Consider a classification problem where we do not have access to labels for individual training examples, but only have average labels over subpopulations. We give practical examples of this setup and show how such a classification task can usefully be analyzed as a weakly supervised clustering problem. We propose three approaches to solving the weakly supervised clustering problem, including a latent variables model that performs well in our experiments. We illustrate our methods on an analysis of aggregated elections data and an industry data set that was the original motivation for this research.

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification.

Ridge regularized linear models (RRLMs), such as ridge regression and the SVM, are a popular group of methods that are used in conjunction with coefficient hypothesis testing to discover explanatory variables with a significant multivariate association to a response. However, many investigators are reluctant to draw causal interpretations of the selected variables due to the incomplete knowledge of the capabilities of RRLMs in causal inference. Under reasonable assumptions, we show that a modified form of RRLMs can get very close to identifying a subset of the Markov boundary by providing a worst-case bound on the space of possible solutions. The results hold for any convex loss, even when the underlying functional relationship is nonlinear, and the solution is not unique. Our approach combines ideas in Markov boundary and sufficient dimension reduction theory. Experimental results show that the modified RRLMs are competitive against state-of-the-art algorithms in discovering part of the Markov boundary from gene expression data.

We develop a sequential low-complexity inference procedure for Dirichlet process mixtures of Gaussians for online clustering and parameter estimation when the number of clusters are unknown a-priori. We present an easily computable, closed form parametric expression for the conditional likelihood, in which hyperparameters are recursively updated as a function of the streaming data assuming conjugate priors. Motivated by large-sample asymptotics, we propose a novel adaptive low-complexity design for the Dirichlet process concentration parameter and show that the number of classes grow at most at a logarithmic rate. We further prove that in the large-sample limit, the conditional likelihood and data predictive distribution become asymptotically Gaussian. We demonstrate through experiments on synthetic and real data sets that our approach is superior to other online state-of-the-art methods.

Abstract--In this paper we propose a strategy for semi-supervised image classification that leverages unsupervised representation learning and co-training. The strategy, that is called CURL from Co-trained Unsupervised Representation Learning, iteratively builds two classifiers on two different views of the data. The two views correspond to different representations learned from both labeled and unlabeled data and differ in the fusion scheme used to combine the image features. T o assess the performance of our proposal, we conducted several experiments on widely used data sets for scene and object recognition. We considered three scenarios (inductive, transductive and self-taught learning) that differ in the strategy followed to exploit the unlabeled data. As image features we considered a combination of GIST, PHOG, and LBP as well as features extracted from a Con-volutional Neural Network. Moreover, two embodiments of CURL are investigated: one using Ensemble Projection as unsupervised representation learning coupled with Logistic Regression, and one based on LapSVM. The results show that CURL clearly outperforms other supervised and semi-supervised learning methods in the state of the art. Semi-supervised learning [1] consists in taking into account both labeled and unlabeled data when training machine learning models. It is particularly effective when there is plenty of training data, but only a few instances are labeled. In the last years, many semi-supervised learning approaches have been proposed including generative methods [2], [3], graph-based methods [4], [5], and methods based on Support V ector Machines [6], [7]. Co-training is another example of semi-supervised technique [8].

Abstract--In the co-sparse analysis model a set of filters is applied to a signal out of the signal class of interest yielding sparse filter responses. As such, it may serve as a prior in inverse problems, or for structural analysis of signals that are known to belong to the signal class. The more the model is adapted to the class, the more reliable it is for these purposes. The task of learning such operators for a given class is therefore a crucial problem. In many applications, it is also required that the filter responses are obtained in a timely manner, which can be achieved by filters with a separable structure. Not only can operators of this sort be efficiently used for computing the filter responses, but they also have the advantage that less training samples are required to obtain a reliable estimate of the operator . The first contribution of this work is to give theoretical evidence for this claim by providing an upper bound for the sample complexity of the learning process. The second is a stochastic gradient descent (SGD) method designed to learn an analysis operator with separable structures, which includes a novel and efficient step size selection rule. Numerical experiments are provided that link the sample complexity to the convergence speed of the SGD algorithm. HE ability to sparsely represent signals has become standard practice in signal processing over the last decade. The commonly used synthesis approach has been extensively investigated and has proven its validity in many applications. Its closely related counterpart, the co-sparse analysis approach, was at first not treated with as much interest. In recent years this has changed and more and more work regarding the application and the theoretical validity of the co-sparse analysis model has been published. Both models assume that the signalss of a certain class are (approximately) contained in a union of subspaces. In the synthesis model, this reads as s Dx, x is sparse. Personal use of this material is permitted.

