arXiv subjects

Ming Yuan

Publications and source records attributed to Ming Yuan.

At least 73 records · Page 4Linked to original sources

arXiv2019

Controlling the Minimal Feature Sizes in Adjoint Optimization of Nanophotonic Devices Using B-spline Surfaces

Adjoint optimization is an effective method in the inverse design of nanophotonic devices. In order to ensure the manufacturability, one would like to have control over the minimal feature sizes. Here we propose utilizing a level-set method based on b-spline surfaces in order to control the feature sizes. This approach is first used to design a wavelength demultiplexer. It is also used to implement a nanophotonic structure for artificial neural computing. In both cases, we show that the minimal feature sizes can be easily parameterized and controlled.

physics.optics↗

arXiv2019

Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence Microscopy

Colocalization analysis aims to study complex spatial associations between bio-molecules via optical imaging techniques. However, existing colocalization analysis workflows only assess an average degree of colocalization within a certain region of interest and ignore the unique and valuable spatial information offered by microscopy. In the current work, we introduce a new framework for colocalization analysis that allows us to quantify colocalization levels at each individual location and automatically identify pixels or regions where colocalization occurs. The framework, referred to as spatially adaptive colocalization analysis (SACA), integrates a pixel-wise local kernel model for colocalization quantification and a multi-scale adaptive propagation-separation strategy for utilizing spatial information to detect colocalization in a spatially adaptive fashion. Applications to simulated and real biological datasets demonstrate the practical merits of SACA in what we hope to be an easily applicable and robust colocalization analysis method. In addition, theoretical properties of SACA are investigated to provide rigorous statistical justification.

stat.ME↗

arXiv2018

Statistically Optimal and Computationally Efficient Low Rank Tensor Completion from Noisy Entries

In this article, we develop methods for estimating a low rank tensor from noisy observations on a subset of its entries to achieve both statistical and computational efficiencies. There have been a lot of recent interests in this problem of noisy tensor completion. Much of the attention has been focused on the fundamental computational challenges often associated with problems involving higher order tensors, yet very little is known about their statistical performance. To fill in this void, in this article, we characterize the fundamental statistical limits of noisy tensor completion by establishing minimax optimal rates of convergence for estimating a $k$th order low rank tensor under the general $\ell_p$ ($1\le p\le 2$) norm which suggest significant room for improvement over the existing approaches. Furthermore, we propose a polynomial-time computable estimating procedure based upon power iteration and a second-order spectral initialization that achieves the optimal rates of convergence. Our method is fairly easy to implement and numerical experiments are presented to further demonstrate the practical merits of our estimator.

stat.ML↗

arXiv2017

Finding Differentially Covarying Needles in a Temporally Evolving Haystack: A Scan Statistics Perspective

Recent results in coupled or temporal graphical models offer schemes for estimating the relationship structure between features when the data come from related (but distinct) longitudinal sources. A novel application of these ideas is for analyzing group-level differences, i.e., in identifying if trends of estimated objects (e.g., covariance or precision matrices) are different across disparate conditions (e.g., gender or disease). Often, poor effect sizes make detecting the differential signal over the full set of features difficult: for example, dependencies between only a subset of features may manifest differently across groups. In this work, we first give a parametric model for estimating trends in the space of SPD matrices as a function of one or more covariates. We then generalize scan statistics to graph structures, to search over distinct subsets of features (graph partitions) whose temporal dependency structure may show statistically significant group-wise differences. We theoretically analyze the Family Wise Error Rate (FWER) and bounds on Type 1 and Type 2 error. On a cohort of individuals with risk factors for Alzheimer's disease (but otherwise cognitively healthy), we find scientifically interesting group differences where the default analysis, i.e., models estimated on the full graph, do not survive reasonable significance thresholds.

