We present the nested Chinese restaurant process (nCRP), a stochastic process which assigns probability distributions to infinitely-deep, infinitely-branching trees. We show how this stochastic process can be used as a prior distribution in a Bayesian nonparametric model of document collections. Specifically, we present an application to information retrieval in which documents are modeled as paths down a random tree, and the preferential attachment dynamics of the nCRP leads to clustering of documents according to sharing of topics at multiple levels of abstraction. Given a corpus of documents, a posterior inference algorithm finds an approximation to a posterior distribution over trees, topics and allocations of words to levels of the tree. We demonstrate this algorithm on collections of scientific abstracts from several journals. This model exemplifies a recent trend in statistical machine learning--the use of Bayesian nonparametric methods to infer distributions on flexible data structures.
Factorized Information Criterion (FIC) is a recently developed information criterion, based on which a novel model selection methodology, namely Factorized Asymptotic Bayesian (FAB) Inference, has been developed and successfully applied to various hierarchical Bayesian models. The Dirichlet Process (DP) prior, and one of its well known representations, the Chinese Restaurant Process (CRP), derive another line of model selection methods. FIC can be viewed as a prior distribution over the latent variable configurations. Under this view, we prove that when the parameter dimensionality $D_{c}=2$, …
We develop the distance dependent Chinese restaurant process (CRP), a flexible class of distributions over partitions that allows for non-exchangeability. This class can be used to model many kinds of dependencies between data in infinite clustering models, including dependencies across time or space. We examine the properties of the distance dependent CRP, discuss its connections to Bayesian nonparametric mixture models, and derive a Gibbs sampler for both observed and mixture settings. We study its performance with three text corpora. We show that relaxing the assumption of exchangeability w…
For a long time, the Dirichlet process has been the gold standard discrete random measure in Bayesian nonparametrics. The Pitman--Yor process provides a simple and mathematically tractable generalization, allowing for a very flexible control of the clustering behaviour. Two commonly used representations of the Pitman--Yor process are the stick-breaking process and the Chinese restaurant process. The former is a constructive representation of the process which turns out very handy for practical implementation, while the latter describes the partition distribution induced. However, the usual pro…
Tree structures are ubiquitous in data across many domains, and many datasets are naturally modelled by unobserved tree structures. In this paper, first we review the theory of random fragmentation processes [Bertoin, 2006], and a number of existing methods for modelling trees, including the popular nested Chinese restaurant process (nCRP). Then we define a general class of probability distributions over trees: the Dirichlet fragmentation process (DFP) through a novel combination of the theory of Dirichlet processes and random fragmentation processes. This DFP presents a stick-breaking constru…
We propose a restricted collapsed draw (RCD) sampler, a general Markov chain Monte Carlo sampler of simultaneous draws from a hierarchical Chinese restaurant process (HCRP) with restriction. Models that require simultaneous draws from a hierarchical Dirichlet process with restriction, such as infinite Hidden markov models (iHMM), were difficult to enjoy benefits of \markerg{the} HCRP due to combinatorial explosion in calculating distributions of coupled draws. By constructing a proposal of seating arrangements (partitioning) and stochastically accepts the proposal by the Metropolis-Hastings al…
Dirichlet process mixture (DPM) models tend to produce many small clusters regardless of whether they are needed to accurately characterize the data - this is particularly true for large data sets. However, interpretability, parsimony, data storage and communication costs all are hampered by having overly many clusters. We propose a powered Chinese restaurant process to limit this kind of problem and penalize over clustering. The method is illustrated using some simulation examples and data with large and small sample size including MNIST and the Old Faithful Geyser data.
The Chinese restaurant process (CRP) and the stick-breaking process are the two most commonly used representations of the Dirichlet process. However, the usual proof of the connection between them is indirect, relying on abstract properties of the Dirichlet process that are difficult for nonexperts to verify. This short note provides a direct proof that the stick-breaking process leads to the CRP, without using any measure theory. We also discuss how the stick-breaking representation arises naturally from the CRP.
