Dataset Information

Comparison of Criteria for Choosing the Number of Classes in Bayesian Finite Mixture Models.

ABSTRACT: Identifying the number of classes in Bayesian finite mixture models is a challenging problem. Several criteria have been proposed, such as adaptations of the deviance information criterion, marginal likelihoods, Bayes factors, and reversible jump MCMC techniques. It was recently shown that in overfitted mixture models, the overfitted latent classes will asymptotically become empty under specific conditions for the prior of the class proportions. This result may be used to construct a criterion for finding the true number of latent classes, based on the removal of latent classes that have negligible proportions. Unlike some alternative criteria, this criterion can easily be implemented in complex statistical models such as latent class mixed-effects models and multivariate mixture models using standard Bayesian software. We performed an extensive simulation study to develop practical guidelines to determine the appropriate number of latent classes based on the posterior distribution of the class proportions, and to compare this criterion with alternative criteria. The performance of the proposed criterion is illustrated using a data set of repeatedly measured hemoglobin values of blood donors.

SUBMITTER: Nasserinejad K

PROVIDER: S-EPMC5231325 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Comparison of Criteria for Choosing the Number of Classes in Bayesian Finite Mixture Models.

Nasserinejad Kazem K van Rosmalen Joost J de Kort Wim W Lesaffre Emmanuel E

PloS one 20170112 1

Identifying the number of classes in Bayesian finite mixture models is a challenging problem. Several criteria have been proposed, such as adaptations of the deviance information criterion, marginal likelihoods, Bayes factors, and reversible jump MCMC techniques. It was recently shown that in overfitted mixture models, the overfitted latent classes will asymptotically become empty under specific conditions for the prior of the class proportions. This result may be used to construct a criterion f ...[more]

PMID: 28081166

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Project description:BackgroundCentral monitoring (CM), in which data across all clinical sites are monitored, has an important role in risk-based monitoring. Several statistical methods have been proposed to compare patient outcomes among the sites for detecting atypical sites that have different trends in observed data. These methods assume that the number of clinical sites is not small, e.g., 100 or more. In addition, the proportion of atypical sites is assumed to be relatively small. However, in actuality, the central statistical monitoring (CSM) has to be implemented in small or moderate sized clinical trials such as small phase II clinical trials. The number of sites is no longer large in such situations. Therefore, it is of concern that existing methods may not work efficiently in CM of small or moderate sized clinical trials. In the light of this problem, we propose a Bayesian CSM method to detect atypical sites as the robust method against the existence of atypical sites.MethodsWe use Bayesian finite mixture models (FMM) to model patient outcome values of both atypical and typical sites. In the method, the distributions of outcome values in normal sites are determined by choosing the body distribution, which has the largest mixture parameter value of finite mixture models based on the assumption that normal sites are in the majority. Atypical sites are detected by the criterion based on the posterior predictive distribution of normal site's outcome values derived from only the chosen body distribution.ResultsProposed method is evaluated by cumulative detection probability and type I error averaged over sites every round of CSM under the various scenarios, being compared with the conventional type analysis. If the total number of patients enrolled is 48, the proposed method is superior at least 10% for any shift sizes at the 2nd and the 3rd rounds. If the total number of patients is 96, both methods show similar detection probability for only one atypical site and large shift size. However, the proposed method is superior for the other scenarios. It is observed that all the type I errors averaged over sites are little difference between the methods at all the scenarios.ConclusionWe propose a Bayesian CSM method which works efficiently in a practical use of CM. It is shown that our method detects atypical sites with high probability regardless of the proportion of the atypical sites under the small clinical trial settings which is the target of our proposed method.

Project description:BackgroundCluster analysis is an integral part of precision medicine and systems biology, used to define groups of patients or biomolecules. Consensus clustering is an ensemble approach that is widely used in these areas, which combines the output from multiple runs of a non-deterministic clustering algorithm. Here we consider the application of consensus clustering to a broad class of heuristic clustering algorithms that can be derived from Bayesian mixture models (and extensions thereof) by adopting an early stopping criterion when performing sampling-based inference for these models. While the resulting approach is non-Bayesian, it inherits the usual benefits of consensus clustering, particularly in terms of computational scalability and providing assessments of clustering stability/robustness.ResultsIn simulation studies, we show that our approach can successfully uncover the target clustering structure, while also exploring different plausible clusterings of the data. We show that, when a parallel computation environment is available, our approach offers significant reductions in runtime compared to performing sampling-based Bayesian inference for the underlying model, while retaining many of the practical benefits of the Bayesian approach, such as exploring different numbers of clusters. We propose a heuristic to decide upon ensemble size and the early stopping criterion, and then apply consensus clustering to a clustering algorithm derived from a Bayesian integrative clustering method. We use the resulting approach to perform an integrative analysis of three 'omics datasets for budding yeast and find clusters of co-expressed genes with shared regulatory proteins. We validate these clusters using data external to the analysis.ConclustionsOur approach can be used as a wrapper for essentially any existing sampling-based Bayesian clustering implementation, and enables meaningful clustering analyses to be performed using such implementations, even when computational Bayesian inference is not feasible, e.g. due to poor exploration of the target density (often as a result of increasing numbers of features) or a limited computational budget that does not along sufficient samples to drawn from a single chain. This enables researchers to straightforwardly extend the applicability of existing software to much larger datasets, including implementations of sophisticated models such as those that jointly model multiple datasets.

Dataset Information

Comparison of Criteria for Choosing the Number of Classes in Bayesian Finite Mixture Models.

Publications

Comparison of Criteria for Choosing the Number of Classes in Bayesian Finite Mixture Models.

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