petab_sciml.problem_utils.neural_ode#

Functions

create_neural_ode(species_all[, ...])

Generate the PEtab files for a neural ODE problem with the given species.

create_neural_ode_problem(model_filename, ...)

Write the PEtab files needed for the neural ODE PEtab problem.
petab_sciml.problem_utils.neural_ode.create_neural_ode(species_all, model_filename='model.xml', network_name='net1', save_directory='.')[source]#

Generate the PEtab files for a neural ODE problem with the given species.

This function will generate the model, hybridization, mapping and parameter files.

Parameters:

  • species_all (Union[Iterable[str], dict]) – List of species names to include in the model, or a dictionary mapping species names to their initial values.

  • model_filename (str) – Name of the SBML file to create.

  • network_name (str) – Name of the neural network to reference in the PEtab files.

  • save_directory (str | Path) – Directory where the generated files will be saved.

Return type:

None

Returns:

None

petab_sciml.problem_utils.neural_ode.create_neural_ode_problem(model_filename, measurements_filename, observables_filename, network_filename, array_filenames, mapping_filenames=['mapping.tsv'], parameters_filename='parameters.tsv', hybridization_filenames=['hybridization.tsv'], save_directory='.')[source]#

Write the PEtab files needed for the neural ODE PEtab problem.

The mappings, parameters and hybridization files can be created using the create_neural_ode function. This function will create the conditions and problem.yaml files. The measurements and observables files need to be provided by the user.

Parameters:

  • model_filename (str) – Name of the SBML file to be referenced in the PEtab problem.

  • measurements_filename (str) – Name of the measurements TSV file to be referenced in the PEtab problem. This file should be located in the same directory where the remaining PEtab files are to be generated.

  • observables_filename (str) – Name of the observables TSV file to be created. This file should be located in the same directory where the remaining PEtab files are to be generated.

  • network_filename (str) – Name of the neural network YAML file defining the network architecture.

  • array_filenames (Iterable[str]) – List of names of array files to be referenced in the PEtab problem.

  • mapping_filenames (Iterable[str]) – List of names of mapping files to be referenced in the PEtab problem.

  • parameters_filename (str) – Name of the parameters TSV file to be referenced in the PEtab problem.

  • hybridization_filenames (Iterable[str]) – List of names of hybridization files to be referenced in the PEtab problem.

  • save_directory (str | Path) – Directory where the generated files will be saved.

Return type:

None

Returns:

None