Stochastic Collapsed Variational Inference for Sequential Data

Stochastic variational inference for collapsed models has recently been successfully applied to large scale topic modelling. In this paper, we propose a stochastic collapsed variational inference algorithm in the sequential data setting. Our algorithm is applicable to both finite hidden Markov models and hierarchical Dirichlet process hidden Markov models, and to any datasets generated by emission distributions in the exponential family. Our experiment results on two discrete datasets show that our inference is both more efficient and more accurate than its uncollapsed version, stochastic variational inference.Comment: NIPS Workshop on Advances in Approximate Bayesian Inference, 201

A Nonparametric Bayesian Approach to Uncovering Rat Hippocampal Population Codes During Spatial Navigation

Rodent hippocampal population codes represent important spatial information about the environment during navigation. Several computational methods have been developed to uncover the neural representation of spatial topology embedded in rodent hippocampal ensemble spike activity. Here we extend our previous work and propose a nonparametric Bayesian approach to infer rat hippocampal population codes during spatial navigation. To tackle the model selection problem, we leverage a nonparametric Bayesian model. Specifically, to analyze rat hippocampal ensemble spiking activity, we apply a hierarchical Dirichlet process-hidden Markov model (HDP-HMM) using two Bayesian inference methods, one based on Markov chain Monte Carlo (MCMC) and the other based on variational Bayes (VB). We demonstrate the effectiveness of our Bayesian approaches on recordings from a freely-behaving rat navigating in an open field environment. We find that MCMC-based inference with Hamiltonian Monte Carlo (HMC) hyperparameter sampling is flexible and efficient, and outperforms VB and MCMC approaches with hyperparameters set by empirical Bayes

Composing Deep Learning and Bayesian Nonparametric Methods

Recent progress in Bayesian methods largely focus on non-conjugate models featured with extensive use of black-box functions: continuous functions implemented with neural networks. Using deep neural networks, Bayesian models can reasonably fit big data while at the same time capturing model uncertainty. This thesis targets at a more challenging problem: how do we model general random objects, including discrete ones, using random functions? Our conclusion is: many (discrete) random objects are in nature a composition of Poisson processes and random functions}. Thus, all discreteness is handled through the Poisson process while random functions captures the rest complexities of the object. Thus the title: composing deep learning and Bayesian nonparametric methods. This conclusion is not a conjecture. In spacial cases such as latent feature models , we can prove this claim by working on infinite dimensional spaces, and that is how Bayesian nonparametric kicks in. Moreover, we will assume some regularity assumptions on random objects such as exchangeability. Then the representations will show up magically using representation theorems. We will see this two times throughout this thesis. One may ask: when a random object is too simple, such as a non-negative random vector in the case of latent feature models, how can we exploit exchangeability? The answer is to aggregate infinite random objects and map them altogether onto an infinite dimensional space. And then assume exchangeability on the infinite dimensional space. We demonstrate two examples of latent feature models by (1) concatenating them as an infinite sequence (Section 2,3) and (2) stacking them as a 2d array (Section 4). Besides, we will see that Bayesian nonparametric methods are useful to model discrete patterns in time series data. We will showcase two examples: (1) using variance Gamma processes to model change points (Section 5), and (2) using Chinese restaurant processes to model speech with switching speakers (Section 6). We also aware that the inference problem can be non-trivial in popular Bayesian nonparametric models. In Section 7, we find a novel solution of online inference for the popular HDP-HMM model

A nonparametric HMM for genetic imputation and coalescent inference

Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self transitions. We develop a new nonparametric model of genetic sequence data, based on the hierarchical Dirichlet process, which supports these self transitions and nonhomogeneity. Our model provides a parameterization of the genetic process that is more parsimonious than other more general nonparametric models which have previously been applied to population genetics. We provide truncation-free MCMC inference for our model using a new auxiliary sampling scheme for Bayesian nonparametric HMMs. In a series of experiments on male X chromosome data from the Thousand Genomes Project and also on data simulated from a population bottleneck we show the benefits of our model over the popular finite model fastPHASE, which can itself be seen as a parametric truncation of our model. We find that the number of HMM states found by our model is correlated with the time to the most recent common ancestor in population bottlenecks. This work demonstrates the flexibility of Bayesian nonparametrics applied to large and complex genetic data