PEtab SciML - Scientific Machine Learning Format and Tooling

Version:

Source code: https://github.com/sebapersson/petab_sciml

User Guide

• Introduction
  • Highlights
  • Installation
  • How to read the documentation
  • Why a SciML data format?
  • Getting Help with and Extending PEtab SciML
• Getting Started
  • Overview
  • Environment
  • Loading the PEtab problem
    • Model File
    • Neural Network File
    • Mapping Table
    • Hybridization Table
    • Parameters Table
    • Array inputs
    • Measurements, Observables and Conditions Tables
    • YAML File
  • Running Simulations
  • Next Steps
• Troubleshooting

How To Guides

• Networks setting ODE parameters
  • Loading the PEtab problem
    • Array input data
    • Network Architecture
    • Parameterizing network inputs
• Observable Formulae
  • Loading the PEtab problem
• Neural ODE
  • Defining the network architecture
  • Generating the PEtab files
  • Loading the PEtab problem

PEtab SciML file format

• Format Specification
  • High Level Overview
  • NN Model Format
    • NN model YAML format
  • Array data
    • Referencing array data
    • Array data file format
  • Mapping Table
    • modelEntityId syntax
    • Indexing
  • Hybridization Table
    • Detailed Field Description
    • Pre-initialization hybridization
    • Simulation hybridization
  • Parameter Table
    • Detailed Field Description
    • Bounds for NN parameters
    • Priors for NN parameters
  • Problem YAML File
  • Notes for developers
    • Alternative model and neural-network formats
    • Dealing with arrays
• Supported Layers and Activation Functions
  • Supported Activation Function
• Tutorial

Python package

• PEtab SciML Python API
  • petab_sciml
  • petab_sciml.standard
  • petab_sciml.problem_utils