Recent studies compare gene expression data across species to identify core and species specific genes in biological systems. To perform such comparisons researchers need to match genes across species. This is a challenging task since the correct matches (orthologs) are not known for most genes. Previous work in this area used deterministic matchings or reduced multidimensional expression data to binary representation. Here we develop a new method that can utilize soft matches (given as priors) to infer both, unique and similar expression patterns across species and a matching for the genes in both species. Our method uses a Dirichlet process mixture model which includes a latent data matching variable. We present learning and inference algorithms based on variational methods for this model. Applying our method to immune response data we show that it can accurately identify common and unique response patterns by improving the matchings between human and mouse genes.

In multi-instance learning, there are two kinds of prediction failure, i.e., false negative and false positive. Current research mainly focus on avoding the former. We attempt to utilize the geometric distribution of instances inside positive bags to avoid both the former and the latter. Based on kernel principal component analysis, we define a projection constraint for each positive bag to classify its constituent instances far away from the separating hyperplane while place positive instances and negative instances at opposite sides. We apply the Constrained Concave-Convex Procedure to solve the resulted problem. Empirical results demonstrate that our approach offers improved generalization performance.

Sodium entry during an action potential determines the energy efficiency of a neuron. The classic Hodgkin-Huxley model of action potential generation is notoriously inefficient in that regard with about 4 times more charges flowing through the membrane than the theoretical minimum required to achieve the observed depolarization. Yet, recent experimental results show that mammalian neurons are close to the optimal metabolic efficiency and that the dynamics of their voltage-gated channels is significantly different than the one exhibited by the classic Hodgkin-Huxley model during the action potential. Nevertheless, the original Hodgkin-Huxley model is still widely used and rarely to model the squid giant axon from which it was extracted. Here, we introduce a novel family of Hodgkin-Huxley models that correctly account for sodium entry, action potential width and whose voltage-gated channels display a dynamics very similar to the most recent experimental observations in mammalian neurons. We speak here about a family of models because the model is parameterized by a unique parameter the variations of which allow to reproduce the entire range of experimental observations from cortical pyramidal neurons to Purkinje cells, yielding a very economical framework to model a wide range of different central neurons. The present paper demonstrates the performances and discuss the properties of this new family of models.

Functional magnetic resonance imaging (fMRI) can be applied to study the functional connectivity of the neural elements which form complex network at a whole brain level. Most analyses of functional resting state networks (RSN) have been based on the analysis of correlation between the temporal dynamics of various regions of the brain. While these models can identify coherently behaving groups in terms of correlation they give little insight into how these groups interact. In this paper we take a different view on the analysis of functional resting state networks. Starting from the definition of resting state as functional coherent groups we search for functional units of the brain that communicate with other parts of the brain in a coherent manner as measured by mutual information. We use the infinite relational model (IRM) to quantify functional coherent groups of resting state networks and demonstrate how the extracted component interactions can be used to discriminate between functional resting state activity in multiple sclerosis and normal subjects.

Matching functional brain regions across individuals is a challenging task, largely due to the variability in their location and extent. It is particularly difficult, but highly relevant, for patients with pathologies such as brain tumors, which can cause substantial reorganization of functional systems. In such cases spatial registration based on anatomical data is only of limited value if the goal is to establish correspondences of functional areas among different individuals, or to localize potentially displaced active regions. Rather than rely on spatial alignment, we propose to perform registration in an alternative space whose geometry is governed by the functional interaction patterns in the brain. We first embed each brain into a functional map that reflects connectivity patterns during a fMRI experiment. The resulting functional maps are then registered, and the obtained correspondences are propagated back to the two brains. In application to a language fMRI experiment, our preliminary results suggest that the proposed method yields improved functional correspondences across subjects. This advantage is pronounced for subjects with tumors that affect the language areas and thus cause spatial reorganization of the functional regions.

Recent studies have shown that multiple kernel learning is very effective for object recognition, leading to the popularity of kernel learning in computer vision problems. In this work, we develop an efficient algorithm for multi-label multiple kernel learning (ML-MKL). We assume that all the classes under consideration share the same combination of kernel functions, and the objective is to find the optimal kernel combination that benefits all the classes. Although several algorithms have been developed for ML-MKL, their computational cost is linear in the number of classes, making them unscalable when the number of classes is large, a challenge frequently encountered in visual object recognition. We address this computational challenge by developing a framework for ML-MKL that combines the worst-case analysis with stochastic approximation. Our analysis shows that the complexity of our algorithm is $O(m^{1/3}\sqrt{ln m})$, where $m$ is the number of classes. Empirical studies with object recognition show that while achieving similar classification accuracy, the proposed method is significantly more efficient than the state-of-the-art algorithms for ML-MKL.

We introduce a new Bayesian nonparametric approach to identification of sparse dynamic linear systems. The impulse responses are modeled as Gaussian processes whose autocovariances encode the BIBO stability constraint, as defined by the recently introduced “Stable Spline kernel”. Sparse solutions are obtained by placing exponential hyperpriors on the scale factors of such kernels. Numerical experiments regarding estimation of ARMAX models show that this technique provides a definite advantage over a group LAR algorithm and state-of-the-art parametric identification techniques based on prediction error minimization.

Likelihood ratio policy gradient methods have been some of the most successful reinforcement learning algorithms, especially for learning on physical systems. We describe how the likelihood ratio policy gradient can be derived from an importance sampling perspective. This derivation highlights how likelihood ratio methods under-use past experience by (a) using the past experience to estimate {\em only} the gradient of the expected return $U(\theta)$ at the current policy parameterization $\theta$, rather than to obtain a more complete estimate of $U(\theta)$, and (b) using past experience under the current policy {\em only} rather than using all past experience to improve the estimates. We present a new policy search method, which leverages both of these observations as well as generalized baselines---a new technique which generalizes commonly used baseline techniques for policy gradient methods. Our algorithm outperforms standard likelihood ratio policy gradient algorithms on several testbeds.

We present a new learning strategy for classification problems in which train and/or test data suffer from missing features. In previous work, instances are represented as vectors from some feature space and one is forced to impute missing values or to consider an instance-specific subspace. In contrast, our method considers instances as sets of (feature,value) pairs which naturally handle the missing value case. Building onto this framework, we propose a classification strategy for sets. Our proposal maps (feature,value) pairs into an embedding space and then non-linearly combines the set of embedded vectors. The embedding and the combination parameters are learned jointly on the final classification objective. This simple strategy allows great flexibility in encoding prior knowledge about the features in the embedding step and yields advantageous results compared to alternative solutions over several datasets.

In this paper we consider the problem of learning from data the support of a probability distribution when the distribution {\em does not} have a density (with respect to some reference measure). We propose a new class of regularized spectral estimators based on a new notion of reproducing kernel Hilbert space, which we call {\em ``completely regular''}. Completely regular kernels allow to capture the relevant geometric and topological properties of an arbitrary probability space. In particular, they are the key ingredient to prove the universal consistency of the spectral estimators and in this respect they are the analogue of universal kernels for supervised problems. Numerical experiments show that spectral estimators compare favorably to state of the art machine learning algorithms for density support estimation.