Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence remains very challenging. Both evolutionary coupling (EC) analysis and supervised machine learning methods are developed to predict contacts, making use of different types of information, respectively. This paper presents a group graphical lasso (GGL) method for contact prediction that integrates joint multi-family EC analysis and supervised learning. Different from existing single-family EC analysis that uses residue co-evolution information in only the target protein family, our joint EC analysis uses residue co-evolution in both the target family and its related families, which may have divergent sequences but similar folds. To implement joint EC analysis, we model a set of related protein families using Gaussian graphical models (GGM) and then co-estimate their precision matrices by maximum-likelihood, subject to the constraint that the precision matrices shall share similar residue co-evolution patterns. To further improve the accuracy of the estimated precision matrices, we employ a supervised learning method to predict contact probability from a variety of evolutionary and non-evolutionary information and then incorporate the predicted probability as prior into our GGL framework. Experiments show that our method can predict contacts much more accurately than existing methods, and that our method performs better on both conserved and family-specific contacts.

Recent years have demonstrated that using random feature maps can significantly decrease the training and testing times of kernel-based algorithms without significantly lowering their accuracy. Regrettably, because random features are target-agnostic, typically thousands of such features are necessary to achieve acceptable accuracies. In this work, we consider the problem of learning a small number of explicit polynomial features. Our approach, named Tensor Machines, finds a parsimonious set of features by optimizing over the hypothesis class introduced by Kar and Karnick for random feature maps in a target-specific manner. Exploiting a natural connection between polynomials and tensors, we provide bounds on the generalization error of Tensor Machines. Empirically, Tensor Machines behave favorably on several real-world datasets compared to other state-of-the-art techniques for learning polynomial features, and deliver significantly more parsimonious models.

Clustering of data sets is a standard problem in many areas of science and engineering. The method of spectral clustering is based on embedding the data set using a kernel function, and using the top eigenvectors of the normalized Laplacian to recover the connected components. We study the performance of spectral clustering in recovering the latent labels of i.i.d. samples from a finite mixture of nonparametric distributions. The difficulty of this label recovery problem depends on the overlap between mixture components and how easily a mixture component is divided into two nonoverlapping components. When the overlap is small compared to the indivisibility of the mixture components, the principal eigenspace of the population-level normalized Laplacian operator is approximately spanned by the square-root kernelized component densities. In the finite sample setting, and under the same assumption, embedded samples from different components are approximately orthogonal with high probability when the sample size is large. As a corollary we control the fraction of samples mislabeled by spectral clustering under finite mixtures with nonparametric components.

We show that accelerated gradient descent, averaged gradient descent and the heavy-ball method for non-strongly-convex problems may be reformulated as constant parameter second-order difference equation algorithms, where stability of the system is equivalent to convergence at rate O(1/n 2), where n is the number of iterations. We provide a detailed analysis of the eigenvalues of the corresponding linear dynamical system , showing various oscillatory and non-oscillatory behaviors, together with a sharp stability result with explicit constants. We also consider the situation where noisy gradients are available, where we extend our general convergence result, which suggests an alternative algorithm (i.e., with different step sizes) that exhibits the good aspects of both averaging and acceleration.

Conditional Random Fields (CRF) have been widely used in a variety of computer vision tasks. Conventional CRFs typically define edges on neighboring image pixels, resulting in a sparse graph such that efficient inference can be performed. However, these CRFs fail to model long-range contextual relationships. Fully-connected CRFs have thus been proposed. While there are efficient approximate inference methods for such CRFs, usually they are sensitive to initialization and make strong assumptions. In this work, we develop an efficient, yet general algorithm for inference on fully-connected CRFs. The algorithm is based on a scalable SDP algorithm and the low- rank approximation of the similarity/kernel matrix. The core of the proposed algorithm is a tailored quasi-Newton method that takes advantage of the low-rank matrix approximation when solving the specialized SDP dual problem. Experiments demonstrate that our method can be applied on fully-connected CRFs that cannot be solved previously, such as pixel-level image co-segmentation.

We show that unconverged stochastic gradient descent can be interpreted as a procedure that samples from a nonparametric variational approximate posterior distribution. This distribution is implicitly defined as the transformation of an initial distribution by a sequence of optimization updates. By tracking the change in entropy over this sequence of transformations during optimization, we form a scalable, unbiased estimate of the variational lower bound on the log marginal likelihood. We can use this bound to optimize hyperparameters instead of using cross-validation. This Bayesian interpretation of SGD suggests improved, overfitting-resistant optimization procedures, and gives a theoretical foundation for popular tricks such as early stopping and ensembling. We investigate the properties of this marginal likelihood estimator on neural network models.

Finding minima of a real valued non-convex function over a high dimensional space is a major challenge in science. We provide evidence that some such functions that are defined on high dimensional domains have a narrow band of values whose pre-image contains the bulk of its critical points. This is in contrast with the low dimensional picture in which this band is wide. Our simulations agree with the previous theoretical work on spin glasses that proves the existence of such a band when the dimension of the domain tends to infinity. Furthermore our experiments on teacher-student networks with the MNIST dataset establish a similar phenomenon in deep networks. We finally observe that both the gradient descent and the stochastic gradient descent methods can reach this level within the same number of steps.

We introduce the hyperparameter search problem in the field of machine learning and discuss its main challenges from an optimization perspective. Machine learning methods attempt to build models that capture some element of interest based on given data. Most common learning algorithms feature a set of hyperparameters that must be determined before training commences. The choice of hyperparameters can significantly affect the resulting model's performance, but determining good values can be complex; hence a disciplined, theoretically sound search strategy is essential.

Performing signal processing tasks on compressive measurements of data has received great attention in recent years. In this paper, we extend previous work on compressive dictionary learning by showing that more general random projections may be used, including sparse ones. More precisely, we examine compressive K-means clustering as a special case of compressive dictionary learning and give theoretical guarantees for its performance for a very general class of random projections. We then propose a memory and computation efficient dictionary learning algorithm, specifically designed for analyzing large volumes of high-dimensional data, which learns the dictionary from very sparse random projections. Experimental results demonstrate that our approach allows for reduction of computational complexity and memory/data access, with controllable loss in accuracy.

Given the rapid growth of social media websites and the ease of aggregating ever-richer social data, an inevitable research question that can be expected to emerge is whether different interaction patterns of individuals and their meaningful interpretation can be captured for social network analysis. In this work, we present a novel solution that discovers occurrences of prototypical 'ego network' patterns from social media and mobile-phone networks, to provide a data-driven instrument to be used in behavioral sciences for graph interpretations. We analyze nine datasets gathered from social media websites and mobile phones, together with 13 network measures, and three unsupervised clustering algorithms. Further, we use an unsupervised feature similarity technique to reduce redundancy and extract compact features from the data. The reduced feature subsets are then used to discover ego patterns using various clustering techniques. By cluster analysis, we discover that eight distinct ego neighborhood patterns or ego graphs have emerged. This categorization allows concise analysis of users' data as they change over time. We provide fine-grained analysis for the validity and quality of clustering results. We perform clustering verification based on the following three intuitions: i) analyzing the clustering patterns for the same set of users crawled from three social media networks, ii) associating metadata information with the clusters and evaluating their performance on real networks, iii) studying selected participants over an extended period to analyze their behavior.