Transfer Learning Bayesian Optimization to Design Competitor DNA Molecules for Use in Diagnostic Assays

With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimiza...

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Bibliographic Details
Published in:arXiv.org 2024-10
Main Authors: Sedgwick, Ruby, Goertz, John P, Stevens, Molly M, Misener, Ruth, van der Wilk, Mark
Format: Article
Language:English
Subjects:
Bayesian analysis
Design optimization
Machine learning
Workflow
Online Access:Get full text
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Summary:With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimization. This paper presents a transfer learning design of experiments workflow to make this development feasible. By combining a transfer learning surrogate model with Bayesian optimization, we show how the total number of experiments can be reduced by sharing information between optimization tasks. We demonstrate the reduction in the number of experiments using data from the development of DNA competitors for use in an amplification-based diagnostic assay. We use cross-validation to compare the predictive accuracy of different transfer learning models, and then compare the performance of the models for both single objective and penalized optimization tasks.
ISSN:2331-8422