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dc.contributor.authorKosarwal, Rahulen
dc.contributor.authorKulasiri, Gamalathge D.en
dc.contributor.authorSamarasinghe, Sandhyaen
dc.date.accessioned2021-01-12T21:26:29Z
dc.date.available2020-11-11en
dc.date.issued2020-11-11en
dc.date.submitted2020-07-17en
dc.identifier.issn1471-2105en
dc.identifier.urihttps://hdl.handle.net/10182/13202
dc.description.abstractBackground: Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizations. Most importantly, the exponential growth of the size of the state-space, with respect to the number of different species in the system makes this a challenging assignment. When the biochemical system has a large number of variables, the CME solution becomes intractable. We introduce the intelligent state projection (ISP) method to use in the stochastic analysis of these systems. For any biochemical reaction network, it is important to capture more than one moment: this allows one to describe the system’s dynamic behaviour. ISP is based on a state-space search and the data structure standards of artificial intelligence (AI). It can be used to explore and update the states of a biochemical system. To support the expansion in ISP, we also develop a Bayesian likelihood node projection (BLNP) function to predict the likelihood of the states. Results: To demonstrate the acceptability and effectiveness of our method, we apply the ISP method to several biological models discussed in prior literature. The results of our computational experiments reveal that the ISP method is effective both in terms of the speed and accuracy of the expansion, and the accuracy of the solution. This method also provides a better understanding of the state-space of the system in terms of blueprint patterns. Conclusions: The ISP is the de-novo method which addresses both accuracy and performance problems for CME solutions. It systematically expands the projection space based on predefined inputs. This ensures accuracy in the approximation and an exact analytical solution for the time of interest. The ISP was more effective both in predicting the behavior of the state-space of the system and in performance management, which is a vital step towards modeling large biochemical systems.en
dc.format.extent42en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relationThe original publication is available from - BioMed Central - https://doi.org/10.1186/s12859-020-03668-2 - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03668-2en
dc.relation.urihttps://doi.org/10.1186/s12859-020-03668-2en
dc.rights© The Author(s). 2020.en
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectbiochemical reaction networksen
dc.subjectchemical master equationen
dc.subjectstochasticen
dc.subjectintelligent state projectionen
dc.subjectBayesian likelihood node projectionen
dc.subjectBioinformaticsen
dc.subject.meshBayes Theoremen
dc.subject.meshMarkov Chainsen
dc.subject.meshStochastic Processesen
dc.subject.meshCatalysisen
dc.subject.meshModels, Biologicalen
dc.titleNovel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networksen
dc.typeJournal Article
lu.contributor.unitLincoln Universityen
lu.contributor.unitFaculty of Agriculture and Life Sciencesen
lu.contributor.unitDepartment of Wine, Food and Molecular Biosciencesen
lu.contributor.unitFaculty of Environment, Society and Designen
lu.contributor.unitDepartment of Environmental Managementen
dc.identifier.doi10.1186/s12859-020-03668-2en
dc.subject.anzsrc060102 Bioinformaticsen
dc.subject.anzsrc010406 Stochastic Analysis and Modellingen
dc.subject.anzsrc01 Mathematical Sciencesen
dc.subject.anzsrc06 Biological Sciencesen
dc.subject.anzsrc08 Information and Computing Sciencesen
dc.relation.isPartOfBMC Bioinformaticsen
pubs.organisational-group/LU
pubs.organisational-group/LU/Agriculture and Life Sciences
pubs.organisational-group/LU/Agriculture and Life Sciences/WFMB
pubs.organisational-group/LU/Faculty of Environment, Society and Design
pubs.organisational-group/LU/Faculty of Environment, Society and Design/DEM
pubs.organisational-group/LU/Research Management Office
pubs.organisational-group/LU/Research Management Office/QE18
pubs.publication-statusPublisheden
pubs.publisher-urlhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03668-2en
pubs.volume21en
dc.rights.licenceAttributionen
dc.rights.licenceAttributionen
lu.identifier.orcid0000-0001-8744-1578
lu.identifier.orcid0000-0003-2943-4331
pubs.article-number515en


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