Cardinality optimization in constraint-based modelling: application to human metabolism
Abstract 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 fl...
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| Published in: | Bioinformatics (Oxford, England) Vol. 39; no. 9 |
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| Main Authors: | , , , , , |
| Format: | Journal Article |
| Language: | English |
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Oxford University Press
02.09.2023
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| ISSN: | 1367-4811, 1367-4803, 1367-4811 |
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| Abstract | Abstract
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_cardOpt with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolbox. |
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| AbstractList | 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.MOTIVATIONSeveral 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.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.RESULTSBy 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.Open source scripts to reproduce the results are here https://github.com/opencobra/COBRA.papers/2023_cardOpt with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolbox.AVAILABILITY AND IMPLEMENTATIONOpen source scripts to reproduce the results are here https://github.com/opencobra/COBRA.papers/2023_cardOpt with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolbox. Abstract 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_cardOpt with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolbox. |
| Author | Thiele, Ines Haraldsdottir, Hulda S Minh, Le Hoai Fleming, Ronan M T Vuong, Phan Tu Hankemeier, Thomas |
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| Cites_doi | 10.1093/bioinformatics/btab194 10.1038/nbt.4072 10.1038/nprot.2009.203 10.1038/nbt1492 10.1038/s41587-020-0446-y 10.1093/bioinformatics/btv096 10.1186/1471-2105-14-240 10.1038/nbt.3703 10.1198/016214501753382273 10.1093/bioinformatics/btn425 10.1016/j.sigpro.2007.08.015 10.1038/nbt.2488 10.1016/j.mib.2010.03.003 10.1109/78.738251 10.1111/j.1432-1033.2004.04213.x 10.1016/S0022-5193(85)80220-4 10.1038/s41596-019-0254-3 10.1038/srep40863 10.1073/pnas.0610772104 10.1016/j.cels.2017.01.010 10.1038/nbt.1614 10.1016/j.jtbi.2004.01.008 10.1371/journal.pcbi.1003424 10.1093/bioinformatics/btq679 10.1023/A:1009777410170 10.1186/1758-2946-6-2 10.1126/scisignal.aaz1482 10.1109/TIT.2003.820031 10.1371/journal.pcbi.1003195 10.1073/pnas.0603364103 10.1093/bioinformatics/btt059 10.1016/j.jtbi.2016.06.033 10.1016/j.bpc.2004.12.001 10.15252/msb.20198982 10.1111/j.2517-6161.1996.tb02080.x 10.1186/s12918-014-0110-6 10.1371/journal.pone.0045635 10.1038/ncomms4083 10.1038/s41596-018-0098-2 10.1016/S0304-3975(97)00115-1 10.1017/CBO9781139854610 10.1016/j.jtbi.2011.09.029 10.1093/bib/bbp011 10.1080/10618600.1998.10474784 10.1007/s11306-016-1051-4 10.1016/j.ejor.2014.11.031 |
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| References | Swainston (2023092306114835900_btad450-B44) 2016; 12 Herrgård (2023092306114835900_btad450-B19) 2008; 26 Beard (2023092306114835900_btad450-B2) 2004; 228 Meléndez-Hevia (2023092306114835900_btad450-B29) 1985; 117 Liu (2023092306114835900_btad450-B25) 2014; 8 Opdam (2023092306114835900_btad450-B32) 2017; 4 Tibshirani (2023092306114835900_btad450-B50) 1996; 58 Norsigian (2023092306114835900_btad450-B31) 2020; 15 Fan (2023092306114835900_btad450-B8) 2001; 96 Thiele (2023092306114835900_btad450-B49) 2020; 16 Gevorgyan (2023092306114835900_btad450-B13) 2008; 24 Duarte (2023092306114835900_btad450-B7) 2007; 104 Weston (2023092306114835900_btad450-B52) 2003; 3 Feist (2023092306114835900_btad450-B9) 2010; 13 Peleg (2023092306114835900_btad450-B35) 2008; 88 Reznik (2023092306114835900_btad450-B41) 2013; 9 Holzhütter (2023092306114835900_btad450-B21) 2004; 271 Orth (2023092306114835900_btad450-B33) 2010; 28 Bradley (2023092306114835900_btad450-B3) 1998 Fleming (2023092306114835900_btad450-B11) 2016; 409 Thiele (2023092306114835900_btad450-B45) 2010; 5 Thiele (2023092306114835900_btad450-B47) 2013; 31 Amaldi (2023092306114835900_btad450-B1) 1998; 209 Rao (2023092306114835900_btad450-B39) 