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ParticleMDI: particle Monte Carlo methods for the cluster analysis of multiple datasets with applications to cancer subtype identification

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  • Nathan Cunningham

    (University of Warwick Coventry)

  • Jim E. Griffin

    (University College London)

  • David L. Wild

    (University of Warwick Coventry)

Abstract

We present a novel nonparametric Bayesian approach for performing cluster analysis in a context where observational units have data arising from multiple sources. Our approach uses a particle Gibbs sampler for inference in which cluster allocations are jointly updated using a conditional particle filter within a Gibbs sampler, improving the mixing of the MCMC chain. We develop several approaches to improving the computational performance of our algorithm. These methods can achieve greater than an order-of-magnitude improvement in performance at no cost to accuracy and can be applied more broadly to Bayesian inference for mixture models with a single dataset. We apply our algorithm to the discovery of risk cohorts amongst 243 patients presenting with kidney renal clear cell carcinoma, using samples from the Cancer Genome Atlas, for which there are gene expression, copy number variation, DNA methylation, protein expression and microRNA data. We identify 4 distinct consensus subtypes and show they are prognostic for survival rate ( $$p

Suggested Citation

  • Nathan Cunningham & Jim E. Griffin & David L. Wild, 2020. "ParticleMDI: particle Monte Carlo methods for the cluster analysis of multiple datasets with applications to cancer subtype identification," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 14(2), pages 463-484, June.
    • Handle: RePEc:spr:advdac:v:14:y:2020:i:2:d:10.1007_s11634-020-00401-y
    DOI: 10.1007/s11634-020-00401-y
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    References listed on IDEAS

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    1. Peter J. Green & Sylvia Richardson, 2001. "Modelling Heterogeneity With and Without the Dirichlet Process," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 28(2), pages 355-375, June.
    2. Christophe Andrieu & Arnaud Doucet & Roman Holenstein, 2010. "Particle Markov chain Monte Carlo methods," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(3), pages 269-342, June.
    3. Evelina Gabasova & John Reid & Lorenz Wernisch, 2017. "Clusternomics: Integrative context-dependent clustering for heterogeneous datasets," PLOS Computational Biology, Public Library of Science, vol. 13(10), pages 1-29, October.
    4. Nicolas Chopin, 2002. "A sequential particle filter method for static models," Biometrika, Biometrika Trust, vol. 89(3), pages 539-552, August.
    5. Huimin Li & Dong Han & Yawen Hou & Huilin Chen & Zheng Chen, 2015. "Statistical Inference Methods for Two Crossing Survival Curves: A Comparison of Methods," PLOS ONE, Public Library of Science, vol. 10(1), pages 1-18, January.
    6. Douglas Steinley & Michael Brusco, 2008. "Selection of Variables in Cluster Analysis: An Empirical Comparison of Eight Procedures," Psychometrika, Springer;The Psychometric Society, vol. 73(1), pages 125-144, March.
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    Cited by:

    1. Lingsong Meng & Dorina Avram & George Tseng & Zhiguang Huo, 2022. "Outcome‐guided sparse K‐means for disease subtype discovery via integrating phenotypic data with high‐dimensional transcriptomic data," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 71(2), pages 352-375, March.
    2. Veronica Distefano & Maria Mannone & Irene Poli, 2023. "Exploring Heterogeneity with Category and Cluster Analyses for Mixed Data," Stats, MDPI, vol. 6(3), pages 1-16, July.

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