3 papers
cs.DM2025
Continuous Petri Nets for Fast Yield Computation: Polynomial-Time and MILP Approaches
Addie Jordon, Juri KolÄák, Daniel Merkle
Petri nets provide accurate analogues to chemical reaction networks, with places representing individual molecules (the resources of the system) and transitions representing chemic…
cs.DM2025
Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks
Stefan Haar, Juri KolÄák
The analysis of biological networks has benefited from the richness of Boolean networks (BNs) and the associated theory. These results have been further fortified in recent years b…
cs.DM2024
Automated Inference of Graph Transformation Rules
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg +8
The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic system…