Computational optimization of associative learning experiments.
With computational biology striving to provide more accurate theoretical accounts of biological systems, use of increasingly complex computational models seems inevitable. However, this trend engenders a challenge of optimal experimental design: due to the flexibility of complex models, it is diffic...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2020-01-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1007593 |
| _version_ | 1818735627917590528 |
|---|---|
| author | Filip Melinscak Dominik R Bach |
| author_facet | Filip Melinscak Dominik R Bach |
| author_sort | Filip Melinscak |
| collection | DOAJ |
| description | With computational biology striving to provide more accurate theoretical accounts of biological systems, use of increasingly complex computational models seems inevitable. However, this trend engenders a challenge of optimal experimental design: due to the flexibility of complex models, it is difficult to intuitively design experiments that will efficiently expose differences between candidate models or allow accurate estimation of their parameters. This challenge is well exemplified in associative learning research. Associative learning theory has a rich tradition of computational modeling, resulting in a growing space of increasingly complex models, which in turn renders manual design of informative experiments difficult. Here we propose a novel method for computational optimization of associative learning experiments. We first formalize associative learning experiments using a low number of tunable design variables, to make optimization tractable. Next, we combine simulation-based Bayesian experimental design with Bayesian optimization to arrive at a flexible method of tuning design variables. Finally, we validate the proposed method through extensive simulations covering both the objectives of accurate parameter estimation and model selection. The validation results show that computationally optimized experimental designs have the potential to substantially improve upon manual designs drawn from the literature, even when prior information guiding the optimization is scarce. Computational optimization of experiments may help address recent concerns over reproducibility by increasing the expected utility of studies, and it may even incentivize practices such as study pre-registration, since optimization requires a pre-specified analysis plan. Moreover, design optimization has the potential not only to improve basic research in domains such as associative learning, but also to play an important role in translational research. For example, design of behavioral and physiological diagnostic tests in the nascent field of computational psychiatry could benefit from an optimization-based approach, similar to the one presented here. |
| first_indexed | 2024-12-18T00:24:16Z |
| format | Article |
| id | doaj.art-1b99ba2ff675437dabad30c432faef5e |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-18T00:24:16Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-1b99ba2ff675437dabad30c432faef5e2022-12-21T21:27:17ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-01-01161e100759310.1371/journal.pcbi.1007593Computational optimization of associative learning experiments.Filip MelinscakDominik R BachWith computational biology striving to provide more accurate theoretical accounts of biological systems, use of increasingly complex computational models seems inevitable. However, this trend engenders a challenge of optimal experimental design: due to the flexibility of complex models, it is difficult to intuitively design experiments that will efficiently expose differences between candidate models or allow accurate estimation of their parameters. This challenge is well exemplified in associative learning research. Associative learning theory has a rich tradition of computational modeling, resulting in a growing space of increasingly complex models, which in turn renders manual design of informative experiments difficult. Here we propose a novel method for computational optimization of associative learning experiments. We first formalize associative learning experiments using a low number of tunable design variables, to make optimization tractable. Next, we combine simulation-based Bayesian experimental design with Bayesian optimization to arrive at a flexible method of tuning design variables. Finally, we validate the proposed method through extensive simulations covering both the objectives of accurate parameter estimation and model selection. The validation results show that computationally optimized experimental designs have the potential to substantially improve upon manual designs drawn from the literature, even when prior information guiding the optimization is scarce. Computational optimization of experiments may help address recent concerns over reproducibility by increasing the expected utility of studies, and it may even incentivize practices such as study pre-registration, since optimization requires a pre-specified analysis plan. Moreover, design optimization has the potential not only to improve basic research in domains such as associative learning, but also to play an important role in translational research. For example, design of behavioral and physiological diagnostic tests in the nascent field of computational psychiatry could benefit from an optimization-based approach, similar to the one presented here.https://doi.org/10.1371/journal.pcbi.1007593 |
| spellingShingle | Filip Melinscak Dominik R Bach Computational optimization of associative learning experiments. PLoS Computational Biology |
| title | Computational optimization of associative learning experiments. |
| title_full | Computational optimization of associative learning experiments. |
| title_fullStr | Computational optimization of associative learning experiments. |
| title_full_unstemmed | Computational optimization of associative learning experiments. |
| title_short | Computational optimization of associative learning experiments. |
| title_sort | computational optimization of associative learning experiments |
| url | https://doi.org/10.1371/journal.pcbi.1007593 |
| work_keys_str_mv | AT filipmelinscak computationaloptimizationofassociativelearningexperiments AT dominikrbach computationaloptimizationofassociativelearningexperiments |