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symident

wheels docs License: MIT

Structural identifiability of ODE models by Lie symmetries over finite fields.

symident finds the non-identifiable directions of an ODE model with observables, conditions, events and inputs, returns them as exact generators where possible, and reduces the model to identifiable parameters. The rank of the OIM is computed over F_p in a C++ kernel; closed forms are reconstructed by sparse interpolation and proven over Q, or checked at random points modulo a large prime, with an error bound where one applies.

Installation

pip install symident

Wheels are built for Linux (x86_64, aarch64, glibc 2.28 or newer; tested on Debian and Fedora), macOS (x86_64, arm64) and Windows (x86_64), for Python 3.10 to 3.14. Elsewhere pip builds from source, which needs a C++17 compiler and CMake; with OpenMP the kernel runs on several threads. The development version installs with pip install git+https://github.com/dModverse/symident.

Steady-state analyses whose resting states need a coupled nonlinear solve use msolve; on Linux and macOS symident.install_msolve() builds it into a per-user cache. The installation page covers Windows and other setups.

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
#>
#> Generators  X = Σᵢ ξ(i) ∂ᵢ
#>
#> Scalings:
#>   X₁  (exact)
#>       ξ(A) :  + A
#>       ξ(B) :  + B
#>       ξ(s) :  - s
#>
#> exact = proven over Q.
res.symmetries[0].generator
#> {'A': 'A', 'B': 'B', 's': '-s'}
print(res.reduce())
#> Reduced 1 of 1 direction.
#>
#> Trafo (non-identity entries)
#>   A = 1
#>
#> Sections:
#>   {X₁}  A = 1
#>   summary(detailed=True) explains each section.

Interface

Model(odes, observables, ...) ODEs or a reaction network with observables, conditions, events, inputs and switches
detect(model, ...) rank, identifiability and the non-identifiable directions (Symmetries)
reduce(result, ...), result.reduce() reparametrization that removes the directions (Reduction)
read_petab(path), Model.from_petab(path) a Model from a PEtab problem, format version 1 or 2 (pip install "symident[petab]")
reconst_control(...) settings of the saturation and the reconstruction
switches(...) diagnostic and route switches for a with block

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

Metadata

Release files for symident 0.11.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for symident 0.11.0
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symident-0.11.0.tar.gz 448.1 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for symident 0.11.0
File
symident-0.11.0-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details
symident-0.11.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
symident-0.11.0-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.14 CPython 3.14 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
symident-0.11.0-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
symident-0.11.0-cp314-cp314-macosx_10_15_x86_64.whl CPython 3.14 CPython 3.14 macOS 10.15+ x86-64 Details
symident-0.11.0-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details
symident-0.11.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 Details
symident-0.11.0-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
symident-0.11.0-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
symident-0.11.0-cp313-cp313-macosx_10_13_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
symident-0.11.0-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
symident-0.11.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
symident-0.11.0-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
symident-0.11.0-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
symident-0.11.0-cp312-cp312-macosx_10_13_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
symident-0.11.0-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
symident-0.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
symident-0.11.0-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
symident-0.11.0-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
symident-0.11.0-cp311-cp311-macosx_10_9_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
symident-0.11.0-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
symident-0.11.0-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
symident-0.11.0-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
symident-0.11.0-cp310-cp310-macosx_11_0_arm64.whl CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
symident-0.11.0-cp310-cp310-macosx_10_9_x86_64.whl CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details

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0.11.0 This release

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0.9.3

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0.9.2

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