structural_simplify fails on SDESystem

[sebapersson]

Describe the bug 🐞

structural_simplify fails on SDESystem generated from a Catalyst ReactionSystem.

Expected behavior

The code should not error.

Minimal Reproducible Example 👇

using ModelingToolkit, Catalyst

rn = @reaction_network begin
    kB, S + E --> SE
    kD, SE --> S + E
    kP, SE --> P + E
end

# Creating an ODEProblem works
u0 = [:S => 50.0, :E => 10.0, :SE => 0.0, :P => 0.0]
tspan = (0., 200.)
ps = [:kB => 0.01, :kD => 0.1, :kP => 0.1]
osys = structural_simplify(convert(ODESystem, rn))
ode = ODEProblem(osys, [50.0, 10.0, 0.0, 0.0], tspan, ps)

ssys = convert(SDESystem, rn)
structural_simplify(ssys)

Error & Stacktrace ⚠️

ERROR: This should never happen. Trying to set DataType with @NamedTuple{substitutions::ModelingToolkit.Substitutions}.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] #s335#288
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/abstractsystem.jl:1132 [inlined]
  [3] var"#s335#288"(::Any, obj::Any, patch::Any)
    @ ModelingToolkit ./none:0
  [4] (::Core.GeneratedFunctionStub)(::UInt64, ::LineNumberNode, ::Any, ::Vararg{Any})
    @ Core ./boot.jl:707
  [5] set
    @ ~/.julia/packages/Setfield/PdKfV/src/lens.jl:122 [inlined]
  [6] macro expansion
    @ ~/.julia/packages/Setfield/PdKfV/src/sugar.jl:197 [inlined]
  [7] tearing_reassemble(state::TearingState{…}, var_eq_matching::ModelingToolkit.BipartiteGraphs.Matching{…}, full_var_eq_matching::Nothing; simplify::Bool, mm::ModelingToolkit.SparseMatrixCLIL{…}, cse_hack::Bool, array_hack::Bool)
    @ ModelingToolkit.StructuralTransformations ~/.julia/packages/ModelingToolkit/0O7FS/src/structural_transformation/symbolics_tearing.jl:601
  [8] tearing_reassemble (repeats 2 times)
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/structural_transformation/symbolics_tearing.jl:240 [inlined]
  [9] #dummy_derivative#140
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/structural_transformation/symbolics_tearing.jl:839 [inlined]
 [10] _structural_simplify!(state::TearingState{…}, io::Nothing; simplify::Bool, check_consistency::Bool, fully_determined::Bool, warn_initialize_determined::Bool, dummy_derivative::Bool, kwargs::@Kwargs{…})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systemstructure.jl:701
 [11] _structural_simplify!
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systemstructure.jl:676 [inlined]
 [12] #structural_simplify!#1353
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systemstructure.jl:669 [inlined]
 [13] __structural_simplify(sys::SDESystem, io::Nothing; simplify::Bool, kwargs::@Kwargs{…})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:94
 [14] __structural_simplify
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:75 [inlined]
 [15] structural_simplify(sys::SDESystem, io::Nothing; simplify::Bool, split::Bool, allow_symbolic::Bool, allow_parameter::Bool, conservative::Bool, fully_determined::Bool, kwargs::@Kwargs{})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:33
 [16] structural_simplify
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:28 [inlined]
 [17] structural_simplify(sys::SDESystem)
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:28
 [18] top-level scope
    @ ~/Dropbox/PhD/tmp/test_fail/MVE.jl:17
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information):

• Output of using Pkg; Pkg.status()

  [479239e8] Catalyst v14.4.1
  [961ee093] ModelingToolkit v9.54.0

• Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)

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• Output of versioninfo()

Julia Version 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 8 × 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, tigerlake)
Threads: 4 default, 0 interactive, 2 GC (on 8 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 4

[sebapersson]

Ping @AayushSabharwal

[AayushSabharwal]

Right, thanks for the ping. I looked into this, and we support/test simplification of "stochastic ODEs" (for lack of a better name) created using @brownian. SDESystems can't be simplified this way. Since you're creating your SDEs through Catalyst, it's reasonable to assume Catalyst will do some simplification on its own. This happens during convert(SDESystem, rn). This specific system also doesn't change when passed through structural_simplify.

[sebapersson]

Thanks for looking into this! So it is not possible (or on the roadmap) to add structural_simplify for more generic SDESystem, and there is no other way to inline equations? Specifically, I am interested in inlinining equations on the form

x ~ ...

into the SDESystem, where x then appears in the model dynamics.

[AayushSabharwal]

I see. It's possible to round-trip through an equivalent ODESystem with @brownian variables instead of noise_eqs. I'll try and get this done soon. In the meantime, can I ask why you're going the SDESystem approach instead of using @brownian?

[sebapersson]

Great thanks!

The reason why I go via the SDESystem is because I want the Chemical Langevin Equation (CLE) for a model imported into a Catalyst ReactionSystem with SBMLImporter. The SDESystem (or SDEProblem which does not work here as I need to inline equations) is the only why I think it is possible to get the CLE (which is a SDE with non-diagonal noise). So in short, I do not think Catalyst works with @brownian.

[AayushSabharwal]

That makes sense