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.
The idea of using hierarchies to improve model flexibility is extensively studied in topic modeling, in models such as latent Dirichlet allocation (LDA) @cite_29 @cite_35 @cite_39 . @cite_29 used a sigmoid link function, introduced in Relational Topic Model to learn fixed networks of documents. These, and further works have exemplified a trend in data-driven machine learning applications -- hierarchical modeling is used to make inferences when the data structure is complex. Our work can be considered as a hierarchical extension of either GCHMMs @cite_2 or topic HMMs @cite_26 with a nested transition function. From this viewpoint, we can also interpret our graphical model in terms of hierarchical LDA modeling.
@cite_35 @cite_26 @cite_29 @cite_39 @cite_2
1991255919 2752711721 2152677317 159693449
Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interest and touches on many important applications in text mining, computer vision and computational biology. This paper represents the collapsed LDA as a factor graph, which enables the classic loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Although two commonly used approximate inference methods, such as variational Bayes (VB) and collapsed Gibbs sampling (GS), have gained great success in learning LDA, the proposed BP is competitive in both speed and accuracy, as validated by encouraging experimental results on four large-scale document datasets. Furthermore, the BP algorithm has the potential to become a generic scheme for learning variants of LDA-based topic models in the collapsed space. To this end, we show how to learn two typical variants of LDA-based topic models, such as author-topic models (ATM) and relational topic models (RTM), using BP based on the factor graph representations. Latent Dirichlet Allocation (LDA) is a popular topic modeling technique for exploring hidden topics in text corpora. Standard LDA model suffers the problem that the topic assignment of each word is independent and lacks the mechanism to utilize the rich prior background knowledge to learn semantically coherent topics. To address this problem, in this paper, we propose a model called Entity Correlation Latent Dirichlet Allocation (EC-LDA) by incorporating constraints derived from entity correlations as the prior knowledge into LDA topic model. Different from other knowledge-based topic models which extract the knowledge information directly from the train dataset itself or even from the human judgements, for our work, we take advantage of the prior knowledge from the external knowledge base (Freebase 1, in our experiment). Hence, our approach is more suitable to widely kinds of text corpora in different scenarios. We fit our proposed model using Gibbs sampling. Experiment results demonstrate the effectiveness of our model compared with standard LDA. Inspired by a two-level theory from political science that unifies agenda setting and ideological framing, we propose supervised hierarchical latent Dirichlet allocation (SHLDA), which jointly captures documents' multi-level topic structure and their polar response variables. Our model extends the nested Chinese restaurant processes to discover tree-structured topic hierarchies and uses both per-topic hierarchical and per-word lexical regression parameters to model response variables. SHLDA improves prediction on political affiliation and sentiment tasks in addition to providing insight into how topics under discussion are framed. Topic models such as the latent Dirichlet allocation (LDA) have become a standard staple in the modeling toolbox of machine learning. They have been applied to a vast variety of data sets, contexts, and tasks to varying degrees of success. However, to date there is almost no formal theory explicating the LDA's behavior, and despite its familiarity there is very little systematic analysis of and guidance on the properties of the data that affect the inferential performance of the model. This paper seeks to address this gap, by providing a systematic analysis of factors which characterize the LDA's performance. We present theorems elucidating the posterior contraction rates of the topics as the amount of data increases, and a thorough supporting empirical study using synthetic and real data sets, including news and web-based articles and tweet messages. Based on these results we provide practical guidance on how to identify suitable data sets for topic models, and how to specify particular model parameters.