arXiv subjects

Robert Nowak

Publications and source records attributed to Robert Nowak.

At least 73 records · Page 4Linked to original sources

arXiv2018

Linking de novo assembly results with long DNA reads by dnaasm-link application

Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, a result of \textit{de novo} assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions, as presented in the paper. Finally, our implementation outperforms other state-of-the-art tools in terms of speed and memory requirements, which may enable the usage of the presented application for organisms with a large genome, which is not possible in~existing applications. The presented application has many advantages as (i) significant memory optimization and reduction of computation time (ii) filling the gaps through the appropriate fragment of a specified long DNA read (iii) reducing number of spanned and unspanned gaps in the existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, docker image and source code are available at http://dnaasm.sourceforge.net.

q-bio.GN↗

arXiv2018

Scalable Sparse Subspace Clustering via Ordered Weighted $\ell_1$ Regression

The main contribution of the paper is a new approach to subspace clustering that is significantly more computationally efficient and scalable than existing state-of-the-art methods. The central idea is to modify the regression technique in sparse subspace clustering (SSC) by replacing the $\ell_1$ minimization with a generalization called Ordered Weighted $\ell_1$ (OWL) minimization which performs simultaneous regression and clustering of correlated variables. Using random geometric graph theory, we prove that OWL regression selects more points within each subspace, resulting in better clustering results. This allows for accurate subspace clustering based on regression solutions for only a small subset of the total dataset, significantly reducing the computational complexity compared to SSC. In experiments, we find that our OWL approach can achieve a speedup of 20$\times$ to 30$\times$ for synthetic problems and 4$\times$ to 8$\times$ on real data problems.

stat.ML↗

arXiv2018

Teacher Improves Learning by Selecting a Training Subset

We call a learner super-teachable if a teacher can trim down an iid training set while making the learner learn even better. We provide sharp super-teaching guarantees on two learners: the maximum likelihood estimator for the mean of a Gaussian, and the large margin classifier in 1D. For general learners, we provide a mixed-integer nonlinear programming-based algorithm to find a super teaching set. Empirical experiments show that our algorithm is able to find good super-teaching sets for both regression and classification problems.

stat.ML↗

arXiv2018

Adaptive Sampling for Coarse Ranking

We consider the problem of active coarse ranking, where the goal is to sort items according to their means into clusters of pre-specified sizes, by adaptively sampling from their reward distributions. This setting is useful in many social science applications involving human raters and the approximate rank of every item is desired. Approximate or coarse ranking can significantly reduce the number of ratings required in comparison to the number needed to find an exact ranking. We propose a computationally efficient PAC algorithm LUCBRank for coarse ranking, and derive an upper bound on its sample complexity. We also derive a nearly matching distribution-dependent lower bound. Experiments on synthetic as well as real-world data show that LUCBRank performs better than state-of-the-art baseline methods, even when these methods have the advantage of knowing the underlying parametric model.

cs.LG↗

arXiv2018

Learning Low-Dimensional Metrics

This paper investigates the theoretical foundations of metric learning, focused on three key questions that are not fully addressed in prior work: 1) we consider learning general low-dimensional (low-rank) metrics as well as sparse metrics; 2) we develop upper and lower (minimax)bounds on the generalization error; 3) we quantify the sample complexity of metric learning in terms of the dimension of the feature space and the dimension/rank of the underlying metric;4) we also bound the accuracy of the learned metric relative to the underlying true generative metric. All the results involve novel mathematical approaches to the metric learning problem, and lso shed new light on the special case of ordinal embedding (aka non-metric multidimensional scaling).

stat.ML↗

arXiv2017

Scalable Generalized Linear Bandits: Online Computation and Hashing

Generalized Linear Bandits (GLBs), a natural extension of the stochastic linear bandits, has been popular and successful in recent years. However, existing GLBs scale poorly with the number of rounds and the number of arms, limiting their utility in practice. This paper proposes new, scalable solutions to the GLB problem in two respects. First, unlike existing GLBs, whose per-time-step space and time complexity grow at least linearly with time $t$, we propose a new algorithm that performs online computations to enjoy a constant space and time complexity. At its heart is a novel Generalized Linear extension of the Online-to-confidence-set Conversion (GLOC method) that takes \emph{any} online learning algorithm and turns it into a GLB algorithm. As a special case, we apply GLOC to the online Newton step algorithm, which results in a low-regret GLB algorithm with much lower time and memory complexity than prior work. Second, for the case where the number $N$ of arms is very large, we propose new algorithms in which each next arm is selected via an inner product search. Such methods can be implemented via hashing algorithms (i.e., "hash-amenable") and result in a time complexity sublinear in $N$. While a Thompson sampling extension of GLOC is hash-amenable, its regret bound for $d$-dimensional arm sets scales with $d^{3/2}$, whereas GLOC's regret bound scales with $d$. Towards closing this gap, we propose a new hash-amenable algorithm whose regret bound scales with $d^{5/4}$. Finally, we propose a fast approximate hash-key computation (inner product) with a better accuracy than the state-of-the-art, which can be of independent interest. We conclude the paper with preliminary experimental results confirming the merits of our methods.

