Physics-based ML for modelling stochastic reaction networks

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9 repositories

physics-based-ml.github.io
Public
Website for the organization
HTML
•0•0•0•0•Updated Jul 6, 2021Jul 6, 2021
LatticeGillespieCpp
Public
Gillespie Codes on Lattices in C++
simulations lattice gillespie gillespie-algorithm
Mathematica
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MIT License
•1•0•0•0•Updated Jul 6, 2021Jul 6, 2021
gillespie-cpp
Public
Simple as it gets Gillespie library in C++, as a stepping stone for your own Gillespie codes
gillespie gillespie-algorithm
Mathematica
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GNU General Public License v3.0
•1•0•0•0•Updated Jun 1, 2021Jun 1, 2021
DyBoltzReducedModelsPaper
Public
Code for paper: J. Chem. Phys. 149, 034107 (2018) (arXiv:1803.01063)
machine-learning modeling reaction-diffusion boltzmann-machines multiscale reaction-networks
Mathematica
•1•1•0•0•Updated Jun 1, 2021Jun 1, 2021
ReducedLotkaVolterra
Public
Code used in paper "Deep Learning Moment Closure Approximations using Dynamic Boltzmann Distributions" arXiv 1905.12122
machine-learning deep-learning reaction-network boltzmann-machines multiscale
Mathematica
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GNU General Public License v3.0
•1•0•0•0•Updated Jun 1, 2021Jun 1, 2021
DynamicBoltzmannPaper
Public
Code used in arXiv:1808.08630
machine-learning reaction-network reaction-diffusion boltzmann-machines multiscale moment-closure
Mathematica
•1•0•0•0•Updated Jun 1, 2021Jun 1, 2021
DynamicBoltzmann
Public
Dynamic Boltzmann Machine for Lattice Chemical Kinetics
machine-learning modeling simulations reaction-network boltzmann-machines multiscale gillespie
C++
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GNU General Public License v3.0
•1•0•0•0•Updated Jun 1, 2021Jun 1, 2021
physics-based-ml-reaction-networks
Public
Code for paper "Physics-based machine learning for modeling IP3 induced calcium oscillations" - DOI: 10.5281/zenodo.4839127
Mathematica
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MIT License
•1•1•0•0•Updated May 29, 2021May 29, 2021
sample-pairs-gaussian
Public
Python code to sample pairs of a given set of particles in n dims, where the probability for each pair is Gaussian
gaussian sampling mcmc
Python
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GNU General Public License v3.0
•1•0•0•0•Updated Aug 10, 2019Aug 10, 2019