MSc Computational Statistics and Machine Learning, University College London

Modelling and prediction of medical time series from biophysical models and ICU data, using echo state networks (ESN) [1] and ensemble Kalman filters (AD-EnKF) [2].

Requires packages in requirements.txt and Python 3.9.

Currently requires custom branch of torchdiffeq, pending merge of rtqichen/torchdiffeq#210:

pip install git+https://github.com/slishak/torchdiffeq@manually-reject-step

Install torchinterp1d in the same way (only required for fitting biomechanical models with AD-EnKF):

pip install git+https://github.com/aliutkus/torchinterp1d

Two Python packages are included in this respository. time_series_prediction contains code that implements ESN and AD-EnKF with PyTorch. Example ODE problems are the Lorenz and Rössler attractors, and a forced Van der Pol oscillator. biomechanical_models contains Python implementations of Smith's inertial/non-cardiovascular models [3], and Jallon's heart-lung model [4]. Parameters from Paeme [5] are also used. These modules are documented with type hints and docstrings.

The examples folder contains various Python scripts and Jupyter notebooks which call code from the packages above. In VS Code, it is recommended to add the following snippet to your .vscode/settings.json file in order that the packages are visible on the Python path:

{
    "terminal.integrated.env.windows": {"PYTHONPATH": "${workspaceFolder}"}
}

The example scripts are not documented in as much detail as the implementation packages. Some key example scripts are:

• cvs_example.py: Simulate a cardiovascular system ODE model. Requires some commenting/uncommenting to choose the type of simulation to run.
• esn_hyperparameter_sweep.ipynb runs a large sweep of Echo State Networks on the example ODE problems with varied hyperparameters, and plots the results.
• esn_hyperparameter_sweep_jallon.ipynb does the same but using data from the Jallon heart-lung model
• enkf_activation.ipynb is an example sweep of activation function options when training an RNN with AD-EnKF on the three example ODE problems.
• enkf_jallon.ipynb tries to fit RNNs of two different architectures to data from the Jallon heart-lung model

1. Herbert Jaeger. ‘The “echo state” approach to analysing and training recurrent neural networks-with an erratum note’. In: Bonn, Germany: German National Research Center for Information Technology GMD Technical Report 148 (Jan. 2001).
2. Yuming Chen, Daniel Sanz-Alonso and Rebecca Willett. ‘Auto-differentiable Ensemble Kalman Filters’. In: SIAM Journal on Mathematics of Data Science 4.2 (2022), pp. 801–833. doi: 10.1137/21M1434477. url: https://doi.org/10.1137/21M1434477.
3. 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.
4. 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.
5. 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.