Discrete-time hidden Markov models are a broadly useful class of latent-variable models with applications in areas such as speech recognition, bioinformatics, and climate data analysis. It is common in practice to introduce temporal non-homogeneity into such models by making the transition probabilities dependent on time-varying exogenous input variables via a multinomial logistic parametrization. We extend such models to introduce additional non-homogeneity into the emission distribution using a generalized linear model (GLM), with data augmentation for sampling-based inference. However, the presence of the logistic function in the state transition model significantly complicates parameter inference for the overall model, particularly in a Bayesian context. To address this we extend the recently-proposed Polya-Gamma data augmentation approach to handle non-homogeneous hidden Markov models (NHMMs), allowing the development of an efficient Markov chain Monte Carlo (MCMC) sampling scheme. We apply our model and inference scheme to 30 years of daily rainfall in India, leading to a number of insights into rainfall-related phenomena in the region. Our proposed approach allows for fully Bayesian analysis of relatively complex NHMMs on a scale that was not possible with previous methods. Software implementing the methods described in the paper is available via the R package NHMM.
Topic models provide a useful method for dimensionality reduction and exploratory data analysis in large text corpora. Most approaches to topic model inference have been based on a maximum likelihood objective. Efficient algorithms exist that approximate this objective, but they have no provable guarantees. Recently, algorithms have been introduced that provide provable bounds, but these algorithms are not practical because they are inefficient and not robust to violations of model assumptions. In this paper we present an algorithm for topic model inference that is both provable and practical. The algorithm produces results comparable to the best MCMC implementations while running orders of magnitude faster.
We investigate the complexity of logistic regression models which is defined by counting the number of indistinguishable distributions that the model can represent (Balasubramanian, 1997). We find that the complexity of logistic models with binary inputs does not only depend on the number of parameters but also on the distribution of inputs in a non-trivial way which standard treatments of complexity do not address. In particular, we observe that correlations among inputs induce effective dependencies among parameters thus constraining the model and, consequently, reducing its complexity. We derive simple relations for the upper and lower bounds of the complexity. Furthermore, we show analytically that, defining the model parameters on a finite support rather than the entire axis, decreases the complexity in a manner that critically depends on the size of the domain. Based on our findings, we propose a novel model selection criterion which takes into account the entropy of the input distribution. We test our proposal on the problem of selecting the input variables of a logistic regression model in a Bayesian Model Selection framework. In our numerical tests, we find that, while the reconstruction errors of standard model selection approaches (AIC, BIC, $\ell_1$ regularization) strongly depend on the sparsity of the ground truth, the reconstruction error of our method is always close to the minimum in all conditions of sparsity, data size and strength of input correlations. Finally, we observe that, when considering categorical instead of binary inputs, in a simple and mathematically tractable case, the contribution of the alphabet size to the complexity is very small compared to that of parameter space dimension. We further explore the issue by analysing the dataset of the "13 keys to the White House" which is a method for forecasting the outcomes of US presidential elections.
In order to investigate the breast cancer prediction problem on the aging population with the grades of DCIS, we conduct a tree augmented naive Bayesian network experiment trained and tested on a large clinical dataset including consecutive diagnostic mammography examinations, consequent biopsy outcomes and related cancer registry records in the population of women across all ages. The aggregated results of our ten-fold cross validation method recommend a biopsy threshold higher than 2% for the aging population.
We consider an autonomous agent operating in a stochastic, partially-observable, multiagent environment, that explicitly models the other agents as probabilistic deterministic finite-state controllers (PDFCs) in order to predict their actions. We assume that such models are not given to the agent, but instead must be learned from (possibly imperfect) observations of the other agents' behavior. The agent maintains a belief over the other agents' models, that is updated via Bayesian inference. To represent this belief we place a flexible stick-breaking distribution over PDFCs, that allows the posterior to concentrate around controllers whose size is not bounded and scales with the complexity of the observed data. Since this Bayesian inference task is not analytically tractable, we devise a Markov chain Monte Carlo algorithm to approximate the posterior distribution. The agent then embeds the result of this inference into its own decision making process using the interactive POMDP framework. We show that our learning algorithm can learn agent models that are behaviorally accurate for problems of varying complexity, and that the agent's performance increases as a result.