arXiv subjects

Can Yang

Publications and source records attributed to Can Yang.

At least 55 records · Page 3Linked to original sources

arXiv2019

Wasserstein-Wasserstein Auto-Encoders

To address the challenges in learning deep generative models (e.g.,the blurriness of variational auto-encoder and the instability of training generative adversarial networks, we propose a novel deep generative model, named Wasserstein-Wasserstein auto-encoders (WWAE). We formulate WWAE as minimization of the penalized optimal transport between the target distribution and the generated distribution. By noticing that both the prior $P_Z$ and the aggregated posterior $Q_Z$ of the latent code Z can be well captured by Gaussians, the proposed WWAE utilizes the closed-form of the squared Wasserstein-2 distance for two Gaussians in the optimization process. As a result, WWAE does not suffer from the sampling burden and it is computationally efficient by leveraging the reparameterization trick. Numerical results evaluated on multiple benchmark datasets including MNIST, fashion- MNIST and CelebA show that WWAE learns better latent structures than VAEs and generates samples of better visual quality and higher FID scores than VAEs and GANs.

cs.LG↗

arXiv2018

VIMCO: Variational Inference for Multiple Correlated Outcomes in Genome-wide Association Studies

In Genome-Wide Association Studies (GWAS) where multiple correlated traits have been measured on participants, a joint analysis strategy, whereby the traits are analyzed jointly, can improve statistical power over a single-trait analysis strategy. There are two questions of interest to be addressed when conducting a joint GWAS analysis with multiple traits. The first question examines whether a genetic loci is significantly associated with any of the traits being tested. The second question focuses on identifying the specific trait(s) that is associated with the genetic loci. Since existing methods primarily focus on the first question, this paper seeks to provide a complementary method that addresses the second question. We propose a novel method, Variational Inference for Multiple Correlated Outcomes (VIMCO), that focuses on identifying the specific trait that is associated with the genetic loci, when performing a joint GWAS analysis of multiple traits, while accounting for correlation among the multiple traits. We performed extensive numerical studies and also applied VIMCO to analyze two datasets. The numerical studies and real data analysis demonstrate that VIMCO improves statistical power over single-trait analysis strategies when the multiple traits are correlated and has comparable performance when the traits are not correlated.

stat.ME↗

arXiv2018

REMI: Regression with marginal information and its application in genome-wide association studies

In this study, we consider the problem of variable selection and estimation in high-dimensional linear regression models when the complete data are not accessible, but only certain marginal information or summary statistics are available. This problem is motivated from the Genome-wide association studies (GWAS) that have been widely used to identify risk variants underlying complex human traits/diseases. With a large number of completed GWAS, statistical methods using summary statistics become more and more important because of restricted accessibility to individual-level data sets. Theoretically guaranteed methods are highly demanding to advance the statistical inference with a large amount of available marginal information. Here we propose an $\ell_1$ penalized approach, REMI, to estimate high dimensional regression coefficients with marginal information and external reference samples. We establish an upper bound on the error of the REMI estimator, which has the same order as that of the minimax error bound of Lasso with complete individual-level data. In particular, when marginal information is obtained from a large number of samples together with a small number of reference samples, REMI yields good estimation and prediction results, and outperforms the Lasso because the sample size of accessible individual-level data can be limited. Through simulation studies and real data analysis of the NFBC1966 GWAS data set, we demonstrate that REMI can be widely applicable. The developed R package and the codes to reproduce all the results are available at https://github.com/gordonliu810822/REMI

stat.AP↗

arXiv2018

Joint Analysis of Individual-level and Summary-level GWAS Data by Leveraging Pleiotropy

