symident
Structural identifiability of ODE models by Lie symmetries over finite fields.
symident finds the non-identifiable directions of an ODE model with observables, conditions and events, returns them as exact generators where possible, and reduces the model to identifiable parameters. The observability rank is computed modulo primes in a C++ kernel; closed forms are reconstructed by sparse interpolation and verified at fresh primes.
Installation
pip install git+https://github.com/dModverse/symident
This builds from source and needs a C++17 compiler and CMake; with OpenMP the kernel runs
on several threads. Once symident is on PyPI, pip install symident installs a wheel.
Wheels are built for Linux (x86_64, aarch64; tested on Ubuntu, Debian and Fedora), macOS
(x86_64, arm64) and Windows (x86_64).
Steady-state analyses (equilibrate=True) whose resting state is a coupled nonlinear
polynomial system use msolve. On Linux and macOS
import symident
symident.install_msolve()
builds it with GMP, MPFR and FLINT into a per-user cache (needs a C compiler, make, m4
and curl or wget), where symident finds it. Alternatively point SYMIDENT_MSOLVE at an
msolve executable; on Windows that is the only way.
Example
import symident as si
m = si.Model({"A": "-k1*A", "B": "k1*A - k2*B"}, {"y": "s*B"})
res = si.detect(m, reconstruct=True)
print(res)
#> Result: rank 4 / 5 | 1 non-identifiable direction
res.symmetries[0].generator
#> {'A': 'A', 'B': 'B', 's': '-s'}
print(res.reduce())
#> Reduced 1 of 1 direction.
#> Trafo (non-identity entries)
#> A = 1
Interface
Model(odes, observables, ...) |
ODEs or a reaction network, observables, trafo, conditions, events, inputs, fixed |
detect(model, ...) |
rank, identifiability and the non-identifiable directions (Symmetries) |
reduce(result, ...), result.reduce() |
reparametrisation that removes the directions (Reduction) |
reconst_control(...) |
settings of the saturation and the reconstruction |
Both results print a report; summary() adds the computation details and
to_dict() returns the raw result.
Contact
Simon Beyer, simon.beyer@fdm.uni-freiburg.de. Requests for further functions in model equations, questions and bug reports are welcome by e-mail or as an issue; the supported functions are listed in the user guide.
License
MIT
1 maintainer
Metadata
1 maintainer
Release files for symident 0.9.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| symident-0.9.2.tar.gz | 347.8 kB | Details |
Built distributions (wheels)
Total release size: 14.5 MB
Release files / symident-0.9.2.tar.gz
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