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Sparse representation of stoichiometric matrices
functions and matrices in complex-based functions
#387
Conversation
adding SparseArrays dependency for sparse representations of `stoich` matrices
updating `stoichmat` functions and complex network functions for sparse representation
updating tests for sparse representation of `stoichmat` and complexesmat functions
update project.toml for sparsearrays
add using SparseArrays
stoichiometric matrices
functions and matrices in complex-based functions
I think |
@yewalenikhil65 have a deadline today for a report I need to submit -- I'll review both your PRs this weekend. (And yes, the conservation law methods should get a sparse version at some point too, but we can save that for a separate PR just to keep this easier to review.) |
No problem! |
@yewalenikhil65 take a look and let me know your thoughts on the changes. Mainly I made |
I also should have made all matrices have columns = reactions now. |
This looks nice, exactly how i imagined.. Thanks! Anyway, i will get back to fixing PR In ReactionNetworkImporters after you release new Catalyst version |
@@ -179,7 +179,7 @@ coefficient of the ith product within the jth reaction. | |||
Note: | |||
- Set sparse=true for a sparse matrix representation | |||
""" | |||
function prodstoichmat(::Type{SparseMatrixCSC{Int}}, rn::ReactionSystem; smap=speciesmap(rn)) | |||
function prodstoichmat(::Type{SparseMatrixCSC{Int,Int}}, rn::ReactionSystem; smap=speciesmap(rn)) |
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Is it good idea to be using SparseMatrixCSC{Int,Int}
entries ? i also remember some conversation thread in Catalyst issues to leave scope for non-integer stoichiometries later probablt in furture
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For now it's fine. When we get generalized stoichiometry we'll have to think about what to do here. We don't want it to be type Any
, so we may need some extra preprocessing to figure out the type, or we just error and don't allow these functions when there is symbolic stoichiometry.
I don't think this should be a big cost relative to computing the SNF, so using the transpose shouldn't be an issue. I think what @YingboMa was maybe suggesting is that we should implement and use the Bareiss method instead of SNF for finding the nullspace basis. |
from #386 (comment)
example. We use a second function argument of type
Bool
to switchsparsity
on or off. Default is dense representation as earlier, i.e.sparsity=false