stat.ML↗

arXiv2017

A KL-LUCB Bandit Algorithm for Large-Scale Crowdsourcing

This paper focuses on best-arm identification in multi-armed bandits with bounded rewards. We develop an algorithm that is a fusion of lil-UCB and KL-LUCB, offering the best qualities of the two algorithms in one method. This is achieved by proving a novel anytime confidence bound for the mean of bounded distributions, which is the analogue of the LIL-type bounds recently developed for sub-Gaussian distributions. We corroborate our theoretical results with numerical experiments based on the New Yorker Cartoon Caption Contest.

math.ST↗

arXiv2017

Coalescent-based species tree estimation: a stochastic Farris transform

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular sequences corresponding to each gene often provide limited information about the gene trees themselves. In this paper we consider an approach to species tree reconstruction that addresses both these hurdles. Specifically, we propose an algorithm for phylogeny reconstruction under the multispecies coalescent model with a standard model of site substitution. The multispecies coalescent is commonly used to model gene tree discordance due to incomplete lineage sorting, a well-studied population-genetic effect. In previous work, an information-theoretic trade-off was derived in this context between the number of loci, $m$, needed for an accurate reconstruction and the length of the locus sequences, $k$. It was shown that to reconstruct an internal branch of length $f$, one needs $m$ to be of the order of $1/[f^{2} \sqrt{k}]$. That previous result was obtained under the molecular clock assumption, i.e., under the assumption that mutation rates (as well as population sizes) are constant across the species phylogeny. Here we generalize this result beyond the restrictive molecular clock assumption, and obtain a new reconstruction algorithm that has the same data requirement (up to log factors). Our main contribution is a novel reduction to the molecular clock case under the multispecies coalescent. As a corollary, we also obtain a new identifiability result of independent interest: for any species tree with $n \geq 3$ species, the rooted species tree can be identified from the distribution of its unrooted weighted gene trees even in the absence of a molecular clock.

cs.LG↗

arXiv2016

Learning the Interference Graph of a Wireless Network

A key challenge in wireless networking is the management of interference between transmissions. Identifying which transmitters interfere with each other is a crucial first step. In this paper we cast the task of estimating the a wireless interference environment as a graph learning problem. Nodes represent transmitters and edges represent the presence of interference between pairs of transmitters. We passively observe network traffic transmission patterns and collect information on transmission successes and failures. We establish bounds on the number of observations (each a snapshot of a network traffic pattern) required to identify the interference graph reliably with high probability. Our main results are scaling laws that tell us how the number of observations must grow in terms of the total number of nodes $n$ in the network and the maximum number of interfering transmitters $d$ per node (maximum node degree). The effects of hidden terminal interference (i.e., interference not detectable via carrier sensing) on the observation requirements are also quantified. We show that to identify the graph it is necessary and sufficient that the observation period grows like $d^2 \log n$, and we propose a practical algorithm that reliably identifies the graph from this length of observation. The observation requirements scale quite mildly with network size, and networks with sparse interference (small $d$) can be identified more rapidly. Computational experiments based on a realistic simulations of the traffic and protocol lend additional support to these conclusions.

cs.IT↗

arXiv2016

On Learning High Dimensional Structured Single Index Models

Single Index Models (SIMs) are simple yet flexible semi-parametric models for machine learning, where the response variable is modeled as a monotonic function of a linear combination of features. Estimation in this context requires learning both the feature weights and the nonlinear function that relates features to observations. While methods have been described to learn SIMs in the low dimensional regime, a method that can efficiently learn SIMs in high dimensions, and under general structural assumptions, has not been forthcoming. In this paper, we propose computationally efficient algorithms for SIM inference in high dimensions with structural constraints. Our general approach specializes to sparsity, group sparsity, and low-rank assumptions among others. Experiments show that the proposed method enjoys superior predictive performance when compared to generalized linear models, and achieves results comparable to or better than single layer feedforward neural networks with significantly less computational cost.

stat.ML↗

arXiv2016

Graph-Based Active Learning: A New Look at Expected Error Minimization

In graph-based active learning, algorithms based on expected error minimization (EEM) have been popular and yield good empirical performance. The exact computation of EEM optimally balances exploration and exploitation. In practice, however, EEM-based algorithms employ various approximations due to the computational hardness of exact EEM. This can result in a lack of either exploration or exploitation, which can negatively impact the effectiveness of active learning. We propose a new algorithm TSA (Two-Step Approximation) that balances between exploration and exploitation efficiently while enjoying the same computational complexity as existing approximations. Finally, we empirically show the value of balancing between exploration and exploitation in both toy and real-world datasets where our method outperforms several state-of-the-art methods.

stat.ML↗

arXiv2016

Active Algorithms For Preference Learning Problems with Multiple Populations

In this paper we model the problem of learning preferences of a population as an active learning problem. We propose an algorithm can adaptively choose pairs of items to show to users coming from a heterogeneous population, and use the obtained reward to decide which pair of items to show next. We provide computationally efficient algorithms with provable sample complexity guarantees for this problem in both the noiseless and noisy cases. In the process of establishing sample complexity guarantees for our algorithms, we establish new results using a Nystr{ö}m-like method which can be of independent interest. We supplement our theoretical results with experimental comparisons.

