arXiv subjects

Nanwei Wang

Publications and source records attributed to Nanwei Wang.

6 recordsLinked to original sources

arXiv2025

High-Dimensional Covariate-Dependent Discrete Graphical Models and Dynamic Ising Models

We propose a covariate-dependent discrete graphical model for capturing dynamic networks among discrete random variables, allowing the dependence structure among vertices to vary with covariates. This discrete dynamic network encompasses the dynamic Ising model as a special case. We formulate a likelihood-based approach for parameter estimation and statistical inference. We achieve efficient parameter estimation in high-dimensional settings through the use of the pseudo-likelihood method. To perform model selection, a birth-and-death Markov chain Monte Carlo algorithm is proposed to explore the model space and select the most suitable model.

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arXiv2020

The scalable Birth-Death MCMC Algorithm for Mixed Graphical Model Learning with Application to Genomic Data Integration

Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is now distributed through consortia like The Cancer Genome Atlas (TCGA), where specific types of biological information on specific type of tissue or cell are available. In cancer research, the challenge is now to perform integrative analyses of high-dimensional multi-omic data with the goal to better understand genomic processes that correlate with cancer outcomes, e.g. elucidate gene networks that discriminate a specific cancer subgroups (cancer sub-typing) or discovering gene networks that overlap across different cancer types (pan-cancer studies). In this paper, we propose a novel mixed graphical model approach to analyze multi-omic data of different types (continuous, discrete and count) and perform model selection by extending the Birth-Death MCMC (BDMCMC) algorithm initially proposed by \citet{stephens2000bayesian} and later developed by \cite{mohammadi2015bayesian}. We compare the performance of our method to the LASSO method and the standard BDMCMC method using simulations and find that our method is superior in terms of both computational efficiency and the accuracy of the model selection results. Finally, an application to the TCGA breast cancer data shows that integrating genomic information at different levels (mutation and expression data) leads to better subtyping of breast cancers.

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arXiv2020

Penalized composite likelihood for colored graphical Gaussian models

This paper proposes a penalized composite likelihood method for model selection in colored graphical Gaussian models. The method provides a sparse and symmetry-constrained estimator of the precision matrix, and thus conducts model selection and precision matrix estimation simultaneously. In particular, the method uses penalty terms to constrain the elements of the precision matrix, which enables us to transform the model selection problem into a constrained optimization problem. Further, computer experiments are conducted to illustrate the performance of the proposed new methodology. It is shown that the proposed method performs well in both the selection of nonzero elements in the precision matrix and the identification of symmetry structures in graphical models. The feasibility and potential clinical application of the proposed method are demonstrated on a microarray gene expression data set.

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arXiv2018

Approximating faces of marginal polytopes in discrete hierarchical models

The existence of the maximum likelihood estimate in hierarchical loglinear models is crucial to the reliability of inference for this model. Determining whether the estimate exists is equivalent to finding whether the sufficient statistics vector $t$ belongs to the boundary of the marginal polytope of the model. The dimension of the smallest face $F_t$ containing $t$ determines the dimension of the reduced model which should be considered for correct inference. For higher-dimensional problems, it is not possible to compute $F_{t}$ exactly. Massam and Wang (2015) found an outer approximation to $F_t$ using a collection of sub-models of the original model. This paper refines the methodology to find an outer approximation and devises a new methodology to find an inner approximation. The inner approximation is given not in terms of a face of the marginal polytope, but in terms of a subset of the vertices of $F_t$. Knowing $F_t$ exactly indicates which cell probabilities have maximum likelihood estimates equal to $0$. When $F_t$ cannot be obtained exactly, we can use, first, the outer approximation $F_2$ to reduce the dimension of the problem and, then, the inner approximation $F_1$ to obtain correct estimates of cell probabilities corresponding to elements of $F_1$ and improve the estimates of the remaining probabilities corresponding to elements in $F_2\setminus F_1$. Using both real-world and simulated data, we illustrate our results, and show that our methodology scales to high dimensions.

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arXiv2015

A local approach to estimation in discrete loglinear models

We consider two connected aspects of maximum likelihood estimation of the parameter for high-dimensional discrete graphical models: the existence of the maximum likelihood estimate (mle) and its computation. When the data is sparse, there are many zeros in the contingency table and the maximum likelihood estimate of the parameter may not exist. Fienberg and Rinaldo (2012) have shown that the mle does not exists iff the data vector belongs to a face of the so-called marginal cone spanned by the rows of the design matrix of the model. Identifying these faces in high-dimension is challenging. In this paper, we take a local approach : we show that one such face, albeit possibly not the smallest one, can be identified by looking at a collection of marginal graphical models generated by induced subgraphs $G_i,i=1,\ldots,k$ of $G$. This is our first contribution. Our second contribution concerns the composite maximum likelihood estimate. When the dimension of the problem is large, estimating the parameters of a given graphical model through maximum likelihood is challenging, if not impossible. The traditional approach to this problem has been local with the use of composite likelihood based on local conditional likelihoods. A more recent development is to have the components of the composite likelihood be marginal likelihoods centred around each $v$. We first show that the estimates obtained by consensus through local conditional and marginal likelihoods are identical. We then study the asymptotic properties of the composite maximum likelihood estimate when both the dimension of the model and the sample size $N$ go to infinity.

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arXiv2013

Distributed parameter estimation of discrete hierarchical models via marginal likelihoods

We consider discrete graphical models Markov with respect to a graph $G$ and propose two distributed marginal methods to estimate the maximum likelihood estimate of the canonical parameter of the model. Both methods are based on a relaxation of the marginal likelihood obtained by considering the density of the variables represented by a vertex $v$ of $G$ and a neighborhood. The two methods differ by the size of the neighborhood of $v$. We show that the estimates are consistent and that those obtained with the larger neighborhood have smaller asymptotic variance than the ones obtained through the smaller neighborhood.

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