IonBench: a benchmark of optimisation strategies for mathematical models of ion channel currents

Owen, Matt J.; Mirams, Gary R.

Abstract

Ion channel models present many challenging optimisation problems. These include unidentifiable parame- ters, noisy data, unobserved states, and a combination of both fast and slow timescales. This can make it difficult to choose a suitable optimisation routine a priori. Nevertheless, many attempts have been made to design optimisation routines specifically for ion channel models, however, little work has been done to compare these optimisation approaches. We have developed ionBench, an open-source optimisation bench- marking framework, to evaluate and compare these approaches against a standard set of ion channel optimisation problems. We included implementations of thirty-four unique optimisation approaches that have been previously applied to ion channel models and evaluated them against the ionBench test suite, consisting of five parameter optimisation problems derived from the cardiac ion channel literature. Each optimisation approach was initiated from multiple starting parameters and tasked with reproducing a problem-specific simulated dataset. Through ionBench, we tracked and evaluated the performance of these optimisations, identifying the expected run time until a successful optimisation for each approach, which was used for comparisons. Finally, we used these results, in addition to other literature results, to identify a new efficient approach. Its use could reduce computation time by multiple orders of magnitude, while also improving the reliability of ion channel parameter optimisation.

Citation

Owen, M. J., & Mirams, G. R. IonBench: a benchmark of optimisation strategies for mathematical models of ion channel currents

• Working Paper Type: Preprint
• Deposit Date: Mar 11, 2025
• Publicly Available Date: Mar 11, 2025
• DOI: https://doi.org/10.1101/2025.01.31.635876
• Public URL: https://nottingham-repository.worktribe.com/output/44825632