Michael Minyi Zhang

Michael Minyi Zhang, Gregory W. Gundersen, Barbara E. Engelhardt

The Gaussian process latent variable model (GPLVM) is a popular probabilistic method used for nonlinear dimension reduction, matrix factorization, and state-space modeling. Inference for GPLVMs is computationally tractable only when the data likelihood is Gaussian. Moreover, inference for GPLVMs has typically been restricted to obtaining maximum a posteriori point estimates, which can lead to overfitting, or variational approximations, which mischaracterize the posterior uncertainty. Here, we present a method to perform Markov chain Monte Carlo (MCMC) inference for generalized Bayesian nonlinear latent variable modeling. The crucial insight necessary to generalize GPLVMs to arbitrary observation models is that we approximate the kernel function in the Gaussian process mappings with random Fourier features; this allows us to compute the gradient of the posterior in closed form with respect to the latent variables. We show that we can generalize GPLVMs to non-Gaussian observations, such as Poisson, negative binomial, and multinomial distributions, using our random feature latent variable model (RFLVM). Our generalized RFLVMs perform on par with state-of-the-art latent variable models on a wide range of applications, including motion capture, images, and text data for the purpose of estimating the latent structure and imputing the missing data of these complex data sets.

Forough Fazeli-Asl, Michael Minyi Zhang

We propose a novel generative model within the Bayesian non-parametric learning (BNPL) framework to address some notable failure modes in generative adversarial networks (GANs) and variational autoencoders (VAEs)--these being overfitting in the GAN case and noisy samples in the VAE case. We will demonstrate that the BNPL framework enhances training stability and provides robustness and accuracy guarantees when incorporating the Wasserstein distance and maximum mean discrepancy measure (WMMD) into our model's loss function. Moreover, we introduce a so-called ``triple model'' that combines the GAN, the VAE, and further incorporates a code-GAN (CGAN) to explore the latent space of the VAE. This triple model design generates high-quality, diverse samples, while the BNPL framework, leveraging the WMMD loss function, enhances training stability. Together, these components enable our model to achieve superior performance across various generative tasks. These claims are supported by both theoretical analyses and empirical validation on a wide variety of datasets.

Forough Fazeli-Asl, Michael Minyi Zhang, Lizhen Lin

A classic inferential statistical problem is the goodness-of-fit (GOF) test. Such a test can be challenging when the hypothesized parametric model has an intractable likelihood and its distributional form is not available. Bayesian methods for GOF can be appealing due to their ability to incorporate expert knowledge through prior distributions. However, standard Bayesian methods for this test often require strong distributional assumptions on the data and their relevant parameters. To address this issue, we propose a semi-Bayesian nonparametric (semi-BNP) procedure in the context of the maximum mean discrepancy (MMD) measure that can be applied to the GOF test. Our method introduces a novel Bayesian estimator for the MMD, enabling the development of a measure-based hypothesis test for intractable models. Through extensive experiments, we demonstrate that our proposed test outperforms frequentist MMD-based methods by achieving a lower false rejection and acceptance rate of the null hypothesis. Furthermore, we showcase the versatility of our approach by embedding the proposed estimator within a generative adversarial network (GAN) framework. It facilitates a robust BNP learning approach as another significant application of our method. With our BNP procedure, this new GAN approach can enhance sample diversity and improve inferential accuracy compared to traditional techniques.

Michael Minyi Zhang

We propose a non-linear, Bayesian non-parametric latent variable model where the latent space is assumed to be sparse and infinite dimensional a priori using an Indian buffet process prior. A posteriori, the number of instantiated dimensions in the latent space is guaranteed to be finite. The purpose of placing the Indian buffet process on the latent variables is to: 1.) Automatically and probabilistically select the number of latent dimensions. 2.) Impose sparsity in the latent space, where the Indian buffet process will select which elements are exactly zero. Our proposed model allows for sparse, non-linear latent variable modeling where the number of latent dimensions is selected automatically. Inference is made tractable using the random Fourier approximation and we can easily implement posterior inference through Markov chain Monte Carlo sampling. This approach is amenable to many observation models beyond the Gaussian setting. We demonstrate the utility of our method on a variety of synthetic, biological and text datasets and show that we can obtain superior test set performance compared to previous latent variable models.

Taole Sha, Michael Minyi Zhang

Time-dependent data often exhibit characteristics, such as non-stationarity and heavy-tailed errors, that would be inappropriate to model with the typical assumptions used in popular models. Thus, more flexible approaches are required to be able to accommodate such issues. To this end, we propose a Bayesian mixture of student-$t$ processes with an overall-local scale structure for the covariance. Moreover, we use a sequential Monte Carlo (SMC) sampler in order to perform online inference as data arrive in real-time. We demonstrate the superiority of our proposed approach compared to typical Gaussian process-based models on real-world data sets in order to prove the necessity of using mixtures of student-$t$ processes.

Ying Li, Zhidi Lin, Feng Yin et al.

Gaussian process latent variable models (GPLVMs) are a versatile family of unsupervised learning models commonly used for dimensionality reduction. However, common challenges in modeling data with GPLVMs include inadequate kernel flexibility and improper selection of the projection noise, leading to a type of model collapse characterized by vague latent representations that do not reflect the underlying data structure. This paper addresses these issues by, first, theoretically examining the impact of projection variance on model collapse through the lens of a linear GPLVM. Second, we tackle model collapse due to inadequate kernel flexibility by integrating the spectral mixture (SM) kernel and a differentiable random Fourier feature (RFF) kernel approximation, which ensures computational scalability and efficiency through off-the-shelf automatic differentiation tools for learning the kernel hyperparameters, projection variance, and latent representations within the variational inference framework. The proposed GPLVM, named advisedRFLVM, is evaluated across diverse datasets and consistently outperforms various salient competing models, including state-of-the-art variational autoencoders (VAEs) and other GPLVM variants, in terms of informative latent representations and missing data imputation.

Forough Fazeliasl, Michael Minyi Zhang, Bei Jiang et al.

Mutual Information (MI) is a crucial measure for capturing dependencies between variables, but exact computation is challenging in high dimensions with intractable likelihoods, impacting accuracy and robustness. One idea is to use an auxiliary neural network to train an MI estimator; however, methods based on the empirical distribution function (EDF) can introduce sharp fluctuations in the MI loss due to poor out-of-sample performance, destabilizing convergence. We present a Bayesian nonparametric (BNP) solution for training an MI estimator by constructing the MI loss with a finite representation of the Dirichlet process posterior to incorporate regularization in the training process. With this regularization, the MI loss integrates both prior knowledge and empirical data to reduce the loss sensitivity to fluctuations and outliers in the sample data, especially in small sample settings like mini-batches. This approach addresses the challenge of balancing accuracy and low variance by effectively reducing variance, leading to stabilized and robust MI loss gradients during training and enhancing the convergence of the MI approximation while offering stronger theoretical guarantees for convergence. We explore the application of our estimator in maximizing MI between the data space and the latent space of a variational autoencoder. Experimental results demonstrate significant improvements in convergence over EDF-based methods, with applications across synthetic and real datasets, notably in 3D CT image generation, yielding enhanced structure discovery and reduced overfitting in data synthesis. While this paper focuses on generative models in application, the proposed estimator is not restricted to this setting and can be applied more broadly in various BNP learning procedures.

Zi Yang, Ying Li, Zhidi Lin et al.

The multi-view Gaussian process latent variable model (MV-GPLVM) aims to learn a unified representation from multi-view data but is hindered by challenges such as limited kernel expressiveness and low computational efficiency. To overcome these issues, we first introduce a new duality between the spectral density and the kernel function. By modeling the spectral density with a bivariate Gaussian mixture, we then derive a generic and expressive kernel termed Next-Gen Spectral Mixture (NG-SM) for MV-GPLVMs. To address the inherent computational inefficiency of the NG-SM kernel, we propose a random Fourier feature approximation. Combined with a tailored reparameterization trick, this approximation enables scalable variational inference for both the model and the unified latent representations. Numerical evaluations across a diverse range of multi-view datasets demonstrate that our proposed method consistently outperforms state-of-the-art models in learning meaningful latent representations.

Ying Li, Zhidi Lin, Yuhao Liu et al.