A large number of recent genome-wide association studies (GWASs) for complex phenotypes confirm the early conjecture for polygenicity, suggesting the presence of large number of variants with only tiny or moderate effects. However, due to the limited sample size of a single GWAS, many associated genetic variants are too weak to achieve the genome-wide significance. These undiscovered variants further limit the prediction capability of GWAS. Restricted access to the individual-level data and the increasing availability of the published GWAS results motivate the development of methods integrating both the individual-level and summary-level data. How to build the connection between the individual-level and summary-level data determines the efficiency of using the existing abundant summary-level resources with limited individual-level data, and this issue inspires more efforts in the existing area. In this study, we propose a novel statistical approach, LEP, which provides a novel way of modeling the connection between the individual-level data and summary-level data. LEP integrates both types of data by \underline{LE}veraing \underline{P}leiotropy to increase the statistical power of risk variants identification and the accuracy of risk prediction. The algorithm for parameter estimation is developed to handle genome-wide-scale data. Through comprehensive simulation studies, we demonstrated the advantages of LEP over the existing methods. We further applied LEP to perform integrative analysis of Crohn's disease from WTCCC and summary statistics from GWAS of some other diseases, such as Type 1 diabetes, Ulcerative colitis and Primary biliary cirrhosis. LEP was able to significantly increase the statistical power of identifying risk variants and improve the risk prediction accuracy from 63.39\% ($\pm$ 0.58\%) to 68.33\% ($\pm$ 0.32\%) using about 195,000 variants.

q-bio.GN↗

arXiv2018

BIVAS: A scalable Bayesian method for bi-level variable selection with applications

In this paper, we consider a Bayesian bi-level variable selection problem in high-dimensional regressions. In many practical situations, it is natural to assign group membership to each predictor. Examples include that genetic variants can be grouped at the gene level and a covariate from different tasks naturally forms a group. Thus, it is of interest to select important groups as well as important members from those groups. The existing Markov Chain Monte Carlo (MCMC) methods are often computationally intensive and not scalable to large data sets. To address this problem, we consider variational inference for bi-level variable selection (BIVAS). In contrast to the commonly used mean-field approximation, we propose a hierarchical factorization to approximate the posterior distribution, by utilizing the structure of bi-level variable selection. Moreover, we develop a computationally efficient and fully parallelizable algorithm based on this variational approximation. We further extend the developed method to model data sets from multi-task learning. The comprehensive numerical results from both simulation studies and real data analysis demonstrate the advantages of BIVAS for variable selection, parameter estimation and computational efficiency over existing methods. The method is implemented in R package `bivas' available at https://github.com/mxcai/bivas.

stat.AP↗

arXiv2018

Unsupervised Cross-dataset Person Re-identification by Transfer Learning of Spatial-Temporal Patterns

Most of the proposed person re-identification algorithms conduct supervised training and testing on single labeled datasets with small size, so directly deploying these trained models to a large-scale real-world camera network may lead to poor performance due to underfitting. It is challenging to incrementally optimize the models by using the abundant unlabeled data collected from the target domain. To address this challenge, we propose an unsupervised incremental learning algorithm, TFusion, which is aided by the transfer learning of the pedestrians' spatio-temporal patterns in the target domain. Specifically, the algorithm firstly transfers the visual classifier trained from small labeled source dataset to the unlabeled target dataset so as to learn the pedestrians' spatial-temporal patterns. Secondly, a Bayesian fusion model is proposed to combine the learned spatio-temporal patterns with visual features to achieve a significantly improved classifier. Finally, we propose a learning-to-rank based mutual promotion procedure to incrementally optimize the classifiers based on the unlabeled data in the target domain. Comprehensive experiments based on multiple real surveillance datasets are conducted, and the results show that our algorithm gains significant improvement compared with the state-of-art cross-dataset unsupervised person re-identification algorithms.

cs.CV↗

arXiv2017

LPG: a four-groups probabilistic approach to leveraging pleiotropy in genome-wide association studies

