LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models

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dc.catalogadorgjm
dc.contributor.authorSaa Higuera, Pedro Andrés E.
dc.contributor.authorZapararte, Sebastian
dc.contributor.authorDrovandi, Christopher C.
dc.contributor.authorNielsen, Lars K.
dc.date.accessioned2024-01-08T16:17:34Z
dc.date.available2024-01-08T16:17:34Z
dc.date.issued2024
dc.date.updated2024-01-07T01:04:24Z
dc.description.abstractUniform random sampling of mass-balanced flux solutions offers an unbiased appraisal of the capabilities of metabolic networks. Unfortunately, it is impossible to avoid thermodynamically infeasible loops in flux samples when using convex samplers on large metabolic models. Current strategies for randomly sampling the non-convex loopless flux space display limited efficiency and lack theoretical guarantees. Results: Here, we present LooplessFluxSampler, an efficient algorithm for exploring the loopless mass-balanced flux solution space of metabolic models, based on an Adaptive Directions Sampling on a Box (ADSB) algorithm. ADSB is rooted in the general Adaptive Direction Sampling (ADS) framework, specifically the Parallel ADS, for which theoretical convergence and irreducibility results are available for sampling from arbitrary distributions. By sampling directions that adapt to the target distribution, ADSB traverses more efficiently the sample space achieving faster mixing than other methods. Importantly, the presented algorithm is guaranteed to target the uniform distribution over convex regions, and it provably converges on the latter distribution over more general (non-convex) regions provided the sample can have full support. Conclusions: LooplessFluxSampler enables scalable statistical inference of the loopless mass-balanced solution space of large metabolic models. Grounded in a theoretically sound framework, this toolbox provides not only efficient but also reliable results for exploring the properties of the almost surely non-convex loopless flux space. Finally, LooplessFluxSampler includes a Markov Chain diagnostics suite for assessing the quality of the final sample and the performance of the algorithm.
dc.fechaingreso.objetodigital2024-01-08
dc.format.extent8 páginas
dc.fuente.origenBiomed Central
dc.identifier.citationBMC Bioinformatics. 2024 Jan 02;25(1):3
dc.identifier.urihttps://doi.org/10.1186/s12859-023-05616-2
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/75645
dc.information.autorucEscuela de ingeniería; Saa Higuera, Pedro Andrés E.; 0000-0002-1659-9041; 162204
dc.information.autorucEscuela de ingeniería; Zapararte, Sebastián; S/I; 1025649
dc.issue.numero3
dc.language.isoen
dc.nota.accesoContenido completo
dc.revistaBMC Bioinformatics
dc.rightsacceso abierto
dc.rights.holderThe Author(s)
dc.rights.licenseCC BY 4.0 DEED Attribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleLooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models
dc.typeartículo
dc.volumen25
sipa.codpersvinculados162204
sipa.codpersvinculados1025649
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