Random feature latent variable models (RFLVMs) represent the state-of-the-art in latent variable models, capable of handling non-Gaussian likelihoods and effectively uncovering patterns in high-dimensional data. However, their heavy reliance on Monte Carlo sampling results in scalability issues which makes it difficult to use these models for datasets with a massive number of observations. To scale up RFLVMs, we turn to the optimization-based variational Bayesian inference (VBI) algorithm which is known for its scalability compared to sampling-based methods. However, implementing VBI for RFLVMs poses challenges, such as the lack of explicit probability distribution functions (PDFs) for the Dirichlet process (DP) in the kernel learning component, and the incompatibility of existing VBI algorithms with RFLVMs. To address these issues, we introduce a stick-breaking construction for DP to obtain an explicit PDF and a novel VBI algorithm called ``block coordinate descent variational inference" (BCD-VI). This enables the development of a scalable version of RFLVMs, or in short, SRFLVM. Our proposed method shows scalability, computational efficiency, superior performance in generating informative latent representations and the ability of imputing missing data across various real-world datasets, outperforming state-of-the-art competitors.

Lizhen Lin, Bayan Saparbayeva, Michael Minyi Zhang et al.

We propose a general scheme for solving convex and non-convex optimization problems on manifolds. The central idea is that, by adding a multiple of the squared retraction distance to the objective function in question, we "convexify" the objective function and solve a series of convex sub-problems in the optimization procedure. One of the key challenges for optimization on manifolds is the difficulty of verifying the complexity of the objective function, e.g., whether the objective function is convex or non-convex, and the degree of non-convexity. Our proposed algorithm adapts to the level of complexity in the objective function. We show that when the objective function is convex, the algorithm provably converges to the optimum and leads to accelerated convergence. When the objective function is non-convex, the algorithm will converge to a stationary point. Our proposed method unifies insights from Nesterov's original idea for accelerating gradient descent algorithms with recent developments in optimization algorithms in Euclidean space. We demonstrate the utility of our algorithms on several manifold optimization tasks such as estimating intrinsic and extrinsic Fréchet means on spheres and low-rank matrix factorization with Grassmann manifolds applied to the Netflix rating data set.

Gregory W. Gundersen, Michael Minyi Zhang, Barbara E. Engelhardt

Gaussian process-based latent variable models are flexible and theoretically grounded tools for nonlinear dimension reduction, but generalizing to non-Gaussian data likelihoods within this nonlinear framework is statistically challenging. Here, we use random features to develop a family of nonlinear dimension reduction models that are easily extensible to non-Gaussian data likelihoods; we call these random feature latent variable models (RFLVMs). By approximating a nonlinear relationship between the latent space and the observations with a function that is linear with respect to random features, we induce closed-form gradients of the posterior distribution with respect to the latent variable. This allows the RFLVM framework to support computationally tractable nonlinear latent variable models for a variety of data likelihoods in the exponential family without specialized derivations. Our generalized RFLVMs produce results comparable with other state-of-the-art dimension reduction methods on diverse types of data, including neural spike train recordings, images, and text data.

Avinava Dubey, Michael Minyi Zhang, Eric P. Xing et al.

Bayesian nonparametric (BNP) models provide elegant methods for discovering underlying latent features within a data set, but inference in such models can be slow. We exploit the fact that completely random measures, which commonly used models like the Dirichlet process and the beta-Bernoulli process can be expressed as, are decomposable into independent sub-measures. We use this decomposition to partition the latent measure into a finite measure containing only instantiated components, and an infinite measure containing all other components. We then select different inference algorithms for the two components: uncollapsed samplers mix well on the finite measure, while collapsed samplers mix well on the infinite, sparsely occupied tail. The resulting hybrid algorithm can be applied to a wide class of models, and can be easily distributed to allow scalable inference without sacrificing asymptotic convergence guarantees.

Fernando Perez-Cruz, Pablo M. Olmos, Michael Minyi Zhang et al.

In this paper, we take a new approach for time of arrival geo-localization. We show that the main sources of error in metropolitan areas are due to environmental imperfections that bias our solutions, and that we can rely on a probabilistic model to learn and compensate for them. The resulting localization error is validated using measurements from a live LTE cellular network to be less than 10 meters, representing an order-of-magnitude improvement.

Michael Minyi Zhang, Bianca Dumitrascu, Sinead A. Williamson et al.

Many machine learning problems can be framed in the context of estimating functions, and often these are time-dependent functions that are estimated in real-time as observations arrive. Gaussian processes (GPs) are an attractive choice for modeling real-valued nonlinear functions due to their flexibility and uncertainty quantification. However, the typical GP regression model suffers from several drawbacks: 1) Conventional GP inference scales $O(N^{3})$ with respect to the number of observations; 2) Updating a GP model sequentially is not trivial; and 3) Covariance kernels typically enforce stationarity constraints on the function, while GPs with non-stationary covariance kernels are often intractable to use in practice. To overcome these issues, we propose a sequential Monte Carlo algorithm to fit infinite mixtures of GPs that capture non-stationary behavior while allowing for online, distributed inference. Our approach empirically improves performance over state-of-the-art methods for online GP estimation in the presence of non-stationarity in time-series data. To demonstrate the utility of our proposed online Gaussian process mixture-of-experts approach in applied settings, we show that we can sucessfully implement an optimization algorithm using online Gaussian process bandits.