To date, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants among a variety of traits/diseases, shedding a light on the genetic architecture of complex diseases. Polygenicity of complex diseases, which refers to the phenomenon that a vast number of risk variants collectively contribute to the heritability of complex diseases with modest individual effects, have been widely accepted. This imposes a major challenge towards fully characterizing the genetic bases of complex diseases. An immediate implication of polygenicity is that a much larger sample size is required to detect risk variants with weak/moderate effects. Meanwhile, accumulating evidence suggests that different complex diseases can share genetic risk variants, a phenomenon known as pleiotropy. In this study, we propose a statistical framework for Leveraging Pleiotropic effects in large-scale GWAS data (LPG). LPG utilizes a variational Bayesian expectation-maximization (VBEM) algorithm, making it computationally efficient and scalable for genome-wide scale analysis. To demon- strate the advantage of LPG over existing methods that do not leverage pleiotropy, we conducted extensive simulation studies and also applied LPG to analyze three au- toimmune disorders (Crohn's disease, rheumatoid arthritis and Type 1 diabetes). The results indicate that LPG can improve the power of prioritization of risk variants and accuracy of risk prediction by leveraging pleiotropy. The software is available at http- s://github.com/Shufeyangyi2015310117/LPG.

stat.ME↗

arXiv2017

LSMM: A statistical approach to integrating functional annotations with genome-wide association studies

Thousands of risk variants underlying complex phenotypes (quantitative traits and diseases) have been identified in genome-wide association studies (GWAS). However, there are still two major challenges towards deepening our understanding of the genetic architectures of complex phenotypes. First, the majority of GWAS hits are in the non-coding region and their biological interpretation is still unclear. Second, accumulating evidence from GWAS suggests the polygenicity of complex traits, i.e., a complex trait is often affected by many variants with small or moderate effects, whereas a large proportion of risk variants with small effects remains unknown. The availability of functional annotation data enables us to address the above challenges. In this study, we propose a latent sparse mixed model (LSMM) to integrate functional annotations with GWAS data. Not only does it increase statistical power of the identification of risk variants, but also offers more biological insights by detecting relevant functional annotations. To allow LSMM scalable to millions of variants and hundreds of functional annotations, we developed an efficient variational expectation-maximization (EM) algorithm for model parameter estimation and statistical inference. We first conducted comprehensive simulation studies to evaluate the performance of LSMM. Then we applied it to analyze 30 GWAS of complex phenotypes integrated with 9 genic category annotations and 127 tissue-specific functional annotations from the Roadmap project. The results demonstrate that our method possesses more statistical power over conventional methods, and can help researchers achieve deeper understanding of genetic architecture of these complex phenotypes.

stat.ME↗

arXiv2017

Prediction analysis for microbiome sequencing data

One primary goal of human microbiome studies is to predict host traits based on human microbiota. However, microbial community sequencing data present significant challenges to the development of statistical methods. In particular, the samples have different library sizes, the data contain many zeros and are often over-dispersed. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR). An inverse regression model is developed for over-dispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension-reduction structure in the model. An efficient Monte Carlo expectation-maximization algorithm is designed for carrying out maximum likelihood estimation. We demonstrate the advantages of PAMIR through simulations and a real data example.

stat.ME↗

arXiv2017

On the Convergence of the EM Algorithm: A Data-Adaptive Analysis

The Expectation-Maximization (EM) algorithm is an iterative method to maximize the log-likelihood function for parameter estimation. Previous works on the convergence analysis of the EM algorithm have established results on the asymptotic (population level) convergence rate of the algorithm. In this paper, we give a data-adaptive analysis of the sample level local convergence rate of the EM algorithm. In particular, we show that the local convergence rate of the EM algorithm is a random variable $\overline{K}_{n}$ derived from the data generating distribution, which adaptively yields the convergence rate of the EM algorithm on each finite sample data set from the same population distribution. We then give a non-asymptotic concentration bound of $\overline{K}_{n}$ on the population level optimal convergence rate $\overlineκ$ of the EM algorithm, which implies that $\overline{K}_{n}\to\overlineκ$ in probability as the sample size $n\to\infty$. Our theory identifies the effect of sample size on the convergence behavior of sample EM sequence, and explains a surprising phenomenon in applications of the EM algorithm, i.e. the finite sample version of the algorithm sometimes converges faster even than the population version. We apply our theory to the EM algorithm on three canonical models and obtain specific forms of the adaptive convergence theorem for each model.

math.ST↗

arXiv2016

Total Variation Regularized Tensor RPCA for Background Subtraction from Compressive Measurements

