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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
Assembly in Directed Hypergraphs
Christoph Flamm, Daniel Merkle, Peter F. Stadler
Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain min…
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…