This paper develops tools for performing formal statistical inference for predictions generated by a broad class of methods developed under the algorithmic framework of data analysis. In particular, we focus on ensemble methods - combinations of many individual, frequently tree-based, prediction functions - which have played an important role. We present a variant of bagging and random forests, both initially introduced by Breiman [1996, 2001b], in which base learners are built on randomly chosen subsamples of the training data and the final prediction is taken as the average over the individual outputs. We demonstrate that this fits into the statistical framework of U-statistics, which were shown to have minimum variance by Halmos [1946] and later demonstrated to be asymptotically normal by Hoeffding [1948]. This allows us to demonstrate that under weak regularity conditions, predictions generated by these subsample ensemble methods are asymptotically normal. We also provide a method to consistently estimate the variance in the limiting distribution without increasing the computational cost so that we may produce confidence intervals and formally test feature significance in practice. Though not the focus of this paper, it is worth noting that this 1 subbagging procedure - suggested by Andonova et al. [2002] for use in model selection - was shown by Zaman and Hirose [2009] to outperform traditional bagging in many situations.

One significant challenge to scaling entity resolution algorithms to massive datasets is understanding how performance changes after moving beyond the realm of small, manually labeled reference datasets. Unlike traditional machine learning tasks, when an entity resolution algorithm performs well on small hold-out datasets, there is no guarantee this performance holds on larger hold-out datasets. We prove simple bounding properties between the performance of a match function on a small validation set and the performance of a pairwise entity resolution algorithm on arbitrarily sized datasets. Thus, our approach enables optimization of pairwise entity resolution algorithms for large datasets, using a small set of labeled data.

Semi-Non-negative Matrix Factorization is a technique that learns a low-dimensional representation of a dataset that lends itself to a clustering interpretation. It is possible that the mapping between this new representation and our original data matrix contains rather complex hierarchical information with implicit lower-level hidden attributes, that classical one level clustering methodologies can not interpret. In this work we propose a novel model, Deep Semi-NMF, that is able to learn such hidden representations that allow themselves to an interpretation of clustering according to different, unknown attributes of a given dataset. We also present a semi-supervised version of the algorithm, named Deep WSF, that allows the use of (partial) prior information for each of the known attributes of a dataset, that allows the model to be used on datasets with mixed attribute knowledge. Finally, we show that our models are able to learn low-dimensional representations that are better suited for clustering, but also classification, outperforming Semi-Non-negative Matrix Factorization, but also other state-of-the-art methodologies variants.

Optimization problems with rank constraints arise in many applications, including matrix regression, structured PCA, matrix completion and matrix decomposition problems. An attractive heuristic for solving such problems is to factorize the low-rank matrix, and to run projected gradient descent on the nonconvex factorized optimization problem. The goal of this problem is to provide a general theoretical framework for understanding when such methods work well, and to characterize the nature of the resulting fixed point. We provide a simple set of conditions under which projected gradient descent, when given a suitable initialization, converges geometrically to a statistically useful solution. Our results are applicable even when the initial solution is outside any region of local convexity, and even when the problem is globally concave. Working in a non-asymptotic framework, we show that our conditions are satisfied for a wide range of concrete models, including matrix regression, structured PCA, matrix completion with real and quantized observations, matrix decomposition, and graph clustering problems. Simulation results show excellent agreement with the theoretical predictions.