The past years have witnessed many dedicated open-source projects that built and maintain implementations of Support Vector Machines (SVM), parallelized for GPU, multi-core CPUs and distributed systems. Up to this point, no comparable effort has been made to parallelize the Elastic Net, despite its popularity in many high impact applications, including genetics, neuroscience and systems biology. The first contribution in this paper is of theoretical nature. We establish a tight link between two seemingly different algorithms and prove that Elastic Net regression can be reduced to SVM with squared hinge loss classification. Our second contribution is to derive a practical algorithm based on this reduction. The reduction enables us to utilize prior efforts in speeding up and parallelizing SVMs to obtain a highly optimized and parallel solver for the Elastic Net and Lasso. With a simple wrapper, consisting of only 11 lines of MATLAB code, we obtain an Elastic Net implementation that naturally utilizes GPU and multi-core CPUs. We demonstrate on twelve real world data sets, that our algorithm yields identical results as the popular (and highly optimized) glmnet implementation but is one or several orders of magnitude faster.

Classification with a sparsity constraint on the solution plays a central role in many high dimensional machine learning applications. In some cases, the features can be grouped together so that entire subsets of features can be selected or not selected. In many applications, however, this can be too restrictive. In this paper, we are interested in a less restrictive form of structured sparse feature selection: we assume that while features can be grouped according to some notion of similarity, not all features in a group need be selected for the task at hand. When the groups are comprised of disjoint sets of features, this is sometimes referred to as the "sparse group" lasso, and it allows for working with a richer class of models than traditional group lasso methods. Our framework generalizes conventional sparse group lasso further by allowing for overlapping groups, an additional flexiblity needed in many applications and one that presents further challenges. The main contribution of this paper is a new procedure called Sparse Overlapping Group (SOG) lasso, a convex optimization program that automatically selects similar features for classification in high dimensions. We establish model selection error bounds for SOGlasso classification problems under a fairly general setting. In particular, the error bounds are the first such results for classification using the sparse group lasso. Furthermore, the general SOGlasso bound specializes to results for the lasso and the group lasso, some known and some new. The SOGlasso is motivated by multi-subject fMRI studies in which functional activity is classified using brain voxels as features, source localization problems in Magnetoencephalography (MEG), and analyzing gene activation patterns in microarray data analysis. Experiments with real and synthetic data demonstrate the advantages of SOGlasso compared to the lasso and group lasso.

Department of Biomedical Engineering, Biomedical Imaging Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA 2 With the existence of biologically distinctive malignant cells originated within the same tumor, intratumor functional heterogeneity is present in many cancers and is often manifested by the intermingled vascular compartments with distinct pharmacokinetics. However, intratumor vascular heterogeneity cannot be resolved directly by most in vivo dynamic imaging. We developed multi-tissue compartment modeling (MTCM), a completely unsupervised method of deconvoluting dynamic imaging series from heterogeneous tumors that can improve vascular characterization in many biological contexts. Applying MTCM to dynamic contrast-enhanced magnetic resonance imaging of breast cancers revealed characteristic intratumor vascular heterogeneity and therapeutic responses that were otherwise undetectable. MTCM is readily applicable to other dynamic imaging modalities for studying intratumor functional and phenotypic heterogeneity, together with a variety of foreseeable applications in the clinic. A formal mathematical description of the method and its detailed implementation is available in Methods.

We study inference and learning based on a sparse coding model with `spike-and-slab' prior. As in standard sparse coding, the model used assumes independent latent sources that linearly combine to generate data points. However, instead of using a standard sparse prior such as a Laplace distribution, we study the application of a more flexible `spike-and-slab' distribution which models the absence or presence of a source's contribution independently of its strength if it contributes. We investigate two approaches to optimize the parameters of spike-and-slab sparse coding: a novel truncated EM approach and, for comparison, an approach based on standard factored variational distributions. The truncated approach can be regarded as a variational approach with truncated posteriors as variational distributions. In applications to source separation we find that both approaches improve the state-of-the-art in a number of standard benchmarks, which argues for the use of `spike-and-slab' priors for the corresponding data domains. Furthermore, we find that the truncated EM approach improves on the standard factored approach in source separation tasks$-$which hints to biases introduced by assuming posterior independence in the factored variational approach. Likewise, on a standard benchmark for image denoising, we find that the truncated EM approach improves on the factored variational approach. While the performance of the factored approach saturates with increasing numbers of hidden dimensions, the performance of the truncated approach improves the state-of-the-art for higher noise levels.

