arXiv subjects

Yuval Kluger

Publications and source records attributed to Yuval Kluger.

At least 37 records · Page 2Linked to original sources

arXiv2021

Local Two-Sample Testing over Graphs and Point-Clouds by Random-Walk Distributions

Rejecting the null hypothesis in two-sample testing is a fundamental tool for scientific discovery. Yet, aside from concluding that two samples do not come from the same probability distribution, it is often of interest to characterize how the two distributions differ. Given samples from two densities $f_1$ and $f_0$, we consider the task of localizing occurrences of the inequality $f_1 > f_0$. To avoid the challenges associated with high-dimensional space, we propose a general hypothesis testing framework where hypotheses are formulated adaptively to the data by conditioning on the combined sample from the two densities. We then investigate a special case of this framework where the notion of locality is captured by a random walk on a weighted graph constructed over this combined sample. We derive a tractable testing procedure for this case employing a type of scan statistic, and provide non-asymptotic lower bounds on the power and accuracy of our test to detect whether $f_1>f_0$ in a local sense. Furthermore, we characterize the test's consistency according to a certain problem-hardness parameter, and show that our test achieves the minimax detection rate for this parameter. We conduct numerical experiments to validate our method, and demonstrate our approach on two real-world applications: detecting and localizing arsenic well contamination across the United States, and analyzing two-sample single-cell RNA sequencing data from melanoma patients.

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arXiv2021

$\ell_0$-based Sparse Canonical Correlation Analysis

Canonical Correlation Analysis (CCA) models are powerful for studying the associations between two sets of variables. The canonically correlated representations, termed \textit{canonical variates} are widely used in unsupervised learning to analyze unlabeled multi-modal registered datasets. Despite their success, CCA models may break (or overfit) if the number of variables in either of the modalities exceeds the number of samples. Moreover, often a significant fraction of the variables measures modality-specific information, and thus removing them is beneficial for identifying the \textit{canonically correlated variates}. Here, we propose $\ell_0$-CCA, a method for learning correlated representations based on sparse subsets of variables from two observed modalities. Sparsity is obtained by multiplying the input variables by stochastic gates, whose parameters are learned together with the CCA weights via an $\ell_0$-regularized correlation loss. We further propose $\ell_0$-Deep CCA for solving the problem of non-linear sparse CCA by modeling the correlated representations using deep nets. We demonstrate the efficacy of the method using several synthetic and real examples. Most notably, by gating nuisance input variables, our approach improves the extracted representations compared to other linear, non-linear and sparse CCA-based models.

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arXiv2021

On the Efficient Evaluation of the Azimuthal Fourier Components of the Green's Function for Helmholtz's Equation in Cylindrical Coordinates

In this manuscript, we develop an efficient algorithm to evaluate the azimuthal Fourier components of the Green's function for the Helmholtz equation in cylindrical coordinates. A computationally efficient algorithm for this modal Green's function is essential for solvers for electromagnetic scattering from bodies of revolution (e.g., radar cross sections, antennas). Current algorithms to evaluate this modal Green's function become computationally intractable when the source and target are close or when the wavenumber is large. Furthermore, most state of the art methods cannot be easily parallelized. In this manuscript, we present an algorithm for evaluating the modal Green's function that has performance independent of both source-to-target proximity and wavenumber, and whose cost grows as $O(m)$, where $m$ is the Fourier mode. Furthermore, our algorithm is embarrassingly parallelizable.

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arXiv2021

Doubly-Stochastic Normalization of the Gaussian Kernel is Robust to Heteroskedastic Noise

A fundamental step in many data-analysis techniques is the construction of an affinity matrix describing similarities between data points. When the data points reside in Euclidean space, a widespread approach is to from an affinity matrix by the Gaussian kernel with pairwise distances, and to follow with a certain normalization (e.g. the row-stochastic normalization or its symmetric variant). We demonstrate that the doubly-stochastic normalization of the Gaussian kernel with zero main diagonal (i.e., no self loops) is robust to heteroskedastic noise. That is, the doubly-stochastic normalization is advantageous in that it automatically accounts for observations with different noise variances. Specifically, we prove that in a suitable high-dimensional setting where heteroskedastic noise does not concentrate too much in any particular direction in space, the resulting (doubly-stochastic) noisy affinity matrix converges to its clean counterpart with rate $m^{-1/2}$, where $m$ is the ambient dimension. We demonstrate this result numerically, and show that in contrast, the popular row-stochastic and symmetric normalizations behave unfavorably under heteroskedastic noise. Furthermore, we provide examples of simulated and experimental single-cell RNA sequence data with intrinsic heteroskedasticity, where the advantage of the doubly-stochastic normalization for exploratory analysis is evident.

