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Bayesian inference in aggregated hidden Markov models
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
2015 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Single molecule experiments study the kinetics of molecular biological systems. Many such studies generate data that can be described by aggregated hidden Markov models, whereby there is a need of doing inference on such data and models. In this study, model selection in aggregated Hidden Markov models was performed with a criterion of maximum Bayesian evidence. Variational Bayes inference was seen to underestimate the evidence for aggregated model fits. Estimation of the evidence integral by brute force Monte Carlo integration theoretically always converges to the correct value, but it converges in far from tractable time. Nested sampling is a promising method for solving this problem by doing faster Monte Carlo integration, but it was here seen to have difficulties generating uncorrelated samples.

Place, publisher, year, edition, pages
2015. , 54 p.
Series
UPTEC X, 15 001
Keyword [en]
Bayesian inference, aggregated hidden Markov models, model selection, variational Bayes, nested sampling, single molecule data
National Category
Biophysics Other Computer and Information Science
Identifiers
URN: urn:nbn:se:uu:diva-243090OAI: oai:DiVA.org:uu-243090DiVA: diva2:785947
Educational program
Molecular Biotechnology Engineering Programme
Supervisors
Examiners
Available from: 2015-02-04 Created: 2015-02-04 Last updated: 2015-02-04Bibliographically approved

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf