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CVSX

Cardiovascular system models in JAX with Diffrax

Introduction

This repository contains code for the paper "A variable heart rate multi-compartmental coupled model of the cardiovascular and respiratory systems", submitted to Journal of the Royal Society Interface. The codebase is based on https://github.com/slishak/MedicalTimeSeriesPrediction, which was written for a previous MSc thesis; the main difference is that the implementation is now in JAX rather than PyTorch.

The work contains Python implementations of Smith's inertial/non-cardiovascular models [1] and Jallon's heart-lung model [2]. Parameters from Paeme [3] are also used. Three novel contributions are introduced in this work:

  1. Support for variable heart-rate in the form of a continuous function of time
  2. Stabilisation of Jallon's respiratory model
  3. Support for autodifferentiation through backpropagation (which is intended to enable more efficient parameter estimation)

Installation

Python 3.9+ is recommended for this work. JAX does not need to be compiled for the GPU; in fact, to run the basic examples, it will be faster on the CPU.

We suggest the use of a virtual environment (e.g. conda). The pyproject.toml file describes the dependencies. From within your virtual environment, you can run the following to install the package: pip install -e .

Following this, you can test the installation by running the following command, which will generate all plots in the paper: python examples/generate_paper_plots.py

Architecture

The module cvsx is a library for creating models of the cardiovascular system. It is laid out as follows:

  • cvs.cardiac_drivers defines a variety of functions $e(t)$ which simulate time-varying elasticity of the ventricles. They also allow the definition of a function $e(s \mod 1)$ where $\frac{ds}{dt} = {\rm HR}(t)$, which permits simulation of variable heart rate.
  • cvs.components defines basic componends of the cardiovascular system, for example PressureVolume compartments, BloodVessel, Valve etc. There are also some other more exotic valve configurations which are not covered in the paper.
  • cvs.models composes the components into full models that can be integrated with Diffrax. These are SmithCVS and JallonHeartLungs.
  • cvs.parameters defines parameterisations for the above models, in particular a function build_parameter_tree creates a parameterisation which can be used to instantiate a model.
  • cvs.respiratory contains the components required for simulation of the respiratory system, RespiratoryPatternGenerator and PassiveRespiratorySystem.
  • cvs.unit_conversions is a utility for converting between common units.

The function main in examples/simulate.py demonstrates parameterising and instantiating a model, and then simulating it with diffrax. There is a lot of extra functionality (e.g. parameter estimation, regurgitating valves) which is not yet officially supported, and will be modified in the future - please bear with us!

References

  1. Bram W Smith et al. ‘Minimal haemodynamic system model including ventricular interaction and valve dynamics’. en. In: Med. Eng. Phys. 26.2 (Mar. 2004), pp. 131–139.
  2. Julie Fontecave Jallon et al. ‘A model of mechanical interactions between heart and lungs’. In: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 367.1908 (2009), pp. 4741–4757. doi: 10.1098/rsta.2009.0137. eprint: url: https://royalsocietypublishing.org/doi/abs/10.1098/rsta.2009.0137.
  3. Sabine Paeme et al. ‘Mathematical multi-scale model of the cardiovascular system including mitral valve dynamics. Application to ischemic mitral insufficiency’. In: BioMedical Engineering OnLine 10.1 (Sept. 2011), p. 86. issn: 1475-925X. doi: 10.1186/1475-925X-10-86. url: https://doi.org/10.1186/1475-925X-10-86.