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arXiv2020

The Spectral Underpinning of word2vec

word2vec due to Mikolov \textit{et al.} (2013) is a word embedding method that is widely used in natural language processing. Despite its great success and frequent use, theoretical justification is still lacking. The main contribution of our paper is to propose a rigorous analysis of the highly nonlinear functional of word2vec. Our results suggest that word2vec may be primarily driven by an underlying spectral method. This insight may open the door to obtaining provable guarantees for word2vec. We support these findings by numerical simulations. One fascinating open question is whether the nonlinear properties of word2vec that are not captured by the spectral method are beneficial and, if so, by what mechanism.

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arXiv2020

Differentiable Unsupervised Feature Selection based on a Gated Laplacian

Scientific observations may consist of a large number of variables (features). Identifying a subset of meaningful features is often ignored in unsupervised learning, despite its potential for unraveling clear patterns hidden in the ambient space. In this paper, we present a method for unsupervised feature selection, and we demonstrate its use for the task of clustering. We propose a differentiable loss function that combines the Laplacian score, which favors low-frequency features, with a gating mechanism for feature selection. We improve the Laplacian score, by replacing it with a gated variant computed on a subset of features. This subset is obtained using a continuous approximation of Bernoulli variables whose parameters are trained to gate the full feature space. We mathematically motivate the proposed approach and demonstrate that in the high noise regime, it is crucial to compute the Laplacian on the gated inputs, rather than on the full feature set. Experimental demonstration of the efficacy of the proposed approach and its advantage over current baselines is provided using several real-world examples.

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arXiv2020

Spectral neighbor joining for reconstruction of latent tree models

A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a set of observed organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a key challenge is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover the structure of latent tree graphical models. Given a matrix that contains a measure of similarity between all pairs of observed variables, SNJ computes a spectral measure of cohesion between groups of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that in comparison to several other reconstruction methods, SNJ requires fewer samples to accurately recover trees with a large number of leaves or long edges.

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arXiv2020

Feature Selection using Stochastic Gates

Feature selection problems have been extensively studied for linear estimation, for instance, Lasso, but less emphasis has been placed on feature selection for non-linear functions. In this study, we propose a method for feature selection in high-dimensional non-linear function estimation problems. The new procedure is based on minimizing the $\ell_0$ norm of the vector of indicator variables that represent if a feature is selected or not. Our approach relies on the continuous relaxation of Bernoulli distributions, which allows our model to learn the parameters of the approximate Bernoulli distributions via gradient descent. This general framework simultaneously minimizes a loss function while selecting relevant features. Furthermore, we provide an information-theoretic justification of incorporating Bernoulli distribution into our approach and demonstrate the potential of the approach on synthetic and real-life applications.

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arXiv2019

Heavy-tailed kernels reveal a finer cluster structure in t-SNE visualisations

T-distributed stochastic neighbour embedding (t-SNE) is a widely used data visualisation technique. It differs from its predecessor SNE by the low-dimensional similarity kernel: the Gaussian kernel was replaced by the heavy-tailed Cauchy kernel, solving the "crowding problem" of SNE. Here, we develop an efficient implementation of t-SNE for a $t$-distribution kernel with an arbitrary degree of freedom $ν$, with $ν\to\infty$ corresponding to SNE and $ν=1$ corresponding to the standard t-SNE. Using theoretical analysis and toy examples, we show that $ν<1$ can further reduce the crowding problem and reveal finer cluster structure that is invisible in standard t-SNE. We further demonstrate the striking effect of heavier-tailed kernels on large real-life data sets such as MNIST, single-cell RNA-sequencing data, and the HathiTrust library. We use domain knowledge to confirm that the revealed clusters are meaningful. Overall, we argue that modifying the tail heaviness of the t-SNE kernel can yield additional insight into the cluster structure of the data.

