Linter

A list of things that should be checked by extending the libpetab-python PEtab v2 linter.

NN model via NN model YAML format

• NN inputs/outputs are valid/unique PEtab IDs (inputs and outputs can be the same PEtab ID if the NN does nothing -- this is fine)
• layers/activation functions are in this list: https://petab-sciml.readthedocs.io/latest/layers.html

Hybridization table

• targetIds are not also targetIds in the condition table
• targetIds are not also inputIds or parameterIds in the array data files
• NN inputs are not in targetValues
• NN outputs are not targetIds
• targetValues contain valid PEtab math expressions
• pre-initialization--hybridized NNs are evaluable (i.e. only depend on things that are available before simulation)

Condition table

• targetIds are not also inputIds or parameterIds in the array data files
• NN inputs are not in targetValues
• NN outputs are not targetIds

Array data files

• any input in the file must have an array defined for all initial PEtab conditions

Parameter table

• a parameter with nominalValue:=array must be defined by an array
• all parameters of the NN are explicitly specified to be estimated or fixed
• if posterior then all ML parameters require one of the following
  • a proper prior
  • finite bounds