Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages.
Bioinformatics
; 25(21): 2824-30, 2009 Nov 01.
Article
en En
| MEDLINE
| ID: mdl-19628503
ABSTRACT
MOTIVATION Human pluripotent stem cell lines persist in culture as a heterogeneous population of SSEA3 positive and SSEA3 negative cells. Tracking individual stem cells in real time can elucidate the kinetics of cells switching between the SSEA3 positive and negative substates. However, identifying a cell's substate at all time points within a cell lineage tree is technically difficult. RESULTS:
A variational Bayesian Expectation Maximization (EM) with smoothed probabilities (VBEMS) algorithm for hidden Markov trees (HMT) is proposed for incomplete tree structured data. The full posterior of the HMT parameters is determined and the underflow problems associated with previous algorithms are eliminated. Example results for the prediction of the types of cells in synthetic and real stem cell lineage trees are presented.AVAILABILITY:
The Matlab code for the VBEMS algorithm is freely available at http//www.acse.dept.shef.ac.uk/repository/vbems_lineage_tree/VBEMS.ZIP CONTACT visakan@sheffield.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Cadenas de Markov
/
Teorema de Bayes
/
Células Madre Pluripotentes
Tipo de estudio:
Health_economic_evaluation
/
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2009
Tipo del documento:
Article
País de afiliación:
Reino Unido