PNNL

Abstract

CellBox is a hybrid modeling framework that integrates machine-learning approaches with explicit mathematical modeling to determine the behavior of dynamical systems, intended for determining the complex interactions of molecule and phenotype within a cellular environment using perturbation/response-based data. The original work utilized analysis of a melanoma cell line, SK-Mel-133, which we sought to expand to and evaluate effectiveness in describing other nonlinear systems both within and outside of biology. We evaluated with two models. One model is based upon the free-fall of an object under a velocity-dependent drag force; this produced inherent perturbation/response data. The other model is based upon a form of mass-action molecular kinetics; for this, we ran the simulation to steady state in each species for each perturbation and select the steady state as input for CellBox. We determined that CellBox, outside of its original use case, can still strongly predict even non-biological dynamical systems in the small-perturbation regime, with r = 0.99977 to 0.85123, p > 0.05 for freefall. In addition, we performed a naïve comparison of CellBox network structure to known network structure in the mass-action model to assess accuracy.