Composing problem solvers for simulation experimentation: a case study on steady state estimation.
Simulation experiments involve various sub-tasks, e.g., parameter optimization, simulation execution, or output data analysis. Many algorithms can be applied to such tasks, but their performance depends on the given problem. Steady state estimation in systems biology is a typical example for this: s...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0091948 |
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| _version_ | 1849468682917380096 |
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| author | Stefan Leye Roland Ewald Adelinde M Uhrmacher |
| author_facet | Stefan Leye Roland Ewald Adelinde M Uhrmacher |
| author_sort | Stefan Leye |
| collection | DOAJ |
| description | Simulation experiments involve various sub-tasks, e.g., parameter optimization, simulation execution, or output data analysis. Many algorithms can be applied to such tasks, but their performance depends on the given problem. Steady state estimation in systems biology is a typical example for this: several estimators have been proposed, each with its own (dis-)advantages. Experimenters, therefore, must choose from the available options, even though they may not be aware of the consequences. To support those users, we propose a general scheme to aggregate such algorithms to so-called synthetic problem solvers, which exploit algorithm differences to improve overall performance. Our approach subsumes various aggregation mechanisms, supports automatic configuration from training data (e.g., via ensemble learning or portfolio selection), and extends the plugin system of the open source modeling and simulation framework James II. We show the benefits of our approach by applying it to steady state estimation for cell-biological models. |
| format | Article |
| id | doaj-art-a1a137a9b9b44d01b80f8a72646f22c4 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-a1a137a9b9b44d01b80f8a72646f22c42025-08-20T03:25:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9194810.1371/journal.pone.0091948Composing problem solvers for simulation experimentation: a case study on steady state estimation.Stefan LeyeRoland EwaldAdelinde M UhrmacherSimulation experiments involve various sub-tasks, e.g., parameter optimization, simulation execution, or output data analysis. Many algorithms can be applied to such tasks, but their performance depends on the given problem. Steady state estimation in systems biology is a typical example for this: several estimators have been proposed, each with its own (dis-)advantages. Experimenters, therefore, must choose from the available options, even though they may not be aware of the consequences. To support those users, we propose a general scheme to aggregate such algorithms to so-called synthetic problem solvers, which exploit algorithm differences to improve overall performance. Our approach subsumes various aggregation mechanisms, supports automatic configuration from training data (e.g., via ensemble learning or portfolio selection), and extends the plugin system of the open source modeling and simulation framework James II. We show the benefits of our approach by applying it to steady state estimation for cell-biological models.https://doi.org/10.1371/journal.pone.0091948 |
| spellingShingle | Stefan Leye Roland Ewald Adelinde M Uhrmacher Composing problem solvers for simulation experimentation: a case study on steady state estimation. PLoS ONE |
| title | Composing problem solvers for simulation experimentation: a case study on steady state estimation. |
| title_full | Composing problem solvers for simulation experimentation: a case study on steady state estimation. |
| title_fullStr | Composing problem solvers for simulation experimentation: a case study on steady state estimation. |
| title_full_unstemmed | Composing problem solvers for simulation experimentation: a case study on steady state estimation. |
| title_short | Composing problem solvers for simulation experimentation: a case study on steady state estimation. |
| title_sort | composing problem solvers for simulation experimentation a case study on steady state estimation |
| url | https://doi.org/10.1371/journal.pone.0091948 |
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