From data to QSP models: a pipeline for using Boolean networks for hypothesis inference and dynamic model building

Abstract

Quantitative Systems Pharmacology (QSP) models capture the physiological underpinnings driving the response to a drug and express those in a semi-mechanistic way, often involving ordinary differential equations (ODEs). The process of developing a QSP model generally starts with the definition of a set of reasonable hypotheses that would support a mechanistic interpretation of the expected response which are used to form a network of interacting elements. This is a hypothesis-driven and knowledge-driven approach, relying on prior information about the structure of the network. However, with recent advances in our ability to generate large datasets rapidly, often in a hypothesis-neutral manner, the opportunity emerges to explore data-driven approaches to establish the network topologies and models in a robust, repeatable manner. In this paper, we explore the possibility of developing complex network representations of physiological responses to pharmaceuticals using a logic-based analysis of available data and then convert the logic relations to dynamic ODE-based models. We discuss an integrated pipeline for converting data to QSP models. This pipeline includes using k-means clustering to binarize continuous data, inferring likely network relationships using a Best-Fit Extension method to create a Boolean network, and finally converting the Boolean network to a continuous ODE model. We utilized an existing QSP model for the dual-affinity re-targeting antibody flotetuzumab to demonstrate the robustness of the process. Key output variables from the QSP model were used to generate a continuous data set for use in the pipeline. This dataset was used to reconstruct a possible model. This reconstruction had no false-positive relationships, and the output of each of the species was similar to that of the original QSP model. This demonstrates the ability to accurately infer relationships in a hypothesis-neutral manner without prior knowledge of a system using this pipeline.

Keywords: Boolean network; Dynamic models; Machine learning; QSP.