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Non-mmcs sampling fails #117
Description
I noticed that when using generate_steady_states_no_multiphase() with any method except mmcs, you would get a zero-array of shape equal to the expected one - that's why the tests do not fail.
(base) u0156635@gbw-l-l0074:ext_data$ python
Python 3.9.5 | packaged by conda-forge | (default, Jun 19 2021, 00:32:32)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import dingo
>>> model = dingo.MetabolicNetwork.from_sbml("e_coli_core.xml")
>>> sampler = dingo.PolytopeSampler(model)
>>> samples = sampler.generate_steady_states_no_multiphase()
>>> samples
array([[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
...,
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]])
- OS: Ubuntu 24
Activity
fixes GeomScale#117
AyushDwi commentedon Oct 30, 2025
Hi @hariszaf! I'd like to work on fixing this issue for GSoC 2026.
I've reproduced the bug using e_coli_core.xml and confirmed that
non-mmcs methods return all zeros.
My plan:
Can you help me understand the intended behavior of each sampling method?
ChinmayRout9040895625 commentedon Dec 1, 2025
Hi @hariszaf! I looked into this issue, and I can reproduce the exact same behaviour:
MMCS sampling works correctly, so the failure seems isolated to the non-MMCS path.
so based on initial inspection, the problem is likely happening at the Cython/C++ wrapper layer:
In contrast, the MMCS path seems to correctly fill the output buffer.
What i plan to do -
Let me know if you would like a PR draft with these changes.
Thanks!
hariszaf commentedon Dec 1, 2025
Hi @ChinmayRout9040895625
Thanks for the interest on our project.
Do you still get this error after the cdcb43c commit?
ChinmayRout9040895625 commentedon Dec 1, 2025
I haven’t tested it after commit cdcb43c yet – the behaviour I described was from a build before that commit. I will do the changes (including cdcb43c), re-run the non-MMCS example, and report back here whether I can still reproduce the all-zero samples or if it’s fixed now.
ChinmayRout9040895625 commentedon Dec 1, 2025
Hi @hariszaf!, thanks for the pointer to cdcb43c.
I pulled the latest develop (including cdcb43c) and re-ran non-MMCS sampling with generate_steady_states_no_multiphase using:
model = MetabolicNetwork.from_sbml("ext_data/e_coli_core.xml")
sampler = PolytopeSampler(model)
steady_states = sampler.generate_steady_states_no_multiphase(
method="billiard_walk",
n=500,
burn_in=100,
thinning=2,
)
I still get a matrix with the correct shape, but all entries are zero (I checked with np.any(np.abs(steady_states) > 1e-12) which returns False).
So the generate_steady_states_no_multiphase is calling HPolytope.generate_samples(...) and directly using its return value, so the issue now seems to be in the implementation of HPolytope.generate_samples rather than PolytopeSampler.py.
I’m happy to dig into the Cython / volesti side if you’d like some help.
vissarion commentedon Dec 9, 2025
@ChinmayRout9040895625 sorry I cannot reproduce your issue. However, if the method is "mmcs" then indeed dingo returns a zero matrix. This is fixed in #122. See the tests in #122 for more details.
ChinmayRout9040895625 commentedon Dec 15, 2025
Thanks a lot for checking this and for the clarification!
That makes sense — I see now that the zero-matrix behaviour was specific to using "mmcs" via the non-multiphase path, and it’s great that this is already addressed in #122 (the tests there are very helpful as well).
Thanks again for the quick investigation and fix.
Please let me know if there’s any other issue, testing, or follow-up where I could help — I’d be happy to contribute
vissarion commentedon Jan 9, 2026
OK I am closing this one @hariszaf @ChinmayRout9040895625 feel free to reopen or open another issue if you find something that is not working.