Inference of cell dynamics on perturbation data using adjoint sensitivity

TL;DR

This paper extends the CellBox model inference approach to diverse biological systems by integrating adjoint sensitivity algorithms in Julia, demonstrating high predictive accuracy on simulated data and potential for real biological applications.

Contribution

The work adapts CellBox with adjoint algorithms in Julia, enabling efficient inference of cell dynamics across various biological systems.

Findings

High prediction accuracy on simulated data

Effective recovery of network structure in simulations

Potential applicability to real biological perturbation data

Abstract

Data-driven dynamic models of cell biology can be used to predict cell response to unseen perturbations. Recent work (CellBox) had demonstrated the derivation of interpretable models with explicit interaction terms, in which the parameters were optimized using machine learning techniques. While the previous work was tested only in a single biological setting, this work aims to extend the range of applicability of this model inference approach to a diversity of biological systems. Here we adapted CellBox in Julia differential programming and augmented the method with adjoint algorithms, which has recently been used in the context of neural ODEs. We trained the models using simulated data from both abstract and biology-inspired networks, which afford the ability to evaluate the recovery of the ground truth network structure. The resulting accuracy of prediction by these models is high both in terms of low error against data and excellent agreement with the network structure used for the simulated training data. While there is no analogous ground truth for real life biological systems, this work demonstrates the ability to construct and parameterize a considerable diversity of network models with high predictive ability. The expectation is that this kind of procedure can be used on real perturbation-response data to derive models applicable to diverse biological systems.