Difference between revisions of "Performance of objective functions and optimization procedures for parameter estimation in system biology models"

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== Paper name ==
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Andrea Degasperi, Dirk Fey & Boris N. Kholodenko, [https://www.nature.com/articles/s41540-017-0023-2.pdf : Performance of objective functions and optimisation procedures for parameter estimation in system biology models], 2017, Systems Biology and Applications volume 3, Article number: 20
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=== Citation ===
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Andrea Degasperi, Dirk Fey & Boris N. Kholodenko, [https://www.nature.com/articles/s41540-017-0023-2.pdf Performance of objective functions and optimisation procedures for parameter estimation in system biology models], 2017, Systems Biology and Applications volume 3, Article number: 20
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=== Summary ===
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In systems biology, relative data are a common occurrence. In ODE-based models, this is regarded by either introducing scaling parameters or data-driven normalization to bring data and simulations onto the same scale. It was shown in this article, that data-driven normalization improves optimization performance and does not aggravate non-identifiability problems compared to a scaling factor approach. Furthermore, this article reports that hybrid optimization methods which combine stochastic global and deterministic local search outperforms deterministic local gradient-based strategies.
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=== Study outcomes ===
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==== Identifiability ====
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Employing data-driven normalization instead of scaling factors improved the identifiability of dynamic parameters, providing a computational example to demonstrate how this occurs.
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==== Convergence Speed ====
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As visualized in Fig. 4 and Fig. 5 of the original publication, convergence speed was consistently improved using data driven normalization compared to scaling factors. Combining the data-driven normalization with the hybrid optimization algorithm GLSDC provided the best performance results especially in high-parameter settings.
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=== Study design and evidence level ===
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* The provided claims are tested on 3 parameter estimation problems with varying amount of parameters.
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* The 3 main algorithms tested were GLSDC, LevMar SE, LevMar FD with scaling factors and data normalization each. These were tested in 96 runs each.
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* Although the previously best-performing method using LSQNONLIN with sensitivity equations as found in [[Lessons Learned from Quantitative Dynamical Modeling in Systems Biology]] has been mentioned, but a comparison with GLSDC was restricted to use of their implementation of the algorithm.
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* The study used Least-Squares instead of Likelihood as objective function, omitting error model fits.
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=== Further comments and aspects ===
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* Additionally to the performance advantages of not using scaling factors, it is also stated that the amount of overfitting is reduced.
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* The notion of practical identifiability does deviates from other literature, see for example e.g. [https://doi.org/10.1093/bioinformatics/btp358 Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood]
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* The objective function values in Fig. 4 and Fig. 5 are not entirely obvious to interpret, since stochastic algorithms and multi-start algorithms are analyzed.

Latest revision as of 13:38, 25 February 2020

1 Citation

Andrea Degasperi, Dirk Fey & Boris N. Kholodenko, Performance of objective functions and optimisation procedures for parameter estimation in system biology models, 2017, Systems Biology and Applications volume 3, Article number: 20

2 Summary

In systems biology, relative data are a common occurrence. In ODE-based models, this is regarded by either introducing scaling parameters or data-driven normalization to bring data and simulations onto the same scale. It was shown in this article, that data-driven normalization improves optimization performance and does not aggravate non-identifiability problems compared to a scaling factor approach. Furthermore, this article reports that hybrid optimization methods which combine stochastic global and deterministic local search outperforms deterministic local gradient-based strategies.

3 Study outcomes

3.1 Identifiability

Employing data-driven normalization instead of scaling factors improved the identifiability of dynamic parameters, providing a computational example to demonstrate how this occurs.

3.2 Convergence Speed

As visualized in Fig. 4 and Fig. 5 of the original publication, convergence speed was consistently improved using data driven normalization compared to scaling factors. Combining the data-driven normalization with the hybrid optimization algorithm GLSDC provided the best performance results especially in high-parameter settings.

4 Study design and evidence level

  • The provided claims are tested on 3 parameter estimation problems with varying amount of parameters.
  • The 3 main algorithms tested were GLSDC, LevMar SE, LevMar FD with scaling factors and data normalization each. These were tested in 96 runs each.
  • Although the previously best-performing method using LSQNONLIN with sensitivity equations as found in Lessons Learned from Quantitative Dynamical Modeling in Systems Biology has been mentioned, but a comparison with GLSDC was restricted to use of their implementation of the algorithm.
  • The study used Least-Squares instead of Likelihood as objective function, omitting error model fits.

5 Further comments and aspects