Supplement to a hierarchical dirichlet process mixture model for haplotype reconstruction from multipopulation data. This work proposes a novel approach to model the spatiotemporal distribution of crowd motions and detect anomalous events. Analyzing user trajectories from mobile device data with. Parallel gibbs sampling for hierarchical dirichlet processes. Reliable and scalable variational inference for the.
Each node in a cooperative hierarchical structure is assigned a dirichlet process to model its weights on the infinite hidden factorstopics. This alleviates the rigid, singlepath formulation of the ncrp, allowing a document to more easily. There will be multiple documentlevel atoms which map to the same corpuslevel atom. We construct the hdsp based on the gamma representation of the hierarchical dirichlet process hdp which allows scaling the mixture components. Our new method results in significant speedups on real world text corpora. It might take a few minutes to download any missing dependencies and build the vignettes. Jordan, fellow, ieee abstractwe develop a nested hierarchical dirichlet process nhdp for hierarchical topic modeling. Nested hierarchical dirichlet process for nonparametric entitytopic. In statistics and machine learning, the hierarchical dirichlet process hdp is a nonparametric bayesian approach to clustering grouped data. Sep 05, 2016 we propose the hierarchical dirichlet process hdp, a hierarchical, nonparametric, bayesian model for clustering problems involving multiple groups of data. This library contains java source and class files implementing the latent dirichlet allocation singlethreaded collapsed gibbs sampling and hierarchical dirichlet process multithreaded collapsed variational inference topic models.
A tutorial on dirichlet processes and hierarchical dirichlet. A hierarchical dirichlet process mixture model for. We consider problems involving groups of data where each observation within a group is a draw from a mixture model and where it is desirable to share mixture components between groups. Modeling population structure under hierarchical dirichlet processes. Along with the growth of social media, there have been simultaneous increases in the amounts of textual information and social structural information. International computer music conference, belfast, uk. See general information about how to correct material in repec for technical questions regarding this item, or to correct its authors, title. Hierarchical dirichlet scaling process proceedings of. Such a base measure being discrete, the child dirichlet processes. Thus, as desired, the mixture models in the different groups necessarily share mixture components. Hierarchical dirichlet processes yee whye teh, michael i. Fits hierarchical dirichlet process topic models to massive data. Hierarchical latent dirichlet allocation hlda addresses the problem of learning topic hierarchies from data. We assume that the number of mixture components is unknown a priori and is to be inferred from the data.
Conditional methods impute the dirichlet process and update it as a component of the gibbs sampler. We consider problems involving groups of data, where each observation within a group is a draw from a mixture model, and where it is desirable to share mixture components both within and between groups. This paper proposes hierarchical dirichlet processes hdp, a probabilistic topic model, as an effective method for automatic substory detection. In this setting it is natural to consider sets of dirichlet processes, one for each group. The terminology of hierarchical dirichlet process has also been used by m uller et al. Machine learning and knowledge discovery in databases pp 564579 cite as. Jordan %b proceedings of the eleventh international conference on artificial intelligence and statistics %c proceedings of machine learning research %d 2007 %e marina meila %e xiaotong shen %f pmlrv2thibaux07a %i pmlr %j proceedings of machine learning research %p 564571 %u. Sequential correspondence hierarchical dirichlet processes. The hybrid nested hierarchical dirichlet process and its application to topic modeling with word differentiation.
The main result of this paper is to show that improved parameter estimation allows bncs to outperform leading learning methods such as random forest for both 01 loss and rmse, albeit just on categorical datasets. Specifically, our method focuses on how one topic splits into multiple topics, and how multiple topics merge into one topic. Nonparametric topic models are a powerful approach, but traditional hierarchical dirichlet processes hdps are unable to fully take into account topic sharing across deep hierarchical structure. Bayesian probabilistic tensor factorization code bibtex icml 2015 markov mixed membership model code. Online inference for the hierarchical dirichlet process. Coupled hierarchical dirichlet process mixtures for simultaneous clustering and topic modeling.
Nested hierarchical dirichlet process code bibtex kdd 2015 bptf. The hierarchical dirichlet process hdp is an intuitive and elegant technique to model data with latent groups. Hierarchical dirichlet processes microsoft research. The former integrate out analytically the infinitedimensional component of the hierarchical model and sample from the marginal distribution of the remaining variables using the gibbs sampler. Fast collapsed gibbs sampling for latent dirichlet allocation. However, in many settings the hdphmms strict markovian constraints are undesirable, particularly if we wish to learn or encode nongeometric state durations.