Recently, there has been a burst in the number of research projects on human computation via crowdsourcing. Multiple choice (or labeling) questions could be referred to as a common type of problem which is solved by this approach. As an application, crowd labeling is applied to find true labels for large machine learning datasets. Since crowds are not necessarily experts, the labels they provide are rather noisy and erroneous. This challenge is usually resolved by collecting multiple labels for each sample, and then aggregating them to estimate the true label. Although the mechanism leads to high-quality labels, it is not actually cost-effective. As a result, efforts are currently made to maximize the accuracy in estimating true labels, while fixing the number of acquired labels. This paper surveys methods to aggregate redundant crowd labels in order to estimate unknown true labels. It presents a unified statistical latent model where the differences among popular methods in the field correspond to different choices for the parameters of the model. Afterwards, algorithms to make inference on these models will be surveyed. Moreover, adaptive methods which iteratively collect labels based on the previously collected labels and estimated models will be discussed. In addition, this paper compares the distinguished methods, and provides guidelines for future work required to address the current open issues.

This paper considers networks where relationships between nodes are represented by directed dissimilarities. The goal is to study methods for the determination of hierarchical clusters, i.e., a family of nested partitions indexed by a connectivity parameter, induced by the given dissimilarity structures. Our construction of hierarchical clustering methods is based on defining admissible methods to be those methods that abide by the axioms of value - nodes in a network with two nodes are clustered together at the maximum of the two dissimilarities between them - and transformation - when dissimilarities are reduced, the network may become more clustered but not less. Several admissible methods are constructed and two particular methods, termed reciprocal and nonreciprocal clustering, are shown to provide upper and lower bounds in the space of admissible methods. Alternative clustering methodologies and axioms are further considered. Allowing the outcome of hierarchical clustering to be asymmetric, so that it matches the asymmetry of the original data, leads to the inception of quasi-clustering methods. The existence of a unique quasi-clustering method is shown. Allowing clustering in a two-node network to proceed at the minimum of the two dissimilarities generates an alternative axiomatic construction. There is a unique clustering method in this case too. The paper also develops algorithms for the computation of hierarchical clusters using matrix powers on a min-max dioid algebra and studies the stability of the methods proposed. We proved that most of the methods introduced in this paper are such that similar networks yield similar hierarchical clustering results. Algorithms are exemplified through their application to networks describing internal migration within states of the United States (U.S.) and the interrelation between sectors of the U.S. economy.

Map matching of GPS trajectories from a sequence of noisy observations serves the purpose of recovering the original routes in a road network. In this work in progress, we attempt to share our experience of feature construction in a spatial database by reporting our ongoing experiment of feature extrac-tion in Conditional Random Fields (CRFs) for map matching. Our preliminary results are obtained from real-world taxi GPS trajectories.

Map matching of the GPS trajectory serves the purpose of recovering the original route on a road network from a sequence of noisy GPS observations. It is a fundamental technique to many Location Based Services. However, map matching of a low sampling rate on urban road network is still a challenging task. In this paper, the characteristics of Conditional Random Fields with regard to inducing many contextual features and feature selection are explored for the map matching of the GPS trajectories at a low sampling rate. Experiments on a taxi trajectory dataset show that our method may achieve competitive results along with the success of reducing model complexity for computation-limited applications.

In this paper we propose and investigate a novel nonlinear unit, called $L_p$ unit, for deep neural networks. The proposed $L_p$ unit receives signals from several projections of a subset of units in the layer below and computes a normalized $L_p$ norm. We notice two interesting interpretations of the $L_p$ unit. First, the proposed unit can be understood as a generalization of a number of conventional pooling operators such as average, root-mean-square and max pooling widely used in, for instance, convolutional neural networks (CNN), HMAX models and neocognitrons. Furthermore, the $L_p$ unit is, to a certain degree, similar to the recently proposed maxout unit (Goodfellow et al., 2013) which achieved the state-of-the-art object recognition results on a number of benchmark datasets. Secondly, we provide a geometrical interpretation of the activation function based on which we argue that the $L_p$ unit is more efficient at representing complex, nonlinear separating boundaries. Each $L_p$ unit defines a superelliptic boundary, with its exact shape defined by the order $p$. We claim that this makes it possible to model arbitrarily shaped, curved boundaries more efficiently by combining a few $L_p$ units of different orders. This insight justifies the need for learning different orders for each unit in the model. We empirically evaluate the proposed $L_p$ units on a number of datasets and show that multilayer perceptrons (MLP) consisting of the $L_p$ units achieve the state-of-the-art results on a number of benchmark datasets. Furthermore, we evaluate the proposed $L_p$ unit on the recently proposed deep recurrent neural networks (RNN).

Multi-task learning (MTL) aims to improve generalization performance by learning multiple related tasks simultaneously. While sometimes the underlying task relationship structure is known, often the structure needs to be estimated from data at hand. In this paper, we present a novel family of models for MTL, applicable to regression and classification problems, capable of learning the structure of task relationships. In particular, we consider a joint estimation problem of the task relationship structure and the individual task parameters, which is solved using alternating minimization. The task relationship structure learning component builds on recent advances in structure learning of Gaussian graphical models based on sparse estimators of the precision (inverse covariance) matrix. We illustrate the effectiveness of the proposed model on a variety of synthetic and benchmark datasets for regression and classification. We also consider the problem of combining climate model outputs for better projections of future climate, with focus on temperature in South America, and show that the proposed model outperforms several existing methods for the problem.