Linked Life Data

11023898

Source:http://linkedlifedata.com/resource/pubmed/id/11023898

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2000-11-13
pubmed:abstractText
Hidden Markov modeling (HMM) can be applied to extract single channel kinetics at signal-to-noise ratios that are too low for conventional analysis. There are two general HMM approaches: traditional Baum's reestimation and direct optimization. The optimization approach has the advantage that it optimizes the rate constants directly. This allows setting constraints on the rate constants, fitting multiple data sets across different experimental conditions, and handling nonstationary channels where the starting probability of the channel depends on the unknown kinetics. We present here an extension of this approach that addresses the additional issues of low-pass filtering and correlated noise. The filtering is modeled using a finite impulse response (FIR) filter applied to the underlying signal, and the noise correlation is accounted for using an autoregressive (AR) process. In addition to correlated background noise, the algorithm allows for excess open channel noise that can be white or correlated. To maximize the efficiency of the algorithm, we derive the analytical derivatives of the likelihood function with respect to all unknown model parameters. The search of the likelihood space is performed using a variable metric method. Extension of the algorithm to data containing multiple channels is described. Examples are presented that demonstrate the applicability and effectiveness of the algorithm. Practical issues such as the selection of appropriate noise AR orders are also discussed through examples.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-11023897, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-1379081, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-1698917, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-1701554, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-1702543, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-1703449, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-2471982, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-2852279, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-6311301, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-6317853, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-8608005, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-8770203, http://linkedlifedata.com/resource/pubmed/commentcorrection/11023898-9107053
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Oct
pubmed:issn
0006-3495
pubmed:author
pubmed:issnType
Print
pubmed:volume
79
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1928-44
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2000
pubmed:articleTitle
Hidden Markov modeling for single channel kinetics with filtering and correlated noise.
pubmed:affiliation
Department of Physiology and Biophysical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA. qin@acsu.buffalo.edu
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't, Evaluation Studies