# Browsing by Author "Zhou, M"

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Item Open Access Augment-and-conquer negative binomial processes(Advances in Neural Information Processing Systems, 2012-12-01) Zhou, M; Carin, LBy developing data augmentation methods unique to the negative binomial (NB) distribution, we unite seemingly disjoint count and mixture models under the NB process framework. We develop fundamental properties of the models and derive efficient Gibbs sampling inference. We show that the gamma-NB process can be reduced to the hierarchical Dirichlet process with normalization, highlighting its unique theoretical, structural and computational advantages. A variety of NB processes with distinct sharing mechanisms are constructed and applied to topic modeling, with connections to existing algorithms, showing the importance of inferring both the NB dispersion and probability parameters.Item Open Access Beta-negative binomial process and poisson factor analysis(Journal of Machine Learning Research, 2012-01-01) Zhou, M; Hannah, LA; Dunson, DB; Carin, L© Copyright 2012 by the authors. A beta-negative binomial (BNB) process is proposed, leading to a beta-gamma-Poisson process, which may be viewed as a "multiscoop" generalization of the beta-Bernoulli process. The BNB process is augmented into a beta-gamma-gamma-Poisson hierarchical structure, and applied as a nonparametric Bayesian prior for an infinite Poisson factor analysis model. A finite approximation for the beta process Lévy random measure is constructed for convenient implementation. Efficient MCMC computations are performed with data augmentation and marginalization techniques. Encouraging results are shown on document count matrix factorization.Item Open Access Lognormal and gamma mixed negative binomial regression(Proceedings of the 29th International Conference on Machine Learning, ICML 2012, 2012-10-10) Zhou, M; Li, L; Dunson, D; Carin, LIn regression analysis of counts, a lack of simple and efficient algorithms for posterior computation has made Bayesian approaches appear unattractive and thus underdeveloped. We propose a lognormal and gamma mixed negative binomial (NB) regression model for counts, and present efficient closed-form Bayesian inference; unlike conventional Poisson models, the proposed approach has two free parameters to include two different kinds of random effects, and allows the incorporation of prior information, such as sparsity in the regression coefficients. By placing a gamma distribution prior on the NB dispersion parameter r, and connecting a log-normal distribution prior with the logit of the NB probability parameter p, efficient Gibbs sampling and variational Bayes inference are both developed. The closed-form updates are obtained by exploiting conditional conjugacy via both a compound Poisson representation and a Polya-Gamma distribution based data augmentation approach. The proposed Bayesian inference can be implemented routinely, while being easily generalizable to more complex settings involving multivariate dependence structures. The algorithms are illustrated using real examples. Copyright 2012 by the author(s)/owner(s).Item Open Access Nested dictionary learning for hierarchical organization of imagery and text(Uncertainty in Artificial Intelligence - Proceedings of the 28th Conference, UAI 2012, 2012-12-01) Li, L; Zhang, XX; Zhou, M; Carin, LA tree-based dictionary learning model is developed for joint analysis of imagery and associated text. The dictionary learning may be applied directly to the imagery from patches, or to general feature vectors extracted from patches or superpixels (using any existing method for image feature extraction). Each image is associated with a path through the tree (from root to a leaf), and each of the multiple patches in a given image is associated with one node in that path. Nodes near the tree root are shared between multiple paths, representing image characteristics that are common among different types of images. Moving toward the leaves, nodes become specialized, representing details in image classes. If available, words (text) are also jointly modeled, with a path-dependent probability over words. The tree structure is inferred via a nested Dirichlet process, and a retrospective stick-breaking sampler is used to infer the tree depth and width.Item Open Access Redox rhythm reinforces the circadian clock to gate immune response.(Nature, 2015-07-23) Zhou, M; Wang, W; Karapetyan, S; Mwimba, M; Marques, J; Buchler, NE; Dong, XRecent studies have shown that in addition to the transcriptional circadian clock, many organisms, including Arabidopsis, have a circadian redox rhythm driven by the organism's metabolic activities. It has been hypothesized that the redox rhythm is linked to the circadian clock, but the mechanism and the biological significance of this link have only begun to be investigated. Here we report that the master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant's redox state and regulates transcription of core circadian clock genes even in the absence of pathogen challenge. Surprisingly, acute perturbation in the redox status triggered by the immune signal salicylic acid does not compromise the circadian clock but rather leads to its reinforcement. Mathematical modelling and subsequent experiments show that NPR1 reinforces the circadian clock without changing the period by regulating both the morning and the evening clock genes. This balanced network architecture helps plants gate their immune responses towards the morning and minimize costs on growth at night. Our study demonstrates how a sensitive redox rhythm interacts with a robust circadian clock to ensure proper responsiveness to environmental stimuli without compromising fitness of the organism.Item Open Access Solving high-dimensional eigenvalue problems using deep neural networks: A diffusion Monte Carlo like approach(Journal of Computational Physics, 2020-12-15) Han, J; Lu, J; Zhou, M© 2020 Elsevier Inc. We propose a new method to solve eigenvalue problems for linear and semilinear second order differential operators in high dimensions based on deep neural networks. The eigenvalue problem is reformulated as a fixed point problem of the semigroup flow induced by the operator, whose solution can be represented by Feynman-Kac formula in terms of forward-backward stochastic differential equations. The method shares a similar spirit with diffusion Monte Carlo but augments a direct approximation to the eigenfunction through neural-network ansatz. The criterion of fixed point provides a natural loss function to search for parameters via optimization. Our approach is able to provide accurate eigenvalue and eigenfunction approximations in several numerical examples, including Fokker-Planck operator and the linear and nonlinear Schrödinger operators in high dimensions.