Regularized training of an autoencoder typically results in hidden unit biases that take on large negative values. We show that negative biases are a natural result of using a hidden layer whose responsibility is to both represent the input data and act as a selection mechanism that ensures sparsity of the representation. We then show that negative biases impede the learning of data distributions whose intrinsic dimensionality is high. We also propose a new activation function that decouples the two roles of the hidden layer and that allows us to learn representations on data with very high intrinsic dimensionality, where standard autoencoders typically fail. Since the decoupled activation function acts like an implicit regularizer, the model can be trained by minimizing the reconstruction error of training data, without requiring any additional regularization.

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.

We address the collective matrix completion problem of jointly recovering a collection of matrices with shared structure from partial (and potentially noisy) observations. To ensure well--posedness of the problem, we impose a joint low rank structure, wherein each component matrix is low rank and the latent space of the low rank factors corresponding to each entity is shared across the entire collection. We first develop a rigorous algebra for representing and manipulating collective--matrix structure, and identify sufficient conditions for consistent estimation of collective matrices. We then propose a tractable convex estimator for solving the collective matrix completion problem, and provide the first non--trivial theoretical guarantees for consistency of collective matrix completion. We show that under reasonable assumptions stated in Section 3.1, with high probability, the proposed estimator exactly recovers the true matrices whenever sample complexity requirements dictated by Theorem 1 are met. The sample complexity requirement derived in the paper are optimum up to logarithmic factors, and significantly improve upon the requirements obtained by trivial extensions of standard matrix completion. Finally, we propose a scalable approximate algorithm to solve the proposed convex program, and corroborate our results through simulated experiments.

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.

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.

Machine learning research focuses on the development of methods that are capable of capturing some element of interest from a given data set. Such elements include but are not limited to coherent structures within data (clustering) or the ability to predict certain target values based on given characteristics, which may be discrete (classification) or continuous (regression). A large variety of learning methods exist, ranging from biologically inspired neural networks [7] over kernel methods [29] to ensemble models [9, 11]. A common trait in these methods is that they are parameterized by a set of hyperparameters λ, which must be set appropriately by the user to maximize the usefulness of the learning approach. Hyperparameters are used to configure various aspects of the learning algorithm and can have wildly varying effects on the resulting model and its performance. Hyperparameter search is commonly performed manually, via rules-of-thumb [19, 20] or by testing sets of hyperparameters on a predefined grid [28]. These approaches leave much to be desired in terms of reproducibility and are impractical when the number of hyperparameters is large [10]. Due to these flaws, the idea of automating hyperparameter search is receiving increasing amounts of attention in machine learning, for instance via benchmarking suites [15] and various initiatives.

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.

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.

We consider the classic problem of establishing a statistical ranking of a set of n items given a set of inconsistent and incomplete pairwise comparisons between such items. Instantiations of this problem occur in numerous applications in data analysis (e.g., ranking teams in sports data), computer vision, and machine learning. We formulate the above problem of ranking with incomplete noisy information as an instance of the group synchronization problem over the group SO(2) of planar rotations, whose usefulness has been demonstrated in numerous applications in recent years. Its least squares solution can be approximated by either a spectral or a semidefinite programming (SDP) relaxation, followed by a rounding procedure. We perform extensive numerical simulations on both synthetic and real-world data sets, showing that our proposed method compares favorably to other algorithms from the recent literature. Existing theoretical guarantees on the group synchronization problem imply lower bounds on the largest amount of noise permissible in the ranking data while still achieving exact recovery. We propose a similar synchronization-based algorithm for the rank-aggregation problem, which integrates in a globally consistent ranking pairwise comparisons given by different rating systems on the same set of items. We also discuss the problem of semi-supervised ranking when there is available information on the ground truth rank of a subset of players, and propose an algorithm based on SDP which recovers the ranks of the remaining players. Finally, synchronization-based ranking, combined with a spectral technique for the densest subgraph problem, allows one to extract locally-consistent partial rankings, in other words, to identify the rank of a small subset of players whose pairwise comparisons are less noisy than the rest of the data, which other methods are not able to identify.