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SciML / Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
https://docs.sciml.ai/Catalyst/stable/
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Further decompostion of a system of ODEs coming from mass-action chemical reaction networks #1132

Open adhalanay opened 4 days ago

adhalanay commented 4 days ago

As suggested here I am opening an issue.

Is your feature request related to a problem? Please describe.

In the algebraic approach to mass action chemical reaction networks there is a very useful factorization of the RHS of the ODE system $$ \frac{dx}{dt}=Y\cdot A_k \cdot \Phi(x), $$ where $Y$ is the complex stoichiometric matrix, $A_k=-L_k$ and $\Phi(x)$ is the vector of monomials. In order to define $L_k$ consider the complex graph associated to the CRN as a weighted directed graph with reaction rates as weights and then $L_k$ is its Laplacian matrix.

While there is a function returning $Y$ I don't think there are functions for the other two factors. Describe the solution you’d like

It will be great to have exposed functions for the last factors: $A_k$ and $\Phi(x)$

Describe alternatives you’ve considered

For $A_k$ it will be maybe enough to have the weighted graph of complexes.

isaacsas commented 4 days ago

@vyudu do you want to add an API function for this?