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Multi-objective Bayesian Optimization with Heuristic Objectives for Biomedical and Molecular Data Analysis Workflows

Alina Selega, View ORCID ProfileKieran R. Campbell
doi: https://doi.org/10.1101/2022.06.08.495370
Alina Selega
1Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
2Vector Institute, Toronto, Canada
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Kieran R. Campbell
1Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
2Vector Institute, Toronto, Canada
3Departments of Molecular Genetics, Statistical Sciences, Computer Science, University of Toronto, Toronto, Canada
4Ontario Institute for Cancer Research, Toronto, Canada
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  • ORCID record for Kieran R. Campbell
  • For correspondence: kierancampbell@lunenfeld.ca
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Abstract

Many practical applications require optimization of multiple, computationally expensive, and possibly competing objectives that are well-suited for multi-objective Bayesian optimization (MOBO) procedures. However, for many types of biomedical data, measures of data analysis workflow success are often heuristic and therefore it is not known a priori which objectives are useful. Thus, MOBO methods that return the full Pareto front may be suboptimal in these cases. Here we propose a novel MOBO method that adaptively updates the scalarization function using properties of the posterior of a multi-output Gaussian process surrogate function. This approach selects useful objectives based on a flexible set of desirable criteria, allowing the functional form of each objective to guide optimization. We demonstrate the qualitative behaviour of our method on toy data and perform proof-of-concept analyses of single-cell RNA sequencing and highly multiplexed imaging datasets.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 12, 2022.
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Multi-objective Bayesian Optimization with Heuristic Objectives for Biomedical and Molecular Data Analysis Workflows
Alina Selega, Kieran R. Campbell
bioRxiv 2022.06.08.495370; doi: https://doi.org/10.1101/2022.06.08.495370
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Multi-objective Bayesian Optimization with Heuristic Objectives for Biomedical and Molecular Data Analysis Workflows
Alina Selega, Kieran R. Campbell
bioRxiv 2022.06.08.495370; doi: https://doi.org/10.1101/2022.06.08.495370

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