1999; 47 Hoops (2023092306114835900_btad450-B22) 2006; 22 Qian (2023092306114835900_btad450-B37) 2005; 114 Magnúsdóttir (2023092306114835900_btad450-B27) 2017; 35 Reed (2023092306114835900_btad450-B40) 2006; 103 Hoai An (2023092306114835900_btad450-B20) 1998; 2 Haraldsdóttir (2023092306114835900_btad450-B17) 2014; 6 Brunk (2023092306114835900_btad450-B4) 2018; 36 Gribonval (2023092306114835900_btad450-B16) 2003; 49 Müller (2023092306114835900_btad450-B30) 2013; 29 Palsson (2023092306114835900_btad450-B34) 2015 Fu (2023092306114835900_btad450-B12) 1998; 7 Thiele (2023092306114835900_btad450-B48) 2014; 30 Sun (2023092306114835900_btad450-B43) 2013; 14 Vlassis (2023092306114835900_btad450-B51) 2014; 10 Ma (2023092306114835900_btad450-B26) 2017; 7 Pham Dinh (2023092306114835900_btad450-B36) 1997; 22 Le Thi (2023092306114835900_btad450-B23) 2015; 244 Lieven (2023092306114835900_btad450-B24) 2020; 38 Robinson (2023092306114835900_btad450-B42) 2020; 13 Chinneck (2023092306114835900_btad450-B5) 2008 Gollub (2023092306114835900_btad450-B15) 2021; 37 Mardinoglu (2023092306114835900_btad450-B28) 2014; 5 Desouki (2023092306114835900_btad450-B6) 2015; 31 Fleming (2023092306114835900_btad450-B10) 2012; 292 Gevorgyan (2023092306114835900_btad450-B14) 2011; 27 Thiele (2023092306114835900_btad450-B46) 2012; 7 Raman (2023092306114835900_btad450-B38) 2009; 10 Heirendt (2023092306114835900_btad450-B18) 2019; 14 |
| References_xml | – volume: 37 start-page: 2938 year: 2021 ident: 2023092306114835900_btad450-B15 article-title: Probabilistic thermodynamic analysis of metabolic networks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btab194 – volume: 36 start-page: 272 year: 2018 ident: 2023092306114835900_btad450-B4 article-title: Recon3D enables a three-dimensional view of gene variation in human metabolism publication-title: Nat Biotechnol doi: 10.1038/nbt.4072 – volume: 5 start-page: 93 year: 2010 ident: 2023092306114835900_btad450-B45 article-title: A protocol for generating a high-quality genome-scale metabolic reconstruction publication-title: Nat Protoc doi: 10.1038/nprot.2009.203 – volume: 3 start-page: 1439 year: 2003 ident: 2023092306114835900_btad450-B52 article-title: Use of the zero norm with linear models and kernel methods publication-title: J Mach Learn Res – volume: 26 start-page: 1155 year: 2008 ident: 2023092306114835900_btad450-B19 article-title: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology publication-title: Nat Biotechnol doi: 10.1038/nbt1492 – volume: 38 start-page: 272 year: 2020 ident: 2023092306114835900_btad450-B24 article-title: MEMOTE for standardized genome-scale metabolic model testing publication-title: Nat Biotechnol doi: 10.1038/s41587-020-0446-y – volume: 31 start-page: 2159 year: 2015 ident: 2023092306114835900_btad450-B6 article-title: CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv096 – volume: 30 start-page: 2529 year: 2014 ident: 2023092306114835900_btad450-B48 article-title: fastGapFill: efficient gap filling in metabolic networks publication-title: Bioinformatics (Oxford, England) – volume: 14 start-page: 240 year: 2013 ident: 2023092306114835900_btad450-B43 article-title: Robust flux balance analysis of multiscale biochemical reaction networks publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-240 – volume: 35 start-page: 81 year: 2017 ident: 2023092306114835900_btad450-B27 article-title: Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota publication-title: Nat Biotechnol doi: 10.1038/nbt.3703 – volume: 96 start-page: 1348 year: 2001 ident: 2023092306114835900_btad450-B8 article-title: Variable selection via nonconcave penalized likelihood and its oracle properties publication-title: J Am Stat Assoc doi: 10.1198/016214501753382273 – volume: 24 start-page: 2245 year: 2008 ident: 2023092306114835900_btad450-B13 article-title: Detection of stoichiometric inconsistencies in biomolecular models publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn425 – volume: 88 start-page: 375 year: 2008 ident: 2023092306114835900_btad450-B35 article-title: A bilinear formulation for vector sparsity optimization publication-title: Signal Process doi: 10.1016/j.sigpro.2007.08.015 – volume: 31 start-page: 419 year: 2013 