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arXiv2018

Defending against Adversarial Images using Basis Functions Transformations

We study the effectiveness of various approaches that defend against adversarial attacks on deep networks via manipulations based on basis function representations of images. Specifically, we experiment with low-pass filtering, PCA, JPEG compression, low resolution wavelet approximation, and soft-thresholding. We evaluate these defense techniques using three types of popular attacks in black, gray and white-box settings. Our results show JPEG compression tends to outperform the other tested defenses in most of the settings considered, in addition to soft-thresholding, which performs well in specific cases, and yields a more mild decrease in accuracy on benign examples. In addition, we also mathematically derive a novel white-box attack in which the adversarial perturbation is composed only of terms corresponding a to pre-determined subset of the basis functions, of which a "low frequency attack" is a special case.

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arXiv2018

SpectralNet: Spectral Clustering using Deep Neural Networks

Spectral clustering is a leading and popular technique in unsupervised data analysis. Two of its major limitations are scalability and generalization of the spectral embedding (i.e., out-of-sample-extension). In this paper we introduce a deep learning approach to spectral clustering that overcomes the above shortcomings. Our network, which we call SpectralNet, learns a map that embeds input data points into the eigenspace of their associated graph Laplacian matrix and subsequently clusters them. We train SpectralNet using a procedure that involves constrained stochastic optimization. Stochastic optimization allows it to scale to large datasets, while the constraints, which are implemented using a special-purpose output layer, allow us to keep the network output orthogonal. Moreover, the map learned by SpectralNet naturally generalizes the spectral embedding to unseen data points. To further improve the quality of the clustering, we replace the standard pairwise Gaussian affinities with affinities leaned from unlabeled data using a Siamese network. Additional improvement can be achieved by applying the network to code representations produced, e.g., by standard autoencoders. Our end-to-end learning procedure is fully unsupervised. In addition, we apply VC dimension theory to derive a lower bound on the size of SpectralNet. State-of-the-art clustering results are reported on the Reuters dataset. Our implementation is publicly available at https://github.com/kstant0725/SpectralNet .

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arXiv2018

Learning Binary Latent Variable Models: A Tensor Eigenpair Approach

Latent variable models with hidden binary units appear in various applications. Learning such models, in particular in the presence of noise, is a challenging computational problem. In this paper we propose a novel spectral approach to this problem, based on the eigenvectors of both the second order moment matrix and third order moment tensor of the observed data. We prove that under mild non-degeneracy conditions, our method consistently estimates the model parameters at the optimal parametric rate. Our tensor-based method generalizes previous orthogonal tensor decomposition approaches, where the hidden units were assumed to be either statistically independent or mutually exclusive. We illustrate the consistency of our method on simulated data and demonstrate its usefulness in learning a common model for population mixtures in genetics.

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arXiv2018

Removal of Batch Effects using Distribution-Matching Residual Networks

Sources of variability in experimentally derived data include measurement error in addition to the physical phenomena of interest. This measurement error is a combination of systematic components, originating from the measuring instrument, and random measurement errors. Several novel biological technologies, such as mass cytometry and single-cell RNA-seq, are plagued with systematic errors that may severely affect statistical analysis if the data is not properly calibrated. We propose a novel deep learning approach for removing systematic batch effects. Our method is based on a residual network, trained to minimize the Maximum Mean Discrepancy (MMD) between the multivariate distributions of two replicates, measured in different batches. We apply our method to mass cytometry and single-cell RNA-seq datasets, and demonstrate that it effectively attenuates batch effects.

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arXiv2018

Randomized algorithms for distributed computation of principal component analysis and singular value decomposition

Randomized algorithms provide solutions to two ubiquitous problems: (1) the distributed calculation of a principal component analysis or singular value decomposition of a highly rectangular matrix, and (2) the distributed calculation of a low-rank approximation (in the form of a singular value decomposition) to an arbitrary matrix. Carefully honed algorithms yield results that are uniformly superior to those of the stock, deterministic implementations in Spark (the popular platform for distributed computation); in particular, whereas the stock software will without warning return left singular vectors that are far from numerically orthonormal, a significantly burnished randomized implementation generates left singular vectors that are numerically orthonormal to nearly the machine precision.

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arXiv2017

Efficient Algorithms for t-distributed Stochastic Neighborhood Embedding

t-distributed Stochastic Neighborhood Embedding (t-SNE) is a method for dimensionality reduction and visualization that has become widely popular in recent years. Efficient implementations of t-SNE are available, but they scale poorly to datasets with hundreds of thousands to millions of high dimensional data-points. We present Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE), which dramatically accelerates the computation of t-SNE. The most time-consuming step of t-SNE is a convolution that we accelerate by interpolating onto an equispaced grid and subsequently using the fast Fourier transform to perform the convolution. We also optimize the computation of input similarities in high dimensions using multi-threaded approximate nearest neighbors. We further present a modification to t-SNE called "late exaggeration," which allows for easier identification of clusters in t-SNE embeddings. Finally, for datasets that cannot be loaded into the memory, we present out-of-core randomized principal component analysis (oocPCA), so that the top principal components of a dataset can be computed without ever fully loading the matrix, hence allowing for t-SNE of large datasets to be computed on resource-limited machines.

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arXiv2017

Randomized Near Neighbor Graphs, Giant Components, and Applications in Data Science

If we pick $n$ random points uniformly in $[0,1]^d$ and connect each point to its $k-$nearest neighbors, then it is well known that there exists a giant connected component with high probability. We prove that in $[0,1]^d$ it suffices to connect every point to $ c_{d,1} \log{\log{n}}$ points chosen randomly among its $ c_{d,2} \log{n}-$nearest neighbors to ensure a giant component of size $n - o(n)$ with high probability. This construction yields a much sparser random graph with $\sim n \log\log{n}$ instead of $\sim n \log{n}$ edges that has comparable connectivity properties. This result has nontrivial implications for problems in data science where an affinity matrix is constructed: instead of picking the $k-$nearest neighbors, one can often pick $k' \ll k$ random points out of the $k-$nearest neighbors without sacrificing efficiency. This can massively simplify and accelerate computation, we illustrate this with several numerical examples.

math.CO↗

arXiv2017

Data-Driven Tree Transforms and Metrics

We consider the analysis of high dimensional data given in the form of a matrix with columns consisting of observations and rows consisting of features. Often the data is such that the observations do not reside on a regular grid, and the given order of the features is arbitrary and does not convey a notion of locality. Therefore, traditional transforms and metrics cannot be used for data organization and analysis. In this paper, our goal is to organize the data by defining an appropriate representation and metric such that they respect the smoothness and structure underlying the data. We also aim to generalize the joint clustering of observations and features in the case the data does not fall into clear disjoint groups. For this purpose, we propose multiscale data-driven transforms and metrics based on trees. Their construction is implemented in an iterative refinement procedure that exploits the co-dependencies between features and observations. Beyond the organization of a single dataset, our approach enables us to transfer the organization learned from one dataset to another and to integrate several datasets together. We present an application to breast cancer gene expression analysis: learning metrics on the genes to cluster the tumor samples into cancer sub-types and validating the joint organization of both the genes and the samples. We demonstrate that using our approach to combine information from multiple gene expression cohorts, acquired by different profiling technologies, improves the clustering of tumor samples.

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arXiv2017

Mahalanonbis Distance Informed by Clustering

A fundamental question in data analysis, machine learning and signal processing is how to compare between data points. The choice of the distance metric is specifically challenging for high-dimensional data sets, where the problem of meaningfulness is more prominent (e.g. the Euclidean distance between images). In this paper, we propose to exploit a property of high-dimensional data that is usually ignored - which is the structure stemming from the relationships between the coordinates. Specifically we show that organizing similar coordinates in clusters can be exploited for the construction of the Mahalanobis distance between samples. When the observable samples are generated by a nonlinear transformation of hidden variables, the Mahalanobis distance allows the recovery of the Euclidean distances in the hidden space.We illustrate the advantage of our approach on a synthetic example where the discovery of clusters of correlated coordinates improves the estimation of the principal directions of the samples. Our method was applied to real data of gene expression for lung adenocarcinomas (lung cancer). By using the proposed metric we found a partition of subjects to risk groups with a good separation between their Kaplan-Meier survival plot.

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