Probabilistic Computing Project Massachusetts Institute of Technology（麻省理工学院概率计算项目）
This article proposes a Bayesian nonparametric method for forecasting, imputation, and clustering in sparsely observed, multivariate time series data. The method is appropriate for jointly modeling hundreds of time series with widely varying, non-stationary dynamics. Given a collection of $N$ time series, the Bayesian model first partitions them into independent clusters using a Chinese restaurant process prior. Within a cluster, all time series are modeled jointly using a novel "temporally-reweighted" extension of the Chinese restaurant process mixture. Markov chain Monte Carlo techniques are…
We are concerned with modeling the strength of links in networks by taking into account how often those links are used. Link usage is a strong indicator of how closely two nodes are related, but existing network models in Bayesian Statistics and Machine Learning are able to predict only wether a link exists at all. As priors for latent attributes of network nodes we explore the Chinese Restaurant Process (CRP) and a multivariate Gaussian with fixed dimensionality. The model is applied to a social network dataset and a word coocurrence dataset.
Nested Chinese Restaurant Process (nCRP) topic models are powerful nonparametric Bayesian methods to extract a topic hierarchy from a given text corpus, where the hierarchical structure is automatically determined by the data. Hierarchical Latent Dirichlet Allocation (hLDA) is a popular instance of nCRP topic models. However, hLDA has only been evaluated at small scale, because the existing collapsed Gibbs sampling and instantiated weight variational inference algorithms either are not scalable or sacrifice inference quality with mean-field assumptions. Moreover, an efficient distributed imple…
Insight Centre for Data Analytics（洞察数据分析中心）；University College Dublin（都柏林大学）；Maynooth University（梅努斯大学）
This paper focuses on the problem of hierarchical non-overlapping clustering of a dataset. In such a clustering, each data item is associated with exactly one leaf node and each internal node is associated with all the data items stored in the sub-tree beneath it, so that each level of the hierarchy corresponds to a partition of the dataset. We develop a novel Bayesian nonparametric method combining the nested Chinese Restaurant Process (nCRP) and the Hierarchical Dirichlet Process (HDP). Compared with other existing Bayesian approaches, our solution tackles data with complex latent mixture fe…
Unsupervised clustering of curves according to their shapes is an important problem with broad scientific applications. The existing model-based clustering techniques either rely on simple probability models (e.g., Gaussian) that are not generally valid for shape analysis or assume the number of clusters. We develop an efficient Bayesian method to cluster curve data using an elastic shape metric that is based on joint registration and comparison of shapes of curves. The elastic-inner product matrix obtained from the data is modeled using a Wishart distribution whose parameters are assigned car…
In this work, we propose a new Bayesian spatial homogeneity pursuit method for survival data under the proportional hazards model to detect spatially clustered patterns in baseline hazard and regression coefficients. Specially, regression coefficients and baseline hazard are assumed to have spatial homogeneity pattern over space. To capture such homogeneity, we develop a geographically weighted Chinese restaurant process prior to simultaneously estimate coefficients and baseline hazards and their uncertainty measures. An efficient Markov chain Monte Carlo (MCMC) algorithm is designed for our p…
Vector autoregression model is ubiquitous in classical time series data analysis. With the rapid advance of social network sites, time series data over latent graph is becoming increasingly popular. In this paper, we develop a novel Bayesian grouped network autoregression model to simultaneously estimate group information (number of groups and group configurations) and group-wise parameters. Specifically, a graphically assisted Chinese restaurant process is incorporated under framework of the network autoregression model to improve the statistical inference performance. An efficient Markov cha…
Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick …
This paper introduces a general class of hierarchical nonparametric prior distributions. The random probability measures are constructed by a hierarchy of generalized species sampling processes with possibly non-diffuse base measures. The proposed framework provides a general probabilistic foundation for hierarchical random measures with either atomic or mixed base measures and allows for studying their properties, such as the distribution of the marginal and total number of clusters. We show that hierarchical species sampling models have a Chinese Restaurants Franchise representation and can …
Chongqing University（重庆大学）；National University of Singapore（新加坡国立大学）；Bioinformatics Institute, A*STAR（A*STAR生物信息研究所）；Lanzhou University of Technology（兰州理工大学）；Lanzhou University（兰州大学）
Complex activity recognition is challenging due to the inherent uncertainty and diversity of performing a complex activity. Normally, each instance of a complex activity has its own configuration of atomic actions and their temporal dependencies. We propose in this paper an atomic action-based Bayesian model that constructs Allen's interval relation networks to characterize complex activities with structural varieties in a probabilistic generative way: By introducing latent variables from the Chinese restaurant process, our approach is able to capture all possible styles of a particular comple…
Crowdsourcing has been proven to be an effective and efficient tool to annotate large datasets. User annotations are often noisy, so methods to combine the annotations to produce reliable estimates of the ground truth are necessary. We claim that considering the existence of clusters of users in this combination step can improve the performance. This is especially important in early stages of crowdsourcing implementations, where the number of annotations is low. At this stage there is not enough information to accurately estimate the bias introduced by each annotator separately, so we have to …
This paper describes the hierarchical infinite relational model (HIRM), a new probabilistic generative model for noisy, sparse, and heterogeneous relational data. Given a set of relations defined over a collection of domains, the model first infers multiple non-overlapping clusters of relations using a top-level Chinese restaurant process. Within each cluster of relations, a Dirichlet process mixture is then used to partition the domain entities and model the probability distribution of relation values. The HIRM generalizes the standard infinite relational model and can be used for a variety o…
We developed a new quantum annealing (QA) algorithm for Dirichlet process mixture (DPM) models based on the Chinese restaurant process (CRP). QA is a parallelized extension of simulated annealing (SA), i.e., it is a parallel stochastic optimization technique. Existing approaches [Kurihara et al. UAI2009, Sato et al. UAI2009] and cannot be applied to the CRP because their QA framework is formulated using a fixed number of mixture components. The proposed QA algorithm can handle an unfixed number of classes in mixture models. We applied QA to a DPM model for clustering vertices in a network wher…
The seemingly disjoint problems of count and mixture modeling are united under the negative binomial (NB) process. A gamma process is employed to model the rate measure of a Poisson process, whose normalization provides a random probability measure for mixture modeling and whose marginalization leads to an NB process for count modeling. A draw from the NB process consists of a Poisson distributed finite number of distinct atoms, each of which is associated with a logarithmic distributed number of data samples. We reveal relationships between various count- and mixture-modeling distributions an…
Spatial point pattern data are routinely encountered. A flexible regression model for the underlying intensity is essential to characterizing the spatial point pattern and understanding the impacts of potential risk factors on such pattern. We propose a Bayesian semiparametric regression model where the observed spatial points follow a spatial Poisson process with an intensity function which adjusts a nonparametric baseline intensity with multiplicative covariate effects. The baseline intensity is piecewise constant, approached with a powered Chinese restaurant process prior which prevents an …
The purpose of this work is to describe a unified, and indeed simple, mechanism for non-parametric Bayesian analysis, construction and generative sampling of a large class of latent feature models which one can describe as generalized notions of Indian Buffet Processes(IBP). This is done via the Poisson Process Calculus as it now relates to latent feature models. The IBP was ingeniously devised by Griffiths and Ghahramani in (2005) and its generative scheme is cast in terms of customers entering sequentially an Indian Buffet restaurant and selecting previously sampled dishes as well as new dis…
One of the focal points of the modern literature on Bayesian nonparametrics has been the problem of clustering, or partitioning, where each data point is modeled as being associated with one and only one of some collection of groups called clusters or partition blocks. Underlying these Bayesian nonparametric models are a set of interrelated stochastic processes, most notably the Dirichlet process and the Chinese restaurant process. In this paper we provide a formal development of an analogous problem, called feature modeling, for associating data points with arbitrary nonnegative integer numbe…
Clustering has become a core technology in machine learning, largely due to its application in the field of unsupervised learning, clustering, classification, and density estimation. A frequentist approach exists to hand clustering based on mixture model which is known as the EM algorithm where the parameters of the mixture model are usually estimated into a maximum likelihood estimation framework. Bayesian approach for finite and infinite Gaussian mixture model generates point estimates for all variables as well as associated uncertainty in the form of the whole estimates' posterior distribut…
We develop a nested hierarchical Dirichlet process (nHDP) for hierarchical topic modeling. 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 document-specific distribution on a shared tree. This alleviates the rigid, single-path formulation of the nCRP, allowing a document to more easily express thematic borrowings as a random effect. We demonstrate our algorithm on 1.8 million documents from The New York Times.
We consider predictive inference using a class of temporally dependent Dirichlet processes driven by Fleming--Viot diffusions, which have a natural bearing in Bayesian nonparametrics and lend the resulting family of random probability measures to analytical posterior analysis. Formulating the implied statistical model as a hidden Markov model, we fully describe the predictive distribution induced by these Fleming--Viot-driven dependent Dirichlet processes, for a sequence of observations collected at a certain time given another set of draws collected at several previous times. This is identifi…
Neutral to the right (NTR) processes were introduced by Doksum in 1974 as Bayesian priors on the class of distributions on the real line. Since that time there have been numerous applications to models that arise in survival analysis subject to possible right censoring. However, unlike the Dirichlet process, the larger class of NTR processes has not been used in a wider range of more complex statistical applications. Here, to circumvent some of these limitations, we describe a natural extension of NTR processes to arbitrary Polish spaces, which we call spatial neutral to the right processes. O…
Simulation of rainfall over a region for long time-sequences can be very useful for planning and policy-making, especially in India where the economy is heavily reliant on monsoon rainfall. However, such simulations should be able to preserve the known spatial and temporal characteristics of rainfall over India. General Circulation Models (GCMs) are unable to do so, and various rainfall generators designed by hydrologists using stochastic processes like Gaussian Processes are also difficult to apply over the vast and highly diverse landscape of India. In this paper, we explore a series of Baye…
Many popular random partition models, such as the Chinese restaurant process and its two-parameter extension, fall in the class of exchangeable random partitions, and have found wide applicability in model-based clustering, population genetics, ecology or network analysis. While the exchangeability assumption is sensible in many cases, it has some strong implications. In particular, Kingman's representation theorem implies that the size of the clusters necessarily grows linearly with the sample size; this feature may be undesirable for some applications, as recently pointed out by Miller et al…
Although combination antiretroviral therapy (ART) is highly effective in suppressing viral load for people with HIV (PWH), many ART agents may exacerbate central nervous system (CNS)-related adverse effects including depression. Therefore, understanding the effects of ART drugs on the CNS function, especially mental health, can help clinicians personalize medicine with less adverse effects for PWH and prevent them from discontinuing their ART to avoid undesirable health outcomes and increased likelihood of HIV transmission. The emergence of electronic health records offers researchers unpreced…
NICTA（澳大利亚国家信息与通信技术研究院）；Australian National University（澳大利亚国立大学）
The two parameter Poisson-Dirichlet Process (PDP), a generalisation of the Dirichlet Process, is increasingly being used for probabilistic modelling in discrete areas such as language technology, bioinformatics, and image analysis. There is a rich literature about the PDP and its derivative distributions such as the Chinese Restaurant Process (CRP). This article reviews some of the basic theory and then the major results needed for Bayesian modelling of discrete problems including details of priors, posteriors and computation. The PDP allows one to build distributions over countable partitions…
We describe the combinatorial stochastic process underlying a sequence of conditionally independent Bernoulli processes with a shared beta process hazard measure. As shown by Thibaux and Jordan [TJ07], in the special case when the underlying beta process has a constant concentration function and a finite and nonatomic mean, the combinatorial structure is that of the Indian buffet process (IBP) introduced by Griffiths and Ghahramani [GG05]. By reinterpreting the beta process introduced by Hjort [Hjo90] as a measurable family of Dirichlet processes, we obtain a simple predictive rule for the gen…
Columbia University（哥伦比亚大学）；Voleon Capital Management（Voleon资本管理）；Princeton University（普林斯顿大学）；UC Berkeley（加州大学伯克利分校）
We develop a nested hierarchical Dirichlet process (nHDP) for hierarchical topic modeling. 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 document-specific distribution on a shared tree. This alleviates the rigid, single-path formulation of the nCRP, allowing a document to more easily express thematic borrowings as a random effect. We derive a stochastic variational inference algorithm for the model, in addition to a greedy subtree selection method for each document, which allows for effic…
