دورية أكاديمية
Cardinality optimization in constraint-based modelling: application to human metabolism
| العنوان: | Cardinality optimization in constraint-based modelling: application to human metabolism |
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| المؤلفون: | Fleming, Ronan M T, Haraldsdottir, Hulda S, Minh, Le Hoai, Vuong, Phan Tu, Hankemeier, Thomas, Thiele, Ines |
| المساهمون: | Wren, Jonathan, the European Unions Horizon 2020 research, National Institute on Ageing |
| المصدر: | Bioinformatics ; volume 39, issue 9 ; ISSN 1367-4811 |
| بيانات النشر: | Oxford University Press (OUP) |
| سنة النشر: | 2023 |
| مصطلحات موضوعية: | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| الوصف: | Motivation Several applications in constraint-based modelling can be mathematically formulated as cardinality optimization problems involving the minimization or maximization of the number of nonzeros in a vector. These problems include testing for stoichiometric consistency, testing for flux consistency, testing for thermodynamic flux consistency, computing sparse solutions to flux balance analysis problems and computing the minimum number of constraints to relax to render an infeasible flux balance analysis problem feasible. Such cardinality optimization problems are computationally complex, with no known polynomial time algorithms capable of returning an exact and globally optimal solution. Results By approximating the zero-norm with nonconvex continuous functions, we reformulate a set of cardinality optimization problems in constraint-based modelling into a difference of convex functions. We implemented and numerically tested novel algorithms that approximately solve the reformulated problems using a sequence of convex programs. We applied these algorithms to various biochemical networks and demonstrate that our algorithms match or outperform existing related approaches. In particular, we illustrate the efficiency and practical utility of our algorithms for cardinality optimization problems that arise when extracting a model ready for thermodynamic flux balance analysis given a human metabolic reconstruction. Availability and implementation Open source scripts to reproduce the results are here https://github.com/opencobra/COBRA.papers/2023_cardOptTest with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolboxTest. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.1093/bioinformatics/btad450 |
| الإتاحة: | https://doi.org/10.1093/bioinformatics/btad450Test https://academic.oup.com/bioinformatics/article-pdf/39/9/btad450/51729460/btad450.pdfTest |
| حقوق: | https://creativecommons.org/licenses/by/4.0Test/ |
| رقم الانضمام: | edsbas.563CE16B |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/bioinformatics/btad450 |
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