issues by generalizing the technique, obtaining the first variational algorithm to deal with the hierarchical Dirichlet process and to deal with hyperparameters of Dirichlet variables. Experiments show a significant improvement in accuracy.

The problem of obtaining the maximum a posteriori estimate of a general discrete random field (i.e. a random field defined using a finite and discrete set of labels) is known to be

Machine learning techniques are increasingly being used to produce a wide-range of classifiers for complex real-world applications that involve nonuniform testing costs and misclassification costs. As the complexity of these applications grows, the management of resources during the learning and classification processes becomes a challenging task. In this work we introduce ACT (Anytime Cost-sensitive Trees), a novel framework for operating in such environments. ACT is an anytime algorithm that allows trading computation time for lower classification costs. It builds a tree top-down and exploits additional time resources to obtain better estimations for the utility of the different candidate splits.