Cardiomyocyte emulator
This repository demonstrates the pretrained emulator of the paper Neural network emulation of the human ventricular cardiomyocyte action potential: a tool for more efficient computation in pharmacological studies, which can be found following the link: https://www.biorxiv.org/content/10.1101/2023.08.16.553497.
Installation
The repository provides a python package that can be installed using setuptools. Note that you need a valid python environment that can run the dependencies (pytorch among others). A possible way to ensure this is by using a python environments, such as venv or conda.
The installation itself can then by simple achieved by cloning the repo and installing it through
pip install .Usage example
import numpy as np
import matplotlib.pyplot as plt
from cardiomyocyte_emulator import load_default_emulator_model
emulator = load_default_emulator_model(device="cpu") #Load the pretrained emulator on the CPU
max_conds_default = emulator.max_conds_center #Use the default maximum conductances
t = np.linspace(-10, 500, num=200) #Create a time range which we will emulate
ap_emu = emulator.forward_latent_np(t, max_conds_default) #Emulation
plt.figure()
plt.plot(t, ap_emu[0])
plt.ylabel("$V_m(t)$ [mV]")
plt.xlabel("$t$ [ms]")
plt.show()
Demos
Additional demos are provided in the demos directory for more use cases. To run the demos, additional packages might be required, which can be installed through the command
pip install .[demos]The demos are provided as jupyter-notebooks
License
The package uses the open-source AGPL license.
Citation
If you use the software for scientific projects, please cite our associated publication
@misc{grandits_neural_2023,
title = {Neural network emulation of the human ventricular cardiomyocyte action potential: a tool for more efficient computation in pharmacological studies},
shorttitle = {Neural network emulation of the human ventricular cardiomyocyte action potential},
url = {https://www.biorxiv.org/content/10.1101/2023.08.16.553497},
doi = {10.1101/2023.08.16.553497},
language = {en},
urldate = {2023-08-18},
publisher = {bioRxiv},
author = {Grandits, Thomas and Augustin, Christoph M. and Haase, Gundolf and Jost, Norbert and Mirams, Gary R. and Niederer, Steven A. and Plank, Gernot and Varro, Andras and Virag, Laszlo and Jung, Alexander},
month = aug,
year = {2023}
}