Discovering hierarchical regularities in data is a key problem in interacting with large datasets, modeling cognition, and encoding knowledge. A previous Bayesian solution---Kingman's coalescent---provides a convenient probabilistic model for data represented as a binary tree. Unfortunately, this is inappropriate for data better described by bushier trees. We generalize an existing belief propagation framework of Kingman's coalescent to the beta coalescent, which models a wider range of tree structures. Because of the complex combinatorial search over possible structures, we develop new sampling schemes using sequential Monte Carlo and Dirichlet process mixture models, which render inference efficient and tractable.

Principal component analysis (PCA), a well-established technique for data analysis and processing, provides a convenient form of dimensionality reduction that is effective for cleaning small Gaussian noises presented in the data. However, the applicability of standard principal component analysis in real scenarios is limited by its sensitivity to large errors. In this paper, we tackle the challenge problem of recovering data corrupted with errors of high magnitude by developing a novel robust transfer principal component analysis method. Our method is based on the assumption that useful information for the recovery of a corrupted data matrix can be gained from an uncorrupted related data matrix. Specifically, we formulate the data recovery problem as a joint robust principal component analysis problem on the two data matrices, with shared common principal components across matrices and individual principal components specific to each data matrix.

Multiple hypothesis testing is a significant problem in nearly all neuroimaging studies. In order to correct for this phenomena, we require a reliable estimate of the Family-Wise Error Rate (FWER). The well known Bonferroni correction method, while being simple to implement, is quite conservative, and can substantially under-power a study because it ignores dependencies between test statistics. Permutation testing, on the other hand, is an exact, non parametric method of estimating the FWER for a given α threshold, but for acceptably low thresholds the computational burden can be prohibitive. In this paper, we observe that permutation testing in fact amounts to populating the columns of a very large matrix P. By analyzing the spectrum of this matrix, under certain conditions, we see that P has a low-rank plus a low-variance residual decomposition which makes it suitable for highly sub–sampled -- on the order of 0.5% -- matrix completion methods.

A common assumption in machine vision is that the training and test samples are drawn from the same distribution. However, there are many problems when this assumption is grossly violated, as in bio-medical applications where different acquisitions can generate drastic variations in the appearance of the data due to changing experimental conditions. This problem is accentuated with 3D data, for which annotation is very time-consuming, limiting the amount of data that can be labeled in new acquisitions for training. In this paper we present a multi-task learning algorithm for domain adaptation based on boosting. Unlike previous approaches that learn task-specific decision boundaries, our method learns a single decision boundary in a shared feature space, common to all tasks.

A large number of algorithms in machine learning, from principal component analysis (PCA), and its non-linear (kernel) extensions, to more recent spectral embedding and support estimation methods, rely on estimating a linear subspace from samples. In this paper we introduce a general formulation of this problem and derive novel learning error estimates. Our results rely on natural assumptions on the spectral properties of the covariance operator associated to the data distribution, and hold for a wide class of metrics between subspaces. As special cases, we discuss sharp error estimates for the reconstruction properties of PCA and spectral support estimation. Key to our analysis is an operator theoretic approach that has broad applicability to spectral learning methods.

Stochastic gradient descent is popular for large scale optimization but has slow convergence asymptotically due to the inherent variance. To remedy this problem, we introduce an explicit variance reduction method for stochastic gradient descent which we call stochastic variance reduced gradient (SVRG). For smooth and strongly convex functions, we prove that this method enjoys the same fast convergence rate as those of stochastic dual coordinate ascent (SDCA) and Stochastic Average Gradient (SAG). However, our analysis is significantly simpler and more intuitive. Moreover, unlike SDCA or SAG, our method does not require the storage of gradients, and thus is more easily applicable to complex problems such as some structured prediction problems and neural network learning.

Stochastic gradient optimization is a class of widely used algorithms for training machine learning models. To optimize an objective, it uses the noisy gradient computed from the random data samples instead of the true gradient computed from the entire dataset. However, when the variance of the noisy gradient is large, the algorithm might spend much time bouncing around, leading to slower convergence and worse performance. In this paper, we develop a general approach of using control variate for variance reduction in stochastic gradient. Data statistics such as low-order moments (pre-computed or estimated online) is used to form the control variate.

Dropout is a relatively new algorithm for training neural networks which relies on stochastically dropping out'' neurons during training in order to avoid the co-adaptation of feature detectors. We introduce a general formalism for studying dropout on either units or connections, with arbitrary probability values, and use it to analyze the averaging and regularizing properties of dropout in both linear and non-linear networks. For deep neural networks, the averaging properties of dropout are characterized by three recursive equations, including the approximation of expectations by normalized weighted geometric means. We provide estimates and bounds for these approximations and corroborate the results with simulations. We also show in simple cases how dropout performs stochastic gradient descent on a regularized error function."

We study the problem of reconstructing low-rank matrices from their noisy observations. We formulate the problem in the Bayesian framework, which allows us to exploit structural properties of matrices in addition to low-rankedness, such as sparsity. We propose an efficient approximate message passing algorithm, derived from the belief propagation algorithm, to perform the Bayesian inference for matrix reconstruction. We have also successfully applied the proposed algorithm to a clustering problem, by formulating the problem of clustering as a low-rank matrix reconstruction problem with an additional structural property. Numerical experiments show that the proposed algorithm outperforms Lloyd's K-means algorithm.

This paper presents a novel algorithm, based upon the dependent Dirichlet process mixture model (DDPMM), for clustering batch-sequential data containing an unknown number of evolving clusters. The algorithm is derived via a low-variance asymptotic analysis of the Gibbs sampling algorithm for the DDPMM, and provides a hard clustering with convergence guarantees similar to those of the k-means algorithm. Empirical results from a synthetic test with moving Gaussian clusters and a test with real ADS-B aircraft trajectory data demonstrate that the algorithm requires orders of magnitude less computational time than contemporary probabilistic and hard clustering algorithms, while providing higher accuracy on the examined datasets.