stat.ML↗

arXiv2017

Effective Tensor Sketching via Sparsification

In this paper, we investigate effective sketching schemes via sparsification for high dimensional multilinear arrays or tensors. More specifically, we propose a novel tensor sparsification algorithm that retains a subset of the entries of a tensor in a judicious way, and prove that it can attain a given level of approximation accuracy in terms of tensor spectral norm with a much smaller sample complexity when compared with existing approaches. In particular, we show that for a $k$th order $d\times\cdots\times d$ cubic tensor of {\it stable rank} $r_s$, the sample size requirement for achieving a relative error $\varepsilon$ is, up to a logarithmic factor, of the order $r_s^{1/2} d^{k/2} /\varepsilon$ when $\varepsilon$ is relatively large, and $r_s d /\varepsilon^2$ and essentially optimal when $\varepsilon$ is sufficiently small. It is especially noteworthy that the sample size requirement for achieving a high accuracy is of an order independent of $k$. To further demonstrate the utility of our techniques, we also study how higher order singular value decomposition (HOSVD) of large tensors can be efficiently approximated via sparsification.

stat.ME↗

arXiv2017

Global Testing Against Sparse Alternatives under Ising Models

In this paper, we study the effect of dependence on detecting sparse signals. In particular, we focus on global testing against sparse alternatives for the means of binary outcomes following an Ising model, and establish how the interplay between the strength and sparsity of a signal determines its detectability under various notions of dependence. The profound impact of dependence is best illustrated under the Curie-Weiss model where we observe the effect of a "thermodynamic" phase transition. In particular, the critical state exhibits a subtle "blessing of dependence" phenomenon in that one can detect much weaker signals at criticality than otherwise. Furthermore, we develop a testing procedure that is broadly applicable to account for dependence and show that it is asymptotically minimax optimal under fairly general regularity conditions.

math.ST↗

arXiv2017

Automated and Robust Quantification of Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric Statistical Approach

Colocalization is a powerful tool to study the interactions between fluorescently labeled molecules in biological fluorescence microscopy. However, existing techniques for colocalization analysis have not undergone continued development especially in regards to robust statistical support. In this paper, we examine two of the most popular quantification techniques for colocalization and argue that they could be improved upon using ideas from nonparametric statistics and scan statistics. In particular, we propose a new colocalization metric that is robust, easily implementable, and optimal in a rigorous statistical testing framework. Application to several benchmark datasets, as well as biological examples, further demonstrates the usefulness of the proposed technique.

stat.ME↗

arXiv2017

On the Optimality of Kernel-Embedding Based Goodness-of-Fit Tests

The reproducing kernel Hilbert space (RKHS) embedding of distributions offers a general and flexible framework for testing problems in arbitrary domains and has attracted considerable amount of attention in recent years. To gain insights into their operating characteristics, we study here the statistical performance of such approaches within a minimax framework. Focusing on the case of goodness-of-fit tests, our analyses show that a vanilla version of the kernel-embedding based test could be suboptimal, and suggest a simple remedy by moderating the embedding. We prove that the moderated approach provides optimal tests for a wide range of deviations from the null and can also be made adaptive over a large collection of interpolation spaces. Numerical experiments are presented to further demonstrate the merits of our approach.

stat.ML↗

arXiv2017

Efficient multivariate entropy estimation via $k$-nearest neighbour distances

Many statistical procedures, including goodness-of-fit tests and methods for independent component analysis, rely critically on the estimation of the entropy of a distribution. In this paper, we seek entropy estimators that are efficient and achieve the local asymptotic minimax lower bound with respect to squared error loss. To this end, we study weighted averages of the estimators originally proposed by Kozachenko and Leonenko (1987), based on the $k$-nearest neighbour distances of a sample of $n$ independent and identically distributed random vectors in $\mathbb{R}^d$. A careful choice of weights enables us to obtain an efficient estimator in arbitrary dimensions, given sufficient smoothness, while the original unweighted estimator is typically only efficient when $d \leq 3$. In addition to the new estimator proposed and theoretical understanding provided, our results facilitate the construction of asymptotically valid confidence intervals for the entropy of asymptotically minimal width.

math.ST↗

arXiv2017

Convex Regularization for High-Dimensional Multi-Response Tensor Regression

In this paper we present a general convex optimization approach for solving high-dimensional multiple response tensor regression problems under low-dimensional structural assumptions. We consider using convex and weakly decomposable regularizers assuming that the underlying tensor lies in an unknown low-dimensional subspace. Within our framework, we derive general risk bounds of the resulting estimate under fairly general dependence structure among covariates. Our framework leads to upper bounds in terms of two very simple quantities, the \emph{Gaussian width} of a convex set in tensor space and the \emph{intrinsic dimension} of the low-dimensional tensor subspace. To the best of our knowledge, this is the first general framework that applies to multiple response problems. These general bounds provide useful upper bounds on rates of convergence for a number of fundamental statistical models of interest including multi-response regression, vector auto-regressive models, low-rank tensor models and pairwise interaction models. Moreover, in many of these settings we prove that the resulting estimates are minimax optimal. We also provide a numerical study that both validates our theoretical guarantees and demonstrates the breadth of our framework.

math.ST↗

arXiv2017

Characterizing Spatiotemporal Transcriptome of Human Brain via Low Rank Tensor Decomposition

Spatiotemporal gene expression data of the human brain offer insights on the spa- tial and temporal patterns of gene regulation during brain development. Most existing methods for analyzing these data consider spatial and temporal profiles separately with the implicit assumption that different brain regions develop in similar trajectories, and that the spatial patterns of gene expression remain similar at different time points. Al- though these analyses may help delineate gene regulation either spatially or temporally, they are not able to characterize heterogeneity in temporal dynamics across different brain regions, or the evolution of spatial patterns of gene regulation over time. In this article, we develop a statistical method based on low rank tensor decomposition to more effectively analyze spatiotemporal gene expression data. We generalize the clas- sical principal component analysis (PCA) which is applicable only to data matrices, to tensor PCA that can simultaneously capture spatial and temporal effects. We also propose an efficient algorithm that combines tensor unfolding and power iteration to estimate the tensor principal components, and provide guarantees on their statistical performances. Numerical experiments are presented to further demonstrate the mer- its of the proposed method. An application of our method to a spatiotemporal brain expression data provides insights on gene regulation patterns in the brain.

stat.ME↗

arXiv2017

On Polynomial Time Methods for Exact Low Rank Tensor Completion

In this paper, we investigate the sample size requirement for exact recovery of a high order tensor of low rank from a subset of its entries. We show that a gradient descent algorithm with initial value obtained from a spectral method can, in particular, reconstruct a ${d\times d\times d}$ tensor of multilinear ranks $(r,r,r)$ with high probability from as few as $O(r^{7/2}d^{3/2}\log^{7/2}d+r^7d\log^6d)$ entries. In the case when the ranks $r=O(1)$, our sample size requirement matches those for nuclear norm minimization (Yuan and Zhang, 2016a), or alternating least squares assuming orthogonal decomposability (Jain and Oh, 2014). Unlike these earlier approaches, however, our method is efficient to compute, easy to implement, and does not impose extra structures on the tensor. Numerical results are presented to further demonstrate the merits of the proposed approach.

stat.ML↗

arXiv2016

Non-Convex Projected Gradient Descent for Generalized Low-Rank Tensor Regression

In this paper, we consider the problem of learning high-dimensional tensor regression problems with low-rank structure. One of the core challenges associated with learning high-dimensional models is computation since the underlying optimization problems are often non-convex. While convex relaxations could lead to polynomial-time algorithms they are often slow in practice. On the other hand, limited theoretical guarantees exist for non-convex methods. In this paper we provide a general framework that provides theoretical guarantees for learning high-dimensional tensor regression models under different low-rank structural assumptions using the projected gradient descent algorithm applied to a potentially non-convex constraint set $Θ$ in terms of its \emph{localized Gaussian width}. We juxtapose our theoretical results for non-convex projected gradient descent algorithms with previous results on regularized convex approaches. The two main differences between the convex and non-convex approach are: (i) from a computational perspective whether the non-convex projection operator is computable and whether the projection has desirable contraction properties and (ii) from a statistical upper bound perspective, the non-convex approach has a superior rate for a number of examples. We provide three concrete examples of low-dimensional structure which address these issues and explain the pros and cons for the non-convex and convex approaches. We supplement our theoretical results with simulations which show that, under several common settings of generalized low rank tensor regression, the projected gradient descent approach is superior both in terms of statistical error and run-time provided the step-sizes of the projected descent algorithm are suitably chosen.

