AutoReduce: An Automated Model Reduction Toolbox

AutoReduce banner

Python toolbox to obtain reduced model expressions using time-scale separation, conservation laws, sensitivity analysis, and projection-based interfaces to established reduction libraries.

Overview

AutoReduce is a Python package for automated model reduction of nonlinear dynamical systems. It provides tools for:

Automated model reduction using QSSA (Quasi-Steady State Approximation)
Conservation-law based reductions
Local sensitivity analysis
SBML import/export through python-libsbml
Integration with BioCRNPyler for synthetic biology models
Optional python-control and PyDMD interfaces

See the bioRxiv paper and International Journal of Robust and Nonlinear Control paper for the model-reduction background.

Quick Start

import numpy as np
from sympy import symbols

from autoreduce import System, solve_timescale_separation

S, C, P, k1, k2, k3, E_total = symbols("S C P k1 k2 k3 E_total")

E = E_total - C
x = [S, C, P]
f = [
    -k1 * E * S + k2 * C,
    k1 * E * S - (k2 + k3) * C,
    k3 * C,
]

system = System(
    x,
    f,
    params_dict={k1: 1.0, k2: 0.5, k3: 0.25, E_total: 1.0},
    x_init=[10.0, 0.0, 0.0],
    C=np.array([[1, 0, 0], [0, 0, 1]]),
)

reduced_system, collapsed_system = solve_timescale_separation(
    system,
    [S, P],
    fast_states=[C],
)

params_dict can be used to set, get, and update parameters:

system.set_param(k1, 2.0)
system.get_param(k1)
system.set_param_dict({k2: 1.0, k3: 0.1})

For more examples, check out the documentation.

Installation

Supported Python versions are 3.9 - 3.13.

Install the latest version of AutoReduce:

pip install autoreduce

Install with all optional dependencies:

pip install autoreduce[all]

Install optional integrations explicitly:

pip install "autoreduce[bio]"
pip install "autoreduce[control]"
pip install "autoreduce[dmd]"

For development installation:

git clone https://github.com/ayush9pandey/autoreduce.git
cd autoreduce
pip install -e ".[dev]"

Documentation

Full documentation is available at autoreduce.readthedocs.io.

Contributing

We welcome contributions. Developer notes and release instructions are in the documentation.

Contact

For questions, feedback, or suggestions, please contact:

Ayush Pandey (ayushpandey at ucmerced dot edu)
GitHub Issues

License

Released under the BSD 3-Clause License (see LICENSE)

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

autoreduce-0.9.tar.gz (1.7 MB view details)

Uploaded Aug 12, 2026 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

autoreduce-0.9-py3-none-any.whl (39.5 kB view details)

Uploaded Aug 12, 2026 Python 3

File details

Details for the file autoreduce-0.9.tar.gz.

File metadata

Download URL: autoreduce-0.9.tar.gz
Upload date: Aug 12, 2026
Size: 1.7 MB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for autoreduce-0.9.tar.gz
Algorithm	Hash digest
SHA256	`443989746fe540c0ff04dc34a422dfd2be7ee10ad497b7ee60ac14c675170c81`
MD5	`63a8559de72f4b2e84b5e87b97018a59`
BLAKE2b-256	`c6154da46532a4ece0d3d726cd6d3d380efcf50f108ddebdcf504883f01946df`

See more details on using hashes here.

Provenance

The following attestation bundles were made for autoreduce-0.9.tar.gz:

Publisher: pypi-deploy.yml on ctsd-lab/AutoReduce

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: autoreduce-0.9.tar.gz
- Subject digest: 443989746fe540c0ff04dc34a422dfd2be7ee10ad497b7ee60ac14c675170c81
- Sigstore transparency entry: 2428525687
- Sigstore integration time: Aug 12, 2026
Source repository:
- Permalink: ctsd-lab/AutoReduce@68c09a9015f6c28ba16d4228203a950df8a9265c
- Branch / Tag: refs/heads/main
- Owner: https://github.com/ctsd-lab
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: pypi-deploy.yml@68c09a9015f6c28ba16d4228203a950df8a9265c
- Trigger Event: workflow_dispatch