ident: 2023092306114835900_btad450-B47 article-title: A community-driven global reconstruction of human metabolism publication-title: Nat Biotechnol doi: 10.1038/nbt.2488 – start-page: 82 year: 1998 ident: 2023092306114835900_btad450-B3 – volume: 13 start-page: 344 year: 2010 ident: 2023092306114835900_btad450-B9 article-title: The biomass objective function publication-title: Curr Opin Microbiol doi: 10.1016/j.mib.2010.03.003 – volume: 47 start-page: 187 year: 1999 ident: 2023092306114835900_btad450-B39 article-title: An affine scaling methodology for best basis selection publication-title: IEEE Trans Signal Process doi: 10.1109/78.738251 – volume: 271 start-page: 2905 year: 2004 ident: 2023092306114835900_btad450-B21 article-title: The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks publication-title: Eur J Biochem doi: 10.1111/j.1432-1033.2004.04213.x – volume: 117 start-page: 251 year: 1985 ident: 2023092306114835900_btad450-B29 article-title: The game of the pentose phosphate cycle publication-title: J Theor Biol doi: 10.1016/S0022-5193(85)80220-4 – volume: 15 start-page: 1 year: 2020 ident: 2023092306114835900_btad450-B31 article-title: A workflow for generating multi-strain genome-scale metabolic models of prokaryotes publication-title: Nat Protoc doi: 10.1038/s41596-019-0254-3 – volume: 7 start-page: srep40863 year: 2017 ident: 2023092306114835900_btad450-B26 article-title: Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression publication-title: Sci Rep doi: 10.1038/srep40863 – volume: 104 start-page: 1777 year: 2007 ident: 2023092306114835900_btad450-B7 article-title: Global reconstruction of the human metabolic network based on genomic and bibliomic data publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0610772104 – volume: 4 start-page: 318 year: 2017 ident: 2023092306114835900_btad450-B32 article-title: A systematic evaluation of methods for tailoring genome-scale metabolic models publication-title: Cell Syst doi: 10.1016/j.cels.2017.01.010 – volume: 22 start-page: 289 year: 1997 ident: 2023092306114835900_btad450-B36 article-title: Convex analysis approach to DC programming: theory, algorithms and applications publication-title: Acta Math Vietnamica – volume: 28 start-page: 245 year: 2010 ident: 2023092306114835900_btad450-B33 article-title: What is flux balance analysis? publication-title: Nat Biotechnol doi: 10.1038/nbt.1614 – volume: 228 start-page: 327 year: 2004 ident: 2023092306114835900_btad450-B2 article-title: Thermodynamic constraints for biochemical networks publication-title: J Theor Biol doi: 10.1016/j.jtbi.2004.01.008 – volume: 10 start-page: e1003424 year: 2014 ident: 2023092306114835900_btad450-B51 article-title: Fast reconstruction of compact context-specific metabolic network models publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1003424 – volume: 27 start-page: 433 year: 2011 ident: 2023092306114835900_btad450-B14 article-title: SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq679 – volume: 2 start-page: 9 year: 1998 ident: 2023092306114835900_btad450-B20 article-title: A combined D.C. Optimization—ellipsoidal branch-and-bound algorithm for solving nonconvex quadratic programming problems publication-title: J Combin Optim doi: 10.1023/A:1009777410170 – volume: 6 start-page: 2 year: 2014 ident: 2023092306114835900_btad450-B17 article-title: Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2 publication-title: J Cheminform doi: 10.1186/1758-2946-6-2 – volume: 13 start-page: eaaz1482 year: 2020 ident: 2023092306114835900_btad450-B42 article-title: An atlas of human metabolism publication-title: Sci Signal doi: 10.1126/scisignal.aaz1482 – volume: 49 start-page: 3320 year: 2003 ident: 2023092306114835900_btad450-B16 article-title: Sparse representations in unions of bases publication-title: IEEE Trans Inform Theory doi: 10.1109/TIT.2003.820031 – volume: 9 start-page: e1003195 year: 2013 ident: 2023092306114835900_btad450-B41 article-title: Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1003195 – volume: 103 start-page: 17480 year: 2006 ident: 2023092306114835900_btad450-B40 article-title: Systems approach to refining genome annotation publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0603364103 – volume: 29 start-page: 903 year: 2013 ident: 2023092306114835900_btad450-B30 article-title: Fast thermodynamically constrained flux variability analysis publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt059 – volume: 409 start-page: 1 year: 2016 ident: 2023092306114835900_btad450-B11 article-title: Conditions for duality between fluxes and concentrations in biochemical networks publication-title: J Theor Biol doi: 10.1016/j.jtbi.2016.06.033 – volume: 114 start-page: 213 year: 2005 ident: 2023092306114835900_btad450-B37 article-title: Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium publication-title: Biophys Chem doi: 10.1016/j.bpc.2004.12.001 – volume: 16 start-page: e8982 year: 2020 ident: 2023092306114835900_btad450-B49 article-title: Personalized whole-body models integrate metabolism, physiology, and the gut microbiome publication-title: Mol Syst Biol doi: 10.15252/msb.20198982 – volume-title: Feasibility and Infeasibility in Optimization: Algorithms and Computational Methods year: 2008 ident: 2023092306114835900_btad450-B5 – volume: 58 start-page: 267 year: 1996 ident: 2023092306114835900_btad450-B50 article-title: Regression shrinkage and selection via the lasso publication-title: J R Stat Soc Ser B (Methodological) doi: 10.1111/j.2517-6161.1996.tb02080.x – volume: 8 start-page: 110 year: 2014 ident: 2023092306114835900_btad450-B25 article-title: Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale publication-title: BMC Syst Biol doi: 10.1186/s12918-014-0110-6 – volume: 7 start-page: e45635 year: 2012 ident: 2023092306114835900_btad450-B46 article-title: Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage publication-title: PLoS One doi: 10.1371/journal.pone.0045635 – volume: 22 start-page: 3067 year: 2006 ident: 2023092306114835900_btad450-B22 article-title: COPASI–a COmplex PAthway SImulator publication-title: Bioinformatics (Oxford, England) – volume: 5 start-page: 3083 year: 2014 ident: 2023092306114835900_btad450-B28 article-title: Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease publication-title: Nat Commun doi: 10.1038/ncomms4083 – volume: 14 start-page: 639 year: 2019 ident: 2023092306114835900_btad450-B18 article-title: Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 publication-title: Nat Protoc doi: 10.1038/s41596-018-0098-2 – volume: 209 start-page: 237 year: 1998 ident: 2023092306114835900_btad450-B1 article-title: On the approximability of minimizing nonzero variables or unsatisfied relations in linear systems publication-title: Theor Comput Sci doi: 10.1016/S0304-3975(97)00115-1 – volume-title: Systems Biology: Constraint-Based Reconstruction and Analysis year: 2015 ident: 2023092306114835900_btad450-B34 doi: 10.1017/CBO9781139854610 – volume: 292 start-page: 71 year: 2012 ident: 2023092306114835900_btad450-B10 article-title: A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks publication-title: J Theor Biol doi: 10.1016/j.jtbi.2011.09.029 – volume: 10 start-page: 435 year: 2009 ident: 2023092306114835900_btad450-B38 article-title: Flux balance analysis of biological systems: applications and challenges publication-title: Brief Bioinform doi: 10.1093/bib/bbp011 – volume: 7 start-page: 397 year: 1998 ident: 2023092306114835900_btad450-B12 article-title: Penalized regressions: the bridge versus the lasso publication-title: J Comput Graph Stat doi: 10.1080/10618600.1998.10474784 – volume: 12 start-page: 109 year: 2016 ident: 2023092306114835900_btad450-B44 article-title: Recon 2.2: from reconstruction to model of human metabolism publication-title: Metabolomics doi: 10.1007/s11306-016-1051-4 – volume: 244 start-page: 26 year: 2015 ident: 2023092306114835900_btad450-B23 article-title: DC approximation approaches for sparse optimization publication-title: Eur J Operat Res doi: 10.1016/j.ejor.2014.11.031 |
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Several applications in constraint-based modelling can be mathematically formulated as cardinality optimization problems involving the... Several applications in constraint-based modelling can be mathematically formulated as cardinality optimization problems involving the minimization or... |
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