Topological approximate Bayesian computation for parameter inference of an angiogenesis model.
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Publication Date
2022-04-28Journal Title
Bioinformatics
ISSN
1367-4803
Publisher
Oxford University Press (OUP)
Type
Article
This Version
VoR
Physical Medium
Print-Electronic
Metadata
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Thorne, T., Kirk, P. D., & Harrington, H. A. (2022). Topological approximate Bayesian computation for parameter inference of an angiogenesis model.. Bioinformatics https://doi.org/10.1093/bioinformatics/btac118
Abstract
MOTIVATION: Inferring the parameters of models describing biological systems is an important problem in the reverse engineering of the mechanisms underlying these systems. Much work has focused on parameter inference of stochastic and ordinary differential equation models using Approximate Bayesian Computation (ABC). While there is some recent work on inference in spatial models, this remains an open problem. Simultaneously, advances in topological data analysis (TDA), a field of computational mathematics, have enabled spatial patterns in data to be characterized. RESULTS: Here, we focus on recent work using TDA to study different regimes of parameter space for a well-studied model of angiogenesis. We propose a method for combining TDA with ABC to infer parameters in the Anderson-Chaplain model of angiogenesis. We demonstrate that this topological approach outperforms ABC approaches that use simpler statistics based on spatial features of the data. This is a first step toward a general framework of spatial parameter inference for biological systems, for which there may be a variety of filtrations, vectorizations and summary statistics to be considered. AVAILABILITY AND IMPLEMENTATION: All code used to produce our results is available as a Snakemake workflow from github.com/tt104/tabc_angio.
Keywords
q-bio.QM, q-bio.QM, stat.ME
Sponsorship
European Commission Horizon 2020 (H2020) Societal Challenges (847912)
Identifiers
External DOI: https://doi.org/10.1093/bioinformatics/btac118
This record's URL: https://www.repository.cam.ac.uk/handle/1810/336812
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