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this is the repository for the code of the paper "Tensor-train approximation of the chemical master equation and its application for parameter inference"

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paper-cme-tt

This is the repository for the code of the paper "Tensor-train approximation of the chemical master equation and its application for parameter inference"

See here for an upgraded version

Requirements:

  • numpy (>=1.18.1)
  • ttpy (Intel MKL is recommended)
  • cython
  • scipy
  • matplotlib
  • tensorflow (>=2.0)
  • pickle
  • tikzplotlib

The scripts that produce the results from the paper are:

  • simplegene_tt_convergence.py for the time convergence of the seir model.
  • model_seir_tt.py for the solution of the SEIR model.
  • seir_filtering.py for the filtering and smoothing of the SEIR model.
  • simplegene_tt_convergence.py for the simple gene model time stepping convergence.
  • simple_gene_tt_4_param_projection.py for the Bayesian inference of the simple gene model.
  • simple_gene_tt_4_param_sweep.py for inference using the simple gene for different hyperparameters.
  • 3stage_param_projection.py for the 3 stage gene expression experiment.
  • model_SEIQR_param.py SEIQR experiment.

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this is the repository for the code of the paper "Tensor-train approximation of the chemical master equation and its application for parameter inference"

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