Sinead A. Williamson, Michael Minyi Zhang, Paul Damien

In many applications, observed data are influenced by some combination of latent causes. For example, suppose sensors are placed inside a building to record responses such as temperature, humidity, power consumption and noise levels. These random, observed responses are typically affected by many unobserved, latent factors (or features) within the building such as the number of individuals, the turning on and off of electrical devices, power surges, etc. These latent factors are usually present for a contiguous period of time before disappearing; further, multiple factors could be present at a time. This paper develops new probabilistic methodology and inference methods for random object generation influenced by latent features exhibiting temporal persistence. Every datum is associated with subsets of a potentially infinite number of hidden, persistent features that account for temporal dynamics in an observation. The ensuing class of dynamic models constructed by adapting the Indian Buffet Process --- a probability measure on the space of random, unbounded binary matrices --- finds use in a variety of applications arising in operations, signal processing, biomedicine, marketing, image analysis, etc. Illustrations using synthetic and real data are provided.

Bayan Saparbayeva, Michael Minyi Zhang, Lizhen Lin

The last decade has witnessed an explosion in the development of models, theory and computational algorithms for "big data" analysis. In particular, distributed computing has served as a natural and dominating paradigm for statistical inference. However, the existing literature on parallel inference almost exclusively focuses on Euclidean data and parameters. While this assumption is valid for many applications, it is increasingly more common to encounter problems where the data or the parameters lie on a non-Euclidean space, like a manifold for example. Our work aims to fill a critical gap in the literature by generalizing parallel inference algorithms to optimization on manifolds. We show that our proposed algorithm is both communication efficient and carries theoretical convergence guarantees. In addition, we demonstrate the performance of our algorithm to the estimation of Fréchet means on simulated spherical data and the low-rank matrix completion problem over Grassmann manifolds applied to the Netflix prize data set.

Michael Minyi Zhang, Sinead A. Williamson, Fernando Perez-Cruz

Inference of latent feature models in the Bayesian nonparametric setting is generally difficult, especially in high dimensional settings, because it usually requires proposing features from some prior distribution. In special cases, where the integration is tractable, we can sample new feature assignments according to a predictive likelihood. We present a novel method to accelerate the mixing of latent variable model inference by proposing feature locations based on the data, as opposed to the prior. First, we introduce an accelerated feature proposal mechanism that we show is a valid MCMC algorithm for posterior inference. Next, we propose an approximate inference strategy to perform accelerated inference in parallel. A two-stage algorithm that combines the two approaches provides a computationally attractive method that can quickly reach local convergence to the posterior distribution of our model, while allowing us to exploit parallelization.

Michael Minyi Zhang, Sinead A. Williamson

Training Gaussian process-based models typically involves an $ O(N^3)$ computational bottleneck due to inverting the covariance matrix. Popular methods for overcoming this matrix inversion problem cannot adequately model all types of latent functions, and are often not parallelizable. However, judicious choice of model structure can ameliorate this problem. A mixture-of-experts model that uses a mixture of $K$ Gaussian processes offers modeling flexibility and opportunities for scalable inference. Our embarrassingly parallel algorithm combines low-dimensional matrix inversions with importance sampling to yield a flexible, scalable mixture-of-experts model that offers comparable performance to Gaussian process regression at a much lower computational cost.

Michael Minyi Zhang, Henry Lam, Lizhen Lin

Effective and accurate model selection is an important problem in modern data analysis. One of the major challenges is the computational burden required to handle large data sets that cannot be stored or processed on one machine. Another challenge one may encounter is the presence of outliers and contaminations that damage the inference quality. The parallel "divide and conquer" model selection strategy divides the observations of the full data set into roughly equal subsets and perform inference and model selection independently on each subset. After local subset inference, this method aggregates the posterior model probabilities or other model/variable selection criteria to obtain a final model by using the notion of geometric median. This approach leads to improved concentration in finding the "correct" model and model parameters and also is provably robust to outliers and data contamination.