Background subtraction has been a fundamental and widely studied task in video analysis, with a wide range of applications in video surveillance, teleconferencing and 3D modeling. Recently, motivated by compressive imaging, background subtraction from compressive measurements (BSCM) is becoming an active research task in video surveillance. In this paper, we propose a novel tensor-based robust PCA (TenRPCA) approach for BSCM by decomposing video frames into backgrounds with spatial-temporal correlations and foregrounds with spatio-temporal continuity in a tensor framework. In this approach, we use 3D total variation (TV) to enhance the spatio-temporal continuity of foregrounds, and Tucker decomposition to model the spatio-temporal correlations of video background. Based on this idea, we design a basic tensor RPCA model over the video frames, dubbed as the holistic TenRPCA model (H-TenRPCA). To characterize the correlations among the groups of similar 3D patches of video background, we further design a patch-group-based tensor RPCA model (PG-TenRPCA) by joint tensor Tucker decompositions of 3D patch groups for modeling the video background. Efficient algorithms using alternating direction method of multipliers (ADMM) are developed to solve the proposed models. Extensive experiments on simulated and real-world videos demonstrate the superiority of the proposed approaches over the existing state-of-the-art approaches.

cs.CV↗

arXiv2016

Mathematical design of a novel gesture-based instruction/input device using wave detection

In this paper, we present a conceptual design of a novel gesture-based instruction/input device using wave detection. The device recogonizes/detects gestures from a person and based on which to give the specific orders/inputs to the computing machine that is connected to it. The gestures are modelled as the shapes of some impenetrable or penetrable scatterers from a certain admissible class, called a dictionary. The device generates time-harmonic point signals for the gesture recognition/detection. It then collects the scattered wave in a relatively small backscattering aperture on a bounded surface containing the point sources. The recognition algorithm consists of two steps and requires only two incident waves of different wavenumbers. The approximate location of the scatterer is first determined by using the measured data at a small wavenumber and the shape of the scatterer is then identified using the computed location of the scatterer and the measured data at a regular wavenumber. We provide the mathematical principle with rigorous justifications underlying the design. Numerical experiments show that the proposed device works effectively and efficiently in some practical scenarios.

math.NA↗

arXiv2015

On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data

In this paper, we first propose a Bayesian neighborhood selection method to estimate Gaussian Graphical Models (GGMs). We show the graph selection consistency of this method in the sense that the posterior probability of the true model converges to one. When there are multiple groups of data available, instead of estimating the networks independently for each group, joint estimation of the networks may utilize the shared information among groups and lead to improved estimation for each individual network. Our method is extended to jointly estimate GGMs in multiple groups of data with complex structures, including spatial data, temporal data and data with both spatial and temporal structures. Markov random field (MRF) models are used to efficiently incorporate the complex data structures. We develop and implement an efficient algorithm for statistical inference that enables parallel computing. Simulation studies suggest that our approach achieves better accuracy in network estimation compared with methods not incorporating spatial and temporal dependencies when there are shared structures among the networks, and that it performs comparably well otherwise. Finally, we illustrate our method using the human brain gene expression microarray dataset, where the expression levels of genes are measured in different brain regions across multiple time periods.

stat.AP↗

arXiv2015

The Research and Optimization of Parallel Finite Element Algorithm based on MiniFE

Finite element method (FEM) is one of the most important numerical methods in modern engineering design and analysis. Since traditional serial FEM is difficult to solve large FE problems efficiently and accurately, high-performance parallel FEM has become one of the essential way to solve practical engineering problems. Based on MiniFE program, which is released by National Energy Research Scientific Computing Center(NERSC), this work analyzes concrete steps, key computing pattern and parallel mechanism of parallel FEM. According to experimental results, this work analyzes the proportion of calculation amount of each module and concludes the main performance bottleneck of the program. Based on that, we optimize the MiniFE program on a server platform. The optimization focuses on the bottleneck of the program - SpMV kernel, and uses an efficient storage format named BCRS. Moreover, an improving plan of hybrid MPI+OpenMP programming is provided. Experimental results show that the optimized program performs better in both SpMV kernel and synchronization. It can increase the performance of the program, on average, by 8.31%. Keywords : finite element, parallel, MiniFE, SpMV, performance optimization

cs.DC↗

arXiv2015

Exploring the genetic patterns of complex diseases via the integrative genome-wide approach

Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However, most of the variants that have been identified contribute relatively small increments of risk and only explain a small portion of the genetic variation in complex diseases. This is the so-called missing heritability problem. Evidence has indicated that many complex diseases are genetically related, meaning these diseases share common genetic risk variants. Therefore, exploring the genetic correlations across multiple related studies could be a promising strategy for removing spurious associations and identifying underlying genetic risk variants, and thereby uncovering the mystery of missing heritability in complex diseases. Results: We present a general and robust method to identify genetic patterns from multiple large-scale genomic datasets. We treat the summary statistics as a matrix and demonstrate that genetic patterns will form a low-rank matrix plus a sparse component. Hence, we formulate the problem as a matrix recovering problem, where we aim to discover risk variants shared by multiple diseases/traits and those for each individual disease/trait. We propose a convex formulation for matrix recovery and an efficient algorithm to solve the problem. We demonstrate the advantages of our method using both synthesized datasets and real datasets. The experimental results show that our method can successfully reconstruct both the shared and the individual genetic patterns from summary statistics and achieve better performance compared with alternative methods under a wide range of scenarios.

cs.CE↗

arXiv2014

Low-Rank Modeling and Its Applications in Image Analysis

Low-rank modeling generally refers to a class of methods that solve problems by representing variables of interest as low-rank matrices. It has achieved great success in various fields including computer vision, data mining, signal processing and bioinformatics. Recently, much progress has been made in theories, algorithms and applications of low-rank modeling, such as exact low-rank matrix recovery via convex programming and matrix completion applied to collaborative filtering. These advances have brought more and more attentions to this topic. In this paper, we review the recent advance of low-rank modeling, the state-of-the-art algorithms, and related applications in image analysis. We first give an overview to the concept of low-rank modeling and challenging problems in this area. Then, we summarize the models and algorithms for low-rank matrix recovery and illustrate their advantages and limitations with numerical experiments. Next, we introduce a few applications of low-rank modeling in the context of image analysis. Finally, we conclude this paper with some discussions.

cs.CV↗

arXiv2014

High-dimensional genome-wide association study and misspecified mixed model analysis

We study behavior of the restricted maximum likelihood (REML) estimator under a misspecified linear mixed model (LMM) that has received much attention in recent gnome-wide association studies. The asymptotic analysis establishes consistency of the REML estimator of the variance of the errors in the LMM, and convergence in probability of the REML estimator of the variance of the random effects in the LMM to a certain limit, which is equal to the true variance of the random effects multiplied by the limiting proportion of the nonzero random effects present in the LMM. The aymptotic results also establish convergence rate (in probability) of the REML estimators as well as a result regarding convergence of the asymptotic conditional variance of the REML estimator. The asymptotic results are fully supported by the results of empirical studies, which include extensive simulation studies that compare the performance of the REML estimator (under the misspecified LMM) with other existing methods.

math.ST↗

arXiv2014

GPA: A statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data

Genome-wide association studies (GWAS) suggests that a complex disease is typically affected by many genetic variants with small or moderate effects. Identification of these risk variants remains to be a very challenging problem. Traditional approaches focusing on a single GWAS dataset alone ignore relevant information that could potentially improve our ability to detect these variants. We proposed a novel statistical approach, named GPA, to performing integrative analysis of multiple GWAS datasets and functional annotations. Hypothesis testing procedures were developed to facilitate statistical inference of pleiotropy and enrichment of functional annotation. We applied our approach to perform systematic analysis of five psychiatric disorders. Not only did GPA identify many weak signals missed by the original single phenotype analysis, but also revealed interesting genetic architectures of these disorders. We also applied GPA to the bladder cancer GWAS data with the ENCODE DNase-seq data from 125 cell lines and showed that GPA can detect cell lines that are more biologically relevant to the phenotype of interest.

stat.ME↗