stat.ML↗

arXiv2016

Combined Hypothesis Testing on Graphs with Applications to Gene Set Enrichment Analysis

Motivated by gene set enrichment analysis, we investigate the problem of combined hypothesis testing on a graph. We introduce a general framework to effectively use the structural information of the underlying graph when testing multivariate means. A new testing procedure is proposed within this framework. We show that the test is optimal in that it can consistently detect departure from the collective null at a rate that no other test could improve, for almost all graphs. We also provide general performance bounds for the proposed test under any specific graph, and illustrate their utility through several common types of graphs. Numerical experiments are presented to further demonstrate the merits of our approach.

stat.ME↗

arXiv2016

Incoherent Tensor Norms and Their Applications in Higher Order Tensor Completion

In this paper, we investigate the sample size requirement for a general class of nuclear norm minimization methods for higher order tensor completion. We introduce a class of tensor norms by allowing for different levels of coherence, which allows us to leverage the incoherence of a tensor. In particular, we show that a $k$th order tensor of rank $r$ and dimension $d\times\cdots\times d$ can be recovered perfectly from as few as $O((r^{(k-1)/2}d^{3/2}+r^{k-1}d)(\log(d))^2)$ uniformly sampled entries through an appropriate incoherent nuclear norm minimization. Our results demonstrate some key differences between completing a matrix and a higher order tensor: They not only point to potential room for improvement over the usual nuclear norm minimization but also highlight the importance of explicitly accounting for incoherence, when dealing with higher order tensors.

math.ST↗

arXiv2016

Structured Correlation Detection with Application to Colocalization Analysis in Dual-Channel Fluorescence Microscopic Imaging

Motivated by the problem of colocalization analysis in fluorescence microscopic imaging, we study in this paper structured detection of correlated regions between two random processes observed on a common domain. We argue that although intuitive, direct use of the maximum log-likelihood statistic suffers from potential bias and substantially reduced power, and introduce a simple size-based normalization to overcome this problem. We show that scanning with the proposed size-corrected likelihood ratio statistics leads to optimal correlation detection over a large collection of structured correlation detection problems.

math.ST↗

arXiv2016

Optimal large-scale quantum state tomography with Pauli measurements

Quantum state tomography aims to determine the state of a quantum system as represented by a density matrix. It is a fundamental task in modern scientific studies involving quantum systems. In this paper, we study estimation of high-dimensional density matrices based on Pauli measurements. In particular, under appropriate notion of sparsity, we establish the minimax optimal rates of convergence for estimation of the density matrix under both the spectral and Frobenius norm losses; and show how these rates can be achieved by a common thresholding approach. Numerical performance of the proposed estimator is also investigated.

math.ST↗

arXiv2015

Minimax Optimal Rates of Estimation in High Dimensional Additive Models: Universal Phase Transition

We establish minimax optimal rates of convergence for estimation in a high dimensional additive model assuming that it is approximately sparse. Our results reveal an interesting phase transition behavior universal to this class of high dimensional problems. In the {\it sparse regime} when the components are sufficiently smooth or the dimensionality is sufficiently large, the optimal rates are identical to those for high dimensional linear regression, and therefore there is no additional cost to entertain a nonparametric model. Otherwise, in the so-called {\it smooth regime}, the rates coincide with the optimal rates for estimating a univariate function, and therefore they are immune to the "curse of dimensionality".

math.ST↗