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switchdyn-changepoints-parameters-identification

https://github.com/xiaomingfu2013/switchdyn-changepoints-parameters-identification

Science Score: 41.0%

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: biorxiv.org
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    Scientific vocabulary similarity
    Low similarity (7.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: xiaomingfu2013
  • Language: Julia
  • Default Branch: main
  • Size: 53.6 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme Citation

README.md

Simultaneous Identification of Changepoints and Model Parameters in Switching Dynamical Systems

This repository contains the code for the paper Xiaoming Fu et al. "Simultaneous Identification of Changepoints and Model Parameters in Switching Dynamical Systems" (2024). To run the code repository locally, please check the