The hierarchical dirichlet process model has been successfully used for extracting the topical or semantic content of documents and other kinds of sparse count data. Given multilocus genotype data from a sample of individuals, the proposed model allows inferring and classifying individuals as unadmixed or admixed, inferring the number of subpopulations ancestral to an. A tutorial on dirichlet processes and hierarchical dirichlet processes yee whye teh gatsby computational neuroscience unit university college london mar 1, 2007 cued yee whye teh gatsby dp and hdp tutorial mar 1, 2007 cued 1 53. Hierarchical dirichlet processes, booktitle in advances in neural information processing systems, year 2005, pages 8592, publisher mit press. Datadriven recomposition using the hierarchical dirichlet process hidden markov model. Burns suny at bu alo nonparametric clustering with dirichlet processes mar. There is much interest in the hierarchical dirichlet process hidden markov model hdphmm as a natural bayesian nonparametric extension of the traditional hmm. Data sets involving multiple groups with shared characteristics frequently arise in practice. A two level hierarchical dirichlet process is a collection of dirichlet processes, one for each group, which share a base distribution, which is also a dirichlet process. Like the hierarchical dirichlet process, ndms rely on two tiers of dirichlet processes to explain the data with an unknown number of latent factors.
Such grouped clustering problems occur often in practice, e. Online variational inference for the hierarchical dirichlet process. A tutorial on dirichlet processes and hierarchical. Online variational inference for the hierarchical dirichlet. Introduction to the dirichlet distribution and related processes. Nested hierarchical dirichlet processes john paisley, member, ieee, chong wang, david m. The new model combines the ideas of the hierarchical and the dependent dirichlet process, allowing the estimation of sitespeci. We discuss representations of hierarchical dirichlet processes in terms of.
Dirichlet process dp mixture models are the cornerstone of nonparametric bayesian statistics, and the development of montecarlo markov chain mcmc sampling methods for dp mixtures has enabled the application of nonparametric bayesian methods to a variety of practical data analysis problems. The hierarchical dirichlet processes hdp is a bayesian nonparametric model that provides a flexible mixedmembership to documents. Diln generalizes the hierarchical dirichlet process hdp to model correlation structure between the weights of the atoms at the group level. Hierarchical dirichlet scaling process springerlink. Pdf bayesian hierarchical mixture clustering using. Truncated priors for tempered hierarchical dirichlet process vector autoregression, bank of russia working paper series wps47, bank of russia. In this paper, we explore the feasibility of trajectory clustering, i. The cooperative hierarchical structure is a common and significant data structure observed in, or adopted by, many research areas, such as. We discuss representations of hierarchical dirichlet processes in terms of a. Sequential latent dirichlet allocation springerlink. Tracking and connecting topics via incremental hierarchical. We derive a representation of diln as a normalized collection of gammadistributed random variables and study its statistical properties. A hierarchical dirichlet process mixture model for haplotype reconstruction from multipopulation data sohn, kyungah and.
In this paper, we propose an approach called evolutionary hierarchical dirichlet processes evohdp to discover interesting cluster evolution patterns from such text data. Renowned bayesian approaches for cooperative hierarchical structure modeling are mostly based on topic models. Hierarchical dirichlet processes with social influence. Conventional gibbs sampling schemes for lda require ok operations per sample where k is the number of topics in the model. This method allows groups to share statistical strength via sharing of clusters. Given our desire to tie the mixture models in the various groups, we consider a hierarchical model, specifically one in which the base measure for the child dirichlet processes is itself distributed according to a dirichlet process. Hierarchical beta processes and the indian buffet process. Coupled hierarchical dirichlet process mixtures for. Moreover, there are often several different stories pertaining to a given event, which we refer to as substories and the corresponding task of their automatic detection as substory detection. Dirichlet hierarchical processes 3 has been shown to recognize anomalies in the qmul dataset. We discuss representations of hierarchical dirichlet processes in terms of a stickbreaking process, and a generalization of the chinese restaurant process that we refer to as the chinese restaurant franchise.
Hierarchical beta processes and the indian buffet process pmlr. All material on this site has been provided by the respective publishers and authors. We develop a nested hierarchical dirichlet process nhdp for hierarchical topic modeling. To select superpixels, the author uses the simple linear method of iterative clustering described in. Each cluster of time series data, corresponding to a motion pattern, is modeled by an hmm. However, until now, hierarchical dirichlet process hdp mixtures have not seen. Such progressive sequential dependency is captured by using the hierarchical twoparameter poisson dirichlet process hpdp. This variant directly considers the underlying sequential structure, i. Substory detection in twitter with hierarchical dirichlet. Parallel gibbs sampling for hierarchical dirichlet. Deraining websites tip 2017 bibtex cvpr 2017 bibtex tsp 2017 nonlinear kalman filtering with divergence minimization code bibtex tpami 2015 nhdp. Aug 27, 2004 we propose the hierarchical dirichlet process hdp, a hierarchical, nonparametric, bayesian model for clustering problems involving multiple groups of data.
By using the theory of dirichlet processes we can implicitly integrate out the infinitely many transition parameters, leaving only three hyperparameters which can be learned from data. Each group is assumed to be generated from a template mixture model with group level variability in both the mixing proportions and the component. We propose a bayesian nonparametric model to infer population admixture, extending the hierarchical dirichlet process to allow for correlation between loci due to linkage disequilibrium. Markov chain monte carlo in approximate dirichlet and beta twoparameter process hierarchical models. An online gibbs sampler algorithm for hierarchical. We adopt the hierarchical dirichlet process hdp model, and. Retrospective markov chain monte carlo methods for dirichlet. In proceedings of the 26th annual international conference on machine learning pp. In this paper we extend hierarchical dirichlet processes to model such data. Blei, title hierarchical dirichlet processes, journal journal of the american statistical association, year 2004, volume 101.
To install, first ensure devtools package is installed and the bioconductor repositories are available run setrepositories. Tracking and connecting topics via incremental hierarchical dirichlet processes. Bayesian hierarchical mixture clustering using multilevel hierarchical dirichlet processes. A hierarchical dirichlet process mixture model for haplotype reconstruction. This result shows that the beta process plays the role for the indian buffet process that the dirichlet process plays for the chinese restaurant process, a parallel that guides us in deriving analogs for the beta process of the many known extensions of the dirichlet process. A hierarchical dependent dirichlet process prior for. These three hyperparameters define a hierarchical dirichlet process capable of capturing a rich set of transition dynamics. Treestructured hierarchical dirichlet process springerlink. A tutorial on dirichlet processes and hierarchical dirichlet processes yee whye teh. Blei we consider problems involving groups of data where each observation within a group is a draw from a mixture model and where it is.
Hierarchical dirichlet processes, journal of the american statistical association. We discuss representations of hierarchical dirichlet processes in terms of a stickbreaking process, and a generalization of the chinese restaurant. In this paper we introduce a novel collapsed gibbs sampling method for the widely used latent dirichlet allocation lda model. Download bibtex %0 conference paper %t reliable and scalable variational inference for the hierarchical dirichlet process %a michael hughes %a dae il kim %a erik sudderth %b proceedings of the eighteenth international conference on artificial intelligence and statistics %c proceedings of machine learning research %d 2015 %e guy lebanon %e s. The hierarchical dirichlet process hdp is a bayesian nonparametric prior for grouped. Oct 25, 2012 we develop a nested hierarchical dirichlet process nhdp for hierarchical topic modeling. In this paper, a new nonparametric bayesian model called the dual sticky hierarchical dirichlet process hidden markov model hdphmm is proposed for mining activities from a collection of time series data such as trajectories. We use hierarchical dirichlet processes due to their ability to automatically extract appropriate trajectory segments. The nhdp is a generalization of the nested chinese restaurant process ncrp that allows each word to follow its own path to a topic node according to a documentspecific distribution on a shared tree. The model relies on a nonparametric prior called the nested chinese restaurant process, which allows for arbitrarily large branching factors and readily accommodates growing data collections.
We can extend the hdphmm to capture such structure by drawing. Accounting for decay of linkage disequilibrium in haplotype inference and missingdata imputation. Citeseerx document details isaac councill, lee giles, pradeep teregowda. In this paper, we develop a novel minibatch online gibbs. We present the hierarchical dirichlet scaling process hdsp, a bayesian nonparametric mixed membership model for multilabeled data. Each group of data is modeled with a mixture, with the. However, it has not been widely used for practical applications due to the high computational costs associated with inference. Also, all share the same set of atoms, and only the atom weights differs. I think i understand the main ideas of hierarchical dirichlet processes, but i dont understand the specifics of its application in topic modeling. This paper introduces a novel parameter estimation method for the probability tables of bayesian network classifiers bncs, using hierarchical dirichlet processes hdps. Download bibtex %0 conference paper %t online variational inference for the hierarchical dirichlet process %a chong wang %a john paisley %a david blei %b proceedings of the fourteenth international conference on artificial intelligence and statistics %c proceedings of machine learning research %d 2011 %e geoffrey gordon %e david dunson %e. Find, read and cite all the research you need on researchgate.
The seqchdp model can be considered as an extended hierarchical dirichlet processes hdp model containing two important features. Hierarchical dirichlet process hdp, allowing for the gen eration of an in. It uses a dirichlet process for each group of data, with the dirichlet processes for all groups sharing a base distribution which is itself drawn from a dirichlet process. We propose the treestructured hierarchical dirichlet process, allowing dirichlet process based topic modeling over a given tree structure of. We first learn the regions of interest rois which inform the behavioral patterns by trajectory analysis with hierarchical dirichlet processes hdp, so that the main trends of crowd motions can be modeled. Hierarchical dirichlet processes representations applications extensions and related models yee whye teh gatsby dp and hdp tutorial mar 1, 2007 cued 2 53. Evolutionary hierarchical dirichlet processes for multiple. Dual sticky hierarchical dirichlet process hidden markov. In statistics and machine learning, the hierarchical dirichlet process hdp is a nonparametric. If one returns all the words that compose a topic, all the approximated topic probabilities in that case will be 1 or 0.