In matrix completion, we are given a matrix where the values of only some of the entries are present, and we want to reconstruct the missing ones. Much work has focused on the assumption that the data matrix has low rank. We propose a more general assumption based on denoising, so that we expect that the value of a missing entry can be predicted from the values of neighboring points. We propose a nonparametric version of denoising based on local, iterated averaging with mean-shift, possibly constrained to preserve local low-rank manifold structure. The few user parameters required (the denoising scale, number of neighbors and local dimensionality) and the number of iterations can be estimated by cross-validating the reconstruction error. Using our algorithms as a postprocessing step on an initial reconstruction (provided by e.g. a low-rank method), we show consistent improvements with synthetic, image and motion-capture data.

Given one feature of a novel animal, humans readily make inferences about other features of the animal. For example, winged creatures often fly, and creatures that eat fish often live in the water. We explore the knowledge that supports these inferences and compare two approaches. The first approach proposes that humans rely on abstract representations of dependency relationships between features, and is formalized here as a graphical model. The second approach proposes that humans rely on specific knowledge of previously encountered animals, and is formalized here as a family of exemplar models. We evaluate these models using a task where participants reason about chimeras, or animals with pairs of features that have not previously been observed to co-occur. The results support the hypothesis that humans rely on explicit representations of relationships between features.

Inferring key unobservable features of individuals is an important task in the applied sciences. In particular, an important source of data in fields such as marketing, social sciences and medicine is questionnaires: answers in such questionnaires are noisy measures of target unobserved features. While comprehensive surveys help to better estimate the latent variables of interest, aiming at a high number of questions comes at a price: refusal to participate in surveys can go up, as well as the rate of missing data; quality of answers can decline; costs associated with applying such questionnaires can also increase. In this paper, we cast the problem of refining existing models for questionnaire data as follows: solve a constrained optimization problem of preserving the maximum amount of information found in a latent variable model using only a subset of existing questions. The goal is to find an optimal subset of a given size. For that, we first define an information theoretical measure for quantifying the quality of a reduced questionnaire. Three different approximate inference methods are introduced to solve this problem. Comparisons against a simple but powerful heuristic are presented.

Speech conveys different yet mixed information ranging from linguistic to speaker-specific components, and each of them should be exclusively used in a specific task. However, it is extremely difficult to extract a specific information component given the fact that nearly all existing acoustic representations carry all types of speech information. Thus, the use of the same representation in both speech and speaker recognition hinders a system from producing better performance due to interference of irrelevant information. In this paper, we present a deep neural architecture to extract speaker-specific information from MFCCs. As a result, a multi-objective loss function is proposed for learning speaker-specific characteristics and regularization via normalizing interference of non-speaker related information and avoiding information loss. With LDC benchmark corpora and a Chinese speech corpus, we demonstrate that a resultant speaker-specific representation is insensitive to text/languages spoken and environmental mismatches and hence outperforms MFCCs and other state-of-the-art techniques in speaker recognition. We discuss relevant issues and relate our approach to previous work.

Multi-class Gaussian Process Classifiers (MGPCs) are often affected by over-fitting problems when labeling errors occur far from the decision boundaries. To prevent this, we investigate a robust MGPC (RMGPC) which considers labeling errors independently of their distance to the decision boundaries. Expectation propagation is used for approximate inference. Experiments with several datasets in which noise is injected in the class labels illustrate the benefits of RMGPC. This method performs better than other Gaussian process alternatives based on considering latent Gaussian noise or heavy-tailed processes. When no noise is injected in the labels, RMGPC still performs equal or better than the other methods. Finally, we show how RMGPC can be used for successfully identifying data instances which are difficult to classify accurately in practice.

We propose an approach for linear unsupervised dimensionality reduction, based on the sparse linear model that has been used to probabilistically interpret sparse coding. We formulate an optimization problem for learning a linear projection from the original signal domain to a lower-dimensional one in a way that approximately preserves, in expectation, pairwise inner products in the sparse domain. We derive solutions to the problem, present nonlinear extensions, and discuss relations to compressed sensing. Our experiments using facial images, texture patches, and images of object categories suggest that the approach can improve our ability to recover meaningful structure in many classes of signals.

In discrete undirected graphical models, the conditional independence of node labels Y is specified by the graph structure. We study the case where there is another input random vector X (e.g. observed features) such that the distribution P (Y | X) is determined by functions of X that characterize the (higher-order) interactions among the Y ’s. The main contribution of this paper is to learn the graph structure and the functions conditioned on X at the same time. We prove that discrete undirected graphical models with feature X are equivalent to mul- tivariate discrete models. The reparameterization of the potential functions in graphical models by conditional log odds ratios of the latter offers advantages in representation of the conditional independence structure. The functional spaces can be flexibly determined by kernels. Additionally, we impose a Structure Lasso (SLasso) penalty on groups of functions to learn the graph structure. These groups with overlaps are designed to enforce hierarchical function selection. In this way, we are able to shrink higher order interactions to obtain a sparse graph structure.

Determining interactions between entities and the overall organization and clustering of nodes in networks is a major challenge when analyzing biological and social network data. Here we extend the Indian Buffet Process (IBP), a nonparametric Bayesian model, to integrate noisy interaction scores with properties of individual entities for inferring interaction networks and clustering nodes within these networks. We present an application of this method to study how microRNAs regulate mRNAs in cells. Analysis of synthetic and real data indicates that the method improves upon prior methods, correctly recovers interactions and clusters, and provides accurate biological predictions.

We introduce a Gaussian process model of functions which are additive. An additive function is one which decomposes into a sum of low-dimensional functions, each depending on only a subset of the input variables. Additive GPs generalize both Generalized Additive Models, and the standard GP models which use squared-exponential kernels. Hyperparameter learning in this model can be seen as Bayesian Hierarchical Kernel Learning (HKL). We introduce an expressive but tractable parameterization of the kernel function, which allows efficient evaluation of all input interaction terms, whose number is exponential in the input dimension. The additional structure discoverable by this model results in increased interpretability, as well as state-of-the-art predictive power in regression tasks.

State-of-the-art statistical methods in neuroscience have enabled us to fit mathematical models to experimental data and subsequently to infer the dynamics of hidden parameters underlying the observable phenomena. Here, we develop a Bayesian method for inferring the time-varying mean and variance of the synaptic input, along with the dynamics of each ion channel from a single voltage trace of a neuron. An estimation problem may be formulated on the basis of the state-space model with prior distributions that penalize large fluctuations in these parameters. After optimizing the hyperparameters by maximizing the marginal likelihood, the state-space model provides the time-varying parameters of the input signals and the ion channel states. The proposed method is tested not only on the simulated data from the Hodgkin-Huxley type models but also on experimental data obtained from a cortical slice in vitro.