Incremental parameter estimation of kinetic metabolic network models
Abstract Background An efficient and reliable parameter estimation method is essential for the creation of biological models using ordinary differential equation (ODE). Most of the existing estimation methods involve finding the global minimum of data fitting residuals over the entire parameter spac...
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| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2013
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| Online Access: | http://hdl.handle.net/1721.1/77143 https://orcid.org/0000-0001-6909-4568 |
| _version_ | 1811084528517644288 |
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| author | Jia, Gengjie Stephanopoulos, Gregory Gunawan, Rudiyanto |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Jia, Gengjie Stephanopoulos, Gregory Gunawan, Rudiyanto |
| author_sort | Jia, Gengjie |
| collection | MIT |
| description | Abstract Background An efficient and reliable parameter estimation method is essential for the creation of biological models using ordinary differential equation (ODE). Most of the existing estimation methods involve finding the global minimum of data fitting residuals over the entire parameter space simultaneously. Unfortunately, the associated computational requirement often becomes prohibitively high due to the large number of parameters and the lack of complete parameter identifiability (i.e. not all parameters can be uniquely identified). Results In this work, an incremental approach was applied to the parameter estimation of ODE models from concentration time profiles. Particularly, the method was developed to address a commonly encountered circumstance in the modeling of metabolic networks, where the number of metabolic fluxes (reaction rates) exceeds that of metabolites (chemical species). Here, the minimization of model residuals was performed over a subset of the parameter space that is associated with the degrees of freedom in the dynamic flux estimation from the concentration time-slopes. The efficacy of this method was demonstrated using two generalized mass action (GMA) models, where the method significantly outperformed single-step estimations. In addition, an extension of the estimation method to handle missing data is also presented. Conclusions The proposed incremental estimation method is able to tackle the issue on the lack of complete parameter identifiability and to significantly reduce the computational efforts in estimating model parameters, which will facilitate kinetic modeling of genome-scale cellular metabolism in the future. |
| first_indexed | 2024-09-23T12:52:24Z |
| format | Article |
| id | mit-1721.1/77143 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T12:52:24Z |
| publishDate | 2013 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/771432022-09-28T10:37:02Z Incremental parameter estimation of kinetic metabolic network models Jia, Gengjie Stephanopoulos, Gregory Gunawan, Rudiyanto Massachusetts Institute of Technology. Department of Chemical Engineering Stephanopoulos, Gregory Abstract Background An efficient and reliable parameter estimation method is essential for the creation of biological models using ordinary differential equation (ODE). Most of the existing estimation methods involve finding the global minimum of data fitting residuals over the entire parameter space simultaneously. Unfortunately, the associated computational requirement often becomes prohibitively high due to the large number of parameters and the lack of complete parameter identifiability (i.e. not all parameters can be uniquely identified). Results In this work, an incremental approach was applied to the parameter estimation of ODE models from concentration time profiles. Particularly, the method was developed to address a commonly encountered circumstance in the modeling of metabolic networks, where the number of metabolic fluxes (reaction rates) exceeds that of metabolites (chemical species). Here, the minimization of model residuals was performed over a subset of the parameter space that is associated with the degrees of freedom in the dynamic flux estimation from the concentration time-slopes. The efficacy of this method was demonstrated using two generalized mass action (GMA) models, where the method significantly outperformed single-step estimations. In addition, an extension of the estimation method to handle missing data is also presented. Conclusions The proposed incremental estimation method is able to tackle the issue on the lack of complete parameter identifiability and to significantly reduce the computational efforts in estimating model parameters, which will facilitate kinetic modeling of genome-scale cellular metabolism in the future. Singapore-MIT Alliance 2013-02-15T15:32:44Z 2013-02-15T15:32:44Z 2012-11 2012-06 2013-02-08T16:04:49Z Article http://purl.org/eprint/type/JournalArticle 1752-0509 http://hdl.handle.net/1721.1/77143 Jia, Gengjie, Gregory Stephanopoulos, and Rudiyanto Gunawan. “Incremental Parameter Estimation of Kinetic Metabolic Network Models.” BMC Systems Biology 6.1 (2012). https://orcid.org/0000-0001-6909-4568 en http://dx.doi.org/10.1186/1752-0509-6-142 BMC Systems Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 Gengjie Jia et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Jia, Gengjie Stephanopoulos, Gregory Gunawan, Rudiyanto Incremental parameter estimation of kinetic metabolic network models |
| title | Incremental parameter estimation of kinetic metabolic network models |
| title_full | Incremental parameter estimation of kinetic metabolic network models |
| title_fullStr | Incremental parameter estimation of kinetic metabolic network models |
| title_full_unstemmed | Incremental parameter estimation of kinetic metabolic network models |
| title_short | Incremental parameter estimation of kinetic metabolic network models |
| title_sort | incremental parameter estimation of kinetic metabolic network models |
| url | http://hdl.handle.net/1721.1/77143 https://orcid.org/0000-0001-6909-4568 |
| work_keys_str_mv | AT jiagengjie incrementalparameterestimationofkineticmetabolicnetworkmodels AT stephanopoulosgregory incrementalparameterestimationofkineticmetabolicnetworkmodels AT gunawanrudiyanto incrementalparameterestimationofkineticmetabolicnetworkmodels |