Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models

Jagiella N, Rickert D, Theis FJ, Hasenauer J (2017)

Publication Type: Journal article

Publication year: 2017

Journal

Cell Systems Elsevier

Book Volume: 4

Pages Range: 194-206.e9

Journal Issue: 2

DOI: 10.1016/j.cels.2016.12.002

Abstract

Mechanistic understanding of multi-scale biological processes, such as cell proliferation in a changing biological tissue, is readily facilitated by computational models. While tools exist to construct and simulate multi-scale models, the statistical inference of the unknown model parameters remains an open problem. Here, we present and benchmark a parallel approximate Bayesian computation sequential Monte Carlo (pABC SMC) algorithm, tailored for high-performance computing clusters. pABC SMC is fully automated and returns reliable parameter estimates and confidence intervals. By running the pABC SMC algorithm for ∼106 hr, we parameterize multi-scale models that accurately describe quantitative growth curves and histological data obtained in vivo from individual tumor spheroid growth in media droplets. The models capture the hybrid deterministic-stochastic behaviors of 105–106 of cells growing in a 3D dynamically changing nutrient environment. The pABC SMC algorithm reliably converges to a consistent set of parameters. Our study demonstrates a proof of principle for robust, data-driven modeling of multi-scale biological systems and the feasibility of multi-scale model parameterization through statistical inference.

Involved external institutions

Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE)

How to cite

APA:

Jagiella, N., Rickert, D., Theis, F.J., & Hasenauer, J. (2017). Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models. Cell Systems, 4(2), 194-206.e9. https://doi.org/10.1016/j.cels.2016.12.002

MLA:

Jagiella, Nick, et al. "Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models." Cell Systems 4.2 (2017): 194-206.e9.

BibTeX: Download