The purpose of this study is to leverage modern technology (such as mobile or web apps in (2014)) to enrich epidemiology data and infer the transmission of disease. Homogeneity related research on population level has been intensively studied in previous work. In contrast, we develop hierarchical Graph-Coupled Hidden Markov Models (hGCHMMs) to simultaneously track the spread of infection in a small cell phone community and capture person-specific infection parameters by leveraging a link prior that incorporates additional covariates. We also reexamine the model evolution of the hGCHMM from simple HMMs and LDA, elucidating additional flexibility and interpretability. Due to the non-conjugacy of sparsely coupled HMMs, we design a new approximate distribution, allowing our approach to be more applicable to other application areas. Additionally, we investigate two common link functions, the beta-exponential prior and sigmoid function, both of which allow the development of a principled Bayesian hierarchical framework for disease transmission. The results of our model allow us to predict the probability of infection for each person on each day, and also to infer personal physical vulnerability and the relevant association with covariates. We demonstrate our approach experimentally on both simulation data and real epidemiological records.
Hidden Markov models are widely used in simulating the state space based disease progression @cite_0 @cite_16 @cite_22 @cite_2 , since HMMs actually mimic the behavior of an SIS model with discretized timestamps and are convenient in terms of the development of inference algorithm for different variants. In our work, we also adopt this basic framework to design our model. Other work like @cite_24 @cite_11 proposed a group lasso formulation or multi-task learning framework using optimization, and is far from our domain. A recent work by @cite_38 learned a continuous time series model looking at trajectories for different patients, but ignoring interactions between chains. Our work attempts to unify social network modeling of individuals using a hierarchical structure. @cite_34 utilized a fixed social network analysis on susceptible-infectious-recovered (SIR) models to identify high-risk individuals. @cite_18 's work on close proximity interactions (CPIs) of dynamic social networks at a high school indicated immunization strategies are more credible if extra contact data is provided.
@cite_38 @cite_18 @cite_22 @cite_34 @cite_0 @cite_24 @cite_2 @cite_16 @cite_11
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Hidden Markov models (HMMs) have proven to be one of the most widely used tools for learning probabilistic models of time series data. In an HMM, information about the past is conveyed through a single discrete variable—the hidden state. We discuss a generalization of HMMs in which this state is factored into multiple state variables and is therefore represented in a distributed manner. We describe an exact algorithm for inferring the posterior probabilities of the hidden state variables given the observations, and relate it to the forward–backward algorithm for HMMs and to algorithms for more general graphical models. Due to the combinatorial nature of the hidden state representation, this exact algorithm is intractable. As in other intractable systems, approximate inference can be carried out using Gibbs sampling or variational methods. Within the variational framework, we present a structured approximation in which the the state variables are decoupled, yielding a tractable algorithm for learning the parameters of the model. Empirical comparisons suggest that these approximations are efficient and provide accurate alternatives to the exact methods. Finally, we use the structured approximation to model Bach‘s chorales and show that factorial HMMs can capture statistical structure in this data set which an unconstrained HMM cannot. We have already shown that extracting long-term dependencies from sequential data is difficult, both for determimstic dynamical systems such as recurrent networks, and probabilistic models such as hidden Markov models (HMMs) or input output hidden Markov models (IOHMMs). In practice, to avoid this problem, researchers have used domain specific a-priori knowledge to give meaning to the hidden or state variables representing past context. In this paper, we propose to use a more general type of a-priori knowledge, namely that the temporal dependencies are structured hierarchically. This implies that long-term dependencies are represented by variables with a long time scale. This principle is applied to a recurrent network which includes delays and multiple time scales. Experiments confirm the advantages of such structures. A similar approach is proposed for HMMs and IOHMMs. Dynamic Bayesian networks such as Hidden Markov Models (HMMs) are successfully used as probabilistic models for human motion. The use of hidden variables makes them expressive models, but inference is only approximate and requires procedures such as particle filters or Markov chain Monte Carlo methods. In this work we propose to instead use simple Markov models that only model observed quantities. We retain a highly expressive dynamic model by using interactions that are nonlinear and non-parametric. A presentation of our approach in terms of latent variables shows logarithmic growth for the computation of exact log-likelihoods in the number of latent states. We validate our model on human motion capture data and demonstrate state-of-the-art performance on action recognition and motion completion tasks. Hidden Markov models (HMMs) are a powerful probabilistic tool for modeling sequential data, and have been applied with success to many text-related tasks, such as part-of-speech tagging, text segmentation and information extraction. In these cases, the observations are usually modeled as multinomial distributions over a discrete vocabulary, and the HMM parameters are set to maximize the likelihood of the observations. This paper presents a new Markovian sequence model, closely related to HMMs, that allows observations to be represented as arbitrary overlapping features (such as word, capitalization, formatting, part-of-speech), and defines the conditional probability of state sequences given observation sequences. It does this by using the maximum entropy framework to fit a set of exponential models that represent the probability of a state given an observation and the previous state. We present positive experimental results on the segmentation of FAQ’s.