Parameter estimation of ion current formulations requires hybrid optimization approach to be both accurate and reliable
Computational models of cardiac electrophysiology provided insights into arrhythmogenesis and paved the way towards tailored therapies in the last years. To fully leverage in-silico models in future research, these models need to be adapted to reflect pathologies, genetic alterations, or pharmacolog...
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| Hauptverfasser: | , , , , , , , , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
13 January 2016
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| In: |
Frontiers in Bioengineering and Biotechnology
Year: 2016, Jahrgang: 3 |
| ISSN: | 2296-4185 |
| DOI: | 10.3389/fbioe.2015.00209 |
| Online-Zugang: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.3389/fbioe.2015.00209 Verlag, lizenzpflichtig, Volltext: https://www.frontiersin.org/articles/10.3389/fbioe.2015.00209/full 
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| Verfasserangaben: | Axel Loewe, Mathias Wilhelms, Jochen Schmid, Mathias J. Krause, Fathima Fischer, Dierk Thomas, Eberhard P. Scholz, Olaf Dössel and Gunnar Seemann |
MARC
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| 245 | 1 | 0 | |a Parameter estimation of ion current formulations requires hybrid optimization approach to be both accurate and reliable |c Axel Loewe, Mathias Wilhelms, Jochen Schmid, Mathias J. Krause, Fathima Fischer, Dierk Thomas, Eberhard P. Scholz, Olaf Dössel and Gunnar Seemann |
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| 520 | |a Computational models of cardiac electrophysiology provided insights into arrhythmogenesis and paved the way towards tailored therapies in the last years. To fully leverage in-silico models in future research, these models need to be adapted to reflect pathologies, genetic alterations, or pharmacological effects, however. A common approach is to leave the structure of established models unaltered and estimate the values of a set of parameters. Today's high-throughput patch clamp data acquisition methods require robust, unsupervised algorithms that estimate parameters both accurate and reliably. In this work, two classes of optimization approaches are evaluated: gradient-based trust-region reflective and derivative-free particle swarm algorithms. Using synthetic input data and different ion current formulations from the Courtemanche et al. electrophysiological model of human atrial myocytes, we show that none of the two schemes alone succeeds to meet all requirements. Sequential combination of the two algorithms did improve the performance to some extent but not satisfactorily. Thus, we propose a novel hybrid approach coupling the two algorithms in each iteration. This hybrid approach yielded very accurate estimates with minimal dependency on the initial guess using synthetic input data for which a ground truth parameter set exists. When applied to measured data, the hybrid approach yielded the best fit, again with minimal variation. Using the proposed algorithm, a single run is sufficient to estimate the parameters. The degree of superiority over the other investigated algorithms in terms of accuracy and robustness depended on the type of current. In contrast to the non-hybrid approaches, the proposed method proved to be optimal for data of arbitrary signal to noise ratio. The hybrid algorithm proposed in this work provides an important tool to integrate experimental data into computational models both accurately and robustly allowing to assess the often non-intuitive consequences of ion channel-level changes on higher levels of integration. | ||
| 650 | 4 | |a Electrophysiology | |
| 650 | 4 | |a hybrid optimzation | |
| 650 | 4 | |a ionic currents | |
| 650 | 4 | |a parameter estimation | |
| 650 | 4 | |a Particle Swarm Optimization | |
| 650 | 4 | |a patch clamp | |
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| 700 | 1 | |a Schmid, Jochen |e VerfasserIn |4 aut | |
| 700 | 1 | |a Krause, Mathias J. |e VerfasserIn |4 aut | |
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| 700 | 1 | |a Seemann, Gunnar |e VerfasserIn |4 aut | |
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