stat.ML↗

arXiv2016

Finite Sample Prediction and Recovery Bounds for Ordinal Embedding

The goal of ordinal embedding is to represent items as points in a low-dimensional Euclidean space given a set of constraints in the form of distance comparisons like "item $i$ is closer to item $j$ than item $k$". Ordinal constraints like this often come from human judgments. To account for errors and variation in judgments, we consider the noisy situation in which the given constraints are independently corrupted by reversing the correct constraint with some probability. This paper makes several new contributions to this problem. First, we derive prediction error bounds for ordinal embedding with noise by exploiting the fact that the rank of a distance matrix of points in $\mathbb{R}^d$ is at most $d+2$. These bounds characterize how well a learned embedding predicts new comparative judgments. Second, we investigate the special case of a known noise model and study the Maximum Likelihood estimator. Third, knowledge of the noise model enables us to relate prediction errors to embedding accuracy. This relationship is highly non-trivial since we show that the linear map corresponding to distance comparisons is non-invertible, but there exists a nonlinear map that is invertible. Fourth, two new algorithms for ordinal embedding are proposed and evaluated in experiments.

stat.ML↗

arXiv2015

Learning Single Index Models in High Dimensions

Single Index Models (SIMs) are simple yet flexible semi-parametric models for classification and regression. Response variables are modeled as a nonlinear, monotonic function of a linear combination of features. Estimation in this context requires learning both the feature weights, and the nonlinear function. While methods have been described to learn SIMs in the low dimensional regime, a method that can efficiently learn SIMs in high dimensions has not been forthcoming. We propose three variants of a computationally and statistically efficient algorithm for SIM inference in high dimensions. We establish excess risk bounds for the proposed algorithms and experimentally validate the advantages that our SIM learning methods provide relative to Generalized Linear Model (GLM) and low dimensional SIM based learning methods.

stat.ML↗

arXiv2015

S2: An Efficient Graph Based Active Learning Algorithm with Application to Nonparametric Classification

This paper investigates the problem of active learning for binary label prediction on a graph. We introduce a simple and label-efficient algorithm called S2 for this task. At each step, S2 selects the vertex to be labeled based on the structure of the graph and all previously gathered labels. Specifically, S2 queries for the label of the vertex that bisects the *shortest shortest* path between any pair of oppositely labeled vertices. We present a theoretical estimate of the number of queries S2 needs in terms of a novel parametrization of the complexity of binary functions on graphs. We also present experimental results demonstrating the performance of S2 on both real and synthetic data. While other graph-based active learning algorithms have shown promise in practice, our algorithm is the first with both good performance and theoretical guarantees. Finally, we demonstrate the implications of the S2 algorithm to the theory of nonparametric active learning. In particular, we show that S2 achieves near minimax optimal excess risk for an important class of nonparametric classification problems.

cs.LG↗

arXiv2015

Sparse Dueling Bandits

The dueling bandit problem is a variation of the classical multi-armed bandit in which the allowable actions are noisy comparisons between pairs of arms. This paper focuses on a new approach for finding the "best" arm according to the Borda criterion using noisy comparisons. We prove that in the absence of structural assumptions, the sample complexity of this problem is proportional to the sum of the inverse squared gaps between the Borda scores of each suboptimal arm and the best arm. We explore this dependence further and consider structural constraints on the pairwise comparison matrix (a particular form of sparsity natural to this problem) that can significantly reduce the sample complexity. This motivates a new algorithm called Successive Elimination with Comparison Sparsity (SECS) that exploits sparsity to find the Borda winner using fewer samples than standard algorithms. We also evaluate the new algorithm experimentally with synthetic and real data. The results show that the sparsity model and the new algorithm can provide significant improvements over standard approaches.

stat.ML↗

arXiv2014

Sequential Testing for Sparse Recovery

This paper studies sequential methods for recovery of sparse signals in high dimensions. When compared to fixed sample size procedures, in the sparse setting, sequential methods can result in a large reduction in the number of samples needed for reliable signal support recovery. Starting with a lower bound, we show any coordinate-wise sequential sampling procedure fails in the high dimensional limit provided the average number of measurements per dimension is less then log s/D(P_0||P_1) where s is the level of sparsity and D(P_0||P_1) the Kullback-Leibler divergence between the underlying distributions. A series of Sequential Probability Ratio Tests (SPRT) which require complete knowledge of the underlying distributions is shown to achieve this bound. Motivated by real world experiments and recent work in adaptive sensing, we introduce a simple procedure termed Sequential Thresholding which can be implemented when the underlying testing problem satisfies a monotone likelihood ratio assumption. Sequential Thresholding guarantees exact support recovery provided the average number of measurements per dimension grows faster than log s/ D(P_0||P_1), achieving the lower bound. For comparison, we show any non-sequential procedure fails provided the number of measurements grows at a rate less than log n/D(P_1||P_0), where n is the total dimension of the problem.

cs.IT↗

arXiv2014

Classification with Sparse Overlapping Groups

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.

cs.LG↗