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.
@cite_38: 
@cite_18: The most frequent infectious diseases in humans—and those with the highest potential for rapid pandemic spread—are usually transmitted via droplets during close proximity interactions (CPIs). Despite the importance of this transmission route, very little is known about the dynamic patterns of CPIs. Using wireless sensor network technology, we obtained high-resolution data of CPIs during a typical day at an American high school, permitting the reconstruction of the social network relevant for infectious disease transmission. At 94 coverage, we collected 762,868 CPIs at a maximal distance of 3 m among 788 individuals. The data revealed a high-density network with typical small-world properties and a relatively homogeneous distribution of both interaction time and interaction partners among subjects. Computer simulations of the spread of an influenza-like disease on the weighted contact graph are in good agreement with absentee data during the most recent influenza season. Analysis of targeted immunization strategies suggested that contact network data are required to design strategies that are significantly more effective than random immunization. Immunization strategies based on contact network data were most effective at high vaccination coverage.
@cite_22: The development of novel treatments for many slowly progressing diseases, such as Alzheimer's disease (AD), is dependent on the ability to monitor and detect changes in disease progression. In some diseases the distinct clinical stages of the disease progress far too slowly to enable a quick evaluation of the efficacy of a given proposed treatment. To help improve the assessment of disease progression, we propose using Hidden Markov Models (HMM's) to model, in a more granular fashion, disease progression as compared to the clinical stages of the disease. Unlike many other applications of Hidden Markov Models, we train our HMM in an unsupervised way and then evaluate how effective the model is at uncovering underlying statistical patterns in disease progression by considering HMM states as disease stages. In this study, we focus on AD and show that our model, when evaluated on the cross validation data, can identify more granular disease stages than the three currently accepted clinical stages of “Normal”, “MCI” (Mild Cognitive Impairment), and “AD”.
@cite_34: Simulation studies using susceptible-infectious-recovered models were conducted to estimate individuals’ risk of infection and time to infection in small-world and randomly mixing networks. Infection transmitted more rapidly but ultimately resulted in fewer infected individuals in the small-world, compared with the random, network. The ability of measures of network centrality to identify high-risk individuals was also assessed. ‘‘Centrality’’ describes an individual’s position in a population; numerous parameters are available to assess this attribute. Here, the authors use the centrality measures degree (number of contacts), random-walk betweenness (a measure of the proportion of times an individual lies on the path between other individuals), shortest-path betweenness (the proportion of times an individual lies on the shortest path between other individuals), and farness (the sum of the number of steps between an individual and all other individuals). Each was associated with time to infection and risk of infection in the simulated outbreaks. In the networks examined, degree (which is the most readily measured) was at least as good as other network parameters in predicting risk of infection. Identification of more central individuals in populations may be used to inform surveillance and infection control strategies.
@cite_0: A novel approach is developed for predicting body trajectories for cancer progression, where conditional probabilities of clinical data are modeled using Hidden Markov Model techniques. Basically, each potential body site is encoded by an N-letter code, and a disease trajectory is described in terms of a string of letters. Patient data base records are then represented by such strings with different lengths, start points and end points. The approach is explored using pathology data for non-Hodgkin lymphoma augmented with an artificial data base generated according to observed distributions in the clinical data. For the Hidden Markov Models a Bayesian approach is taken using the Hybrid Monte Carlo method, producing an ensemble of models rather than a single one. Using a test set consisting of both real and random trajectories, we estimate the performance of our Hidden Markov Model models and also extract most probable profiles. Given the limited data set size the results are very encouraging.
@cite_24: 
@cite_2: We develop Graph-Coupled Hidden Markov Models (GCHMMs) for modeling the spread of infectious disease locally within a social network. Unlike most previous research in epidemiology, which typically models the spread of infection at the level of entire populations, we successfully leverage mobile phone data collected from 84 people over an extended period of time to model the spread of infection on an individual level. Our model, the GCHMM, is an extension of widely-used Coupled Hidden Markov Models (CHMMs), which allow dependencies between state transitions across multiple Hidden Markov Models (HMMs), to situations in which those dependencies are captured through the structure of a graph, or to social networks that may change over time. The benefit of making infection predictions on an individual level is enormous, as it allows people to receive more personalized and relevant health advice.
@cite_16: 
@cite_11: 
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.