Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination.
Akman, Ozgur E
BMC Syst Biol
Springer Science and Business Media LLC
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Avramidis, E., & Akman, O. E. (2017). Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination.. BMC Syst Biol, 11 (1), 40. https://doi.org/10.1186/s12918-017-0416-2
BACKGROUND: Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis of normal and abnormal behaviour. In this study, we considered an existing neurobiological model of fast eye movements (saccades), capable of generating realistic simulations of: (i) normal horizontal saccades; and (ii) infantile nystagmus - pathological ocular oscillations that can be subdivided into different waveform classes. By developing appropriate fitness functions, we optimised the model to existing experimental saccade and nystagmus data, using a well-established multi-objective genetic algorithm. This algorithm required the model to be numerically integrated for very large numbers of parameter combinations. To address this computational bottleneck, we implemented a master-slave parallelisation, in which the model integrations were distributed across the compute units of a GPU, under the control of a CPU. RESULTS: While previous nystagmus fitting has been based on reproducing qualitative waveform characteristics, our optimisation protocol enabled us to perform the first direct fits of a model to experimental recordings. The fits to normal eye movements showed that although saccades of different amplitudes can be accurately simulated by individual parameter sets, a single set capable of fitting all amplitudes simultaneously cannot be determined. The fits to nystagmus oscillations systematically identified the parameter regimes in which the model can reproduce a number of canonical nystagmus waveforms to a high accuracy, whilst also identifying some waveforms that the model cannot simulate. Using a GPU to perform the model integrations yielded a speedup of around 20 compared to a high-end CPU. CONCLUSIONS: The results of both optimisation problems enabled us to quantify the predictive capacity of the model, suggesting specific modifications that could expand its repertoire of simulated behaviours. In addition, the optimal parameter distributions we obtained were consistent with previous computational studies that had proposed the saccadic braking signal to be the origin of the instability preceding the development of infantile nystagmus oscillations. Finally, the master-slave parallelisation method we developed to accelerate the optimisation process can be readily adapted to fit other highly parametrised computational biology models to experimental data.
Humans, Ocular Motility Disorders, Computational Biology, Saccades, Algorithms, Models, Biological, Time Factors, Computer Graphics, Infant
External DOI: https://doi.org/10.1186/s12918-017-0416-2
This record's URL: https://www.repository.cam.ac.uk/handle/1810/269512
Attribution 4.0 International
Licence URL: http://creativecommons.org/licenses/by/4.0/
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