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...

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Bibliographic Details
Published in:PLoS computational biology Vol. 16; no. 1; p. e1007593
Main Authors: Melinscak, Filip, Bach, Dominik R.
Format: Journal Article
Language:English
Published: United States Public Library of Science 01.01.2020
Public Library of Science (PLoS)
Subjects:
Algorithms
Associative learning
Bayes Theorem
Bayesian analysis
Biology
Biology and Life Sciences
Computational Biology - methods
Computer applications
Computer Simulation
Datasets
Design of experiments
Design optimization
Diagnostic systems
Expected utility
Experimental design
Experiments
Humans
Learning theory
Mathematical models
Medical imaging
Methods
Models, Psychological
Neurosciences
Optimization
Parameter estimation
Physical Sciences
Psychiatry
Psychotherapy
Research and Analysis Methods
Research Design
Simulation
Social Sciences
Software
Utility functions
Switzerland
ISSN:1553-7358, 1553-734X, 1553-7358
Online Access:Get full text
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Summary: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.
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The authors have declared that no competing interests exist.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1007593