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We investigate methods for learning partial differential equation (PDE) models from spatio-temporal data under biologically realistic levels and forms of noise. Recent progress in learning PDEs from data have used sparse regression to select candidate terms from a denoised set of data, including approximated partial derivatives. We analyse the performance in using previous methods to denoise data for the task of discovering the governing system of PDEs. We also develop a novel methodology that uses artificial neural networks (ANNs) to denoise data and approximate partial derivatives. We test the methodology on three PDE models for biological transport, i.e. the advection–diffusion, classical Fisher–Kolmogorov–Petrovsky–Piskunov (Fisher–KPP) and nonlinear Fisher–KPP equations. We show that the ANN methodology outperforms previous denoising methods, including finite differences and both local and global polynomial regression splines, in the ability to accurately approximate partial derivatives and learn the correct PDE model.
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Biologically-informed neural networks guide mechanistic modeling from sparse experimental data
Biologically-informed neural networks (BINNs), an extension of physics-informed neural networks [1], are introduced and used to discover the underlying dynamics of biological systems from sparse experimental data. In the present work, BINNs are trained in a supervised learning framework to approximate in vitro cell biology assay experiments while respecting a generalized form of the governing reaction-diffusion partial differential equation (PDE). By allowing the diffusion and reaction terms to be multilayer perceptrons (MLPs), the nonlinear forms of these terms can be learned while simultaneously converging to the solution of the governing PDE. Further, the trained MLPs are used to guide the selection of biologically interpretable mechanistic forms of the PDE terms which provides new insights into the biological and physical mechanisms that govern the dynamics of the observed system. The method is evaluated on sparse real-world data from wound healing assays with varying initial cell densities [2].
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- Award ID(s):
- 1838314
- PAR ID:
- 10302339
- Editor(s):
- Lavrik, Inna
- Date Published:
- Journal Name:
- PLOS Computational Biology
- Volume:
- 16
- Issue:
- 12
- ISSN:
- 1553-7358
- Page Range / eLocation ID:
- e1008462
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1371/journal.pcbi.1008462
