Contains the code to reproduce the analysis for the paper Universal differential equations for systems biology: Current state and open problems.
Feel free to reach out if you want to reproduce our results or use parts of the pipeline for your own work.
The application examples from the publication are referenced by the original authors@
- Glycolysis: Ruoff paper reference
- STAT5 dimerisation: Boehm paper reference
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problems.json: Each problem is listed with a short description and the interface between the mechanistic and ANN model components -
1_mechanistic_model: SBML, PEtab problem for each mechanistic, non-UDE model -
2_measurements: Store synthetic data; Funtions for data generation and loading -
3_start_points: Generate start points ($\theta_M$ and$\theta_{\text{ANN}}$ ) for optimisation, and sample hyperparameters for the UDE optimisation -
4_ude: Define the UDE model -
5_optimisation: Hyperparameter settings, scripts to run optimisation on cluster, optimisation results -
6_evaluate: Evaluation and visualisation of the results -
m_mechanistic_modeling: Reference results for the full ODE models