SciML / SciML/StructuralIdentifiability.jl

*very* long identifiability runtime for relatively small model

Open
#419 5 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

enhancement
Dominant language
Julia
Stars
129
Forks
23
Avg merge
9h 35m
Merged PRs (30d)
17

Description

I have the following model:

ode = @ODEmodel(
    X'(t) = p - X(t),
    Y'(t) = -Y(t) + ((K1^3)*v1) / (K1^3 + X(t)^3),
    Z'(t) = -Z(t) + (v2*(Y(t)^3)*(X(t)^3)) / ((K2^3 + X(t)^3)*(K3^3 + Y(t)^3)),
    y(t) = Z(t)
)

for which the runtime of assess_identifiability is incredibly long. I.e.

assess_identifiability(ode)

takes at least 24 hours (I have not actually managed to complete it).

The model is essentially a incoherent feedforward loop (X deactives Y and activets Z, Y activates Z). In Catalyst it can be implemented like

rn = @reaction_network begin
    (p,1.0), 0 <--> X
    hillr(X, v1, K1, 3), 0 --> Y
    v2*hill(X, 1.0, K2, 3)*hill(Y, 1.0, K3, 3), 0 --> Z
    1.0, (Y,Z) --> 0
end

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce assess_identifiability(ode) with the Julia model in the issue and measure where the runtime is spent. Read the implementation of assess_identifiability and its identifiability analysis path, using the supplied incoherent feedforward-loop model as the test case. Done means the example completes in a practical, documented runtime without changing its identifiability result.

Written by the indexing model from the issue text.

Assessment

Tech stack
julia
Domain
performance
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.