Dirichlet process mixture models for unsupervised clustering of symptoms in Parkinson's disease

In this paper, the goal of identifying disease subgroups based on differences in observed symptom profile is considered. Commonly referred to as phenotype identification, solutions to this task often involve the application of unsupervised clustering techniques. In this paper, we investigate the application of a Dirichlet Process mixture (DPM) model for this task. This model is defined by the placement of the Dirichlet Process (DP) on the unknown components of a mixture model, allowing for the expression of uncertainty about the partitioning of observed data into homogeneous subgroups. To exemplify this approach, an application to phenotype identification in Parkinson’s disease (PD) is considered, with symptom profiles collected using the Unified Parkinson’s Disease Rating Scale (UPDRS). Clustering, Dirichlet Process mixture, Parkinson’s disease, UPDRS.

Reliable survival analysis based on the Dirichlet Process

We present a robust Dirichlet process for estimating survival functions from samples with right-censored data. It adopts a prior near-ignorance approach to avoid almost any assumption about the distribution of the population lifetimes, as well as the need of eliciting an infinite dimensional parameter (in case of lack of prior information), as it happens with the usual Dirichlet process prior. We show how such model can be used to derive robust inferences from right-censored lifetime data. Robustness is due to the identification of the decisions that are prior-dependent, and can be interpreted as an analysis of sensitivity with respect to the hypothetical inclusion of fictitious new samples in the data. In particular, we derive a nonparametric estimator of the survival probability and a hypothesis test about the probability that the lifetime of an individual from one population is shorter than the lifetime of an individual from another. We evaluate these ideas on simulated data and on the Australian AIDS survival dataset. The methods are publicly available through an easy-to-use R package.

Streaming variational inference for dirichlet process mixtures

Bayesian nonparametric models are theoretically suitable to learn streaming data due to their complexity relaxation to the volume of observed data. However, most of the existing variational inference algorithms are not applicable to streaming applications since they re-quire truncation on variational distributions. In this paper, we present two truncation-free variational algorithms, one for mix-membership inference called TFVB (truncation-free variational Bayes), and the other for hard clustering inference called TFME (truncation-free maximization expectation). With these algorithms, we further developed a streaming learning framework for the popular Dirichlet process mixture (DPM) models. Our ex-periments demonstrate the usefulness of our framework in both synthetic and real-world data.

Hierarchical dirichlet process for tracking complex topical structure evolution and its application to autism research literature

In this paper we describe a novel framework for the discovery of the topical content of a data corpus, and the tracking of its complex structural changes across the temporal dimension. In contrast to previous work our model does not impose a prior on the rate at which documents are added to the corpus nor does it adopt the Markovian assumption which overly restricts the type of changes that the model can capture. Our key technical contribution is a framework based on (i) discretization of time into epochs, (ii) epoch-wise topic discovery using a hierarchical Dirichlet process-based model, and (iii) a temporal similarity graph which allows for the modelling of complex topic changes: emergence and disappearance, evolution, splitting and merging. The power of the proposed framework is demonstrated on the medical literature corpus concerned with the autism spectrum disorder (ASD) - an increasingly important research subject of significant social and healthcare importance. In addition to the collected ASD literature corpus which we made freely available, our contributions also include two free online tools we built as aids to ASD researchers. These can be used for semantically meaningful navigation and searching, as well as knowledge discovery from this large and rapidly growing corpus of literature.

Dirichlet process mixture models with pairwise constraints for data clustering

The Dirichlet process mixture (DPM) model, a typical Bayesian nonparametric model, can infer the number of clusters automatically, and thus performing priority in data clustering. This paper investigates the influence of pairwise constraints in the DPM model. The pairwise constraint, known as two types: must-link (ML) and cannot-link (CL) constraints, indicates the relationship between two data points. We have proposed two relevant models which incorporate pairwise constraints: the constrained DPM (C-DPM) and the constrained DPM with selected constraints (SC-DPM). In C-DPM, the concept of chunklet is introduced. ML constraints are compiled into chunklets and CL constraints exist between chunklets. We derive the Gibbs sampling of the C-DPM based on chunklets. We further propose a principled approach to select the most useful constraints, which will be incorporated into the SC-DPM. We evaluate the proposed models based on three real datasets: 20 Newsgroups dataset, NUS-WIDE image dataset and Facebook comments datasets we collected by ourselves. Our SC-DPM performs priority in data clustering. In addition, our SC-DPM can be potentially used for short-text clustering.

A simultaneous extraction of context and community from pervasive signals using nested dirichlet process

Understanding user contexts and group structures plays a central role in pervasive computing. These contexts and community structures are complex to mine from data collected in the wild due to the unprecedented growth of data, noise, uncertainties and complexities. Typical existing approaches would first extract the latent patterns to explain human dynamics or behaviors and then use them as a way to consistently formulate numerical representations for community detection, often via a clustering method. While being able to capture high-order and complex representations, these two steps are performed separately. More importantly, they face a fundamental difficulty in determining the correct number of latent patterns and communities. This paper presents an approach that seamlessly addresses these challenges to simultaneously discover latent patterns and communities in a unified Bayesian nonparametric framework. Our Simultaneous Extraction of Context and Community (SECC) model roots in the nested Dirichlet process theory which allows a nested structure to be built to summarize data at multiple levels. We demonstrate our framework on five datasets where the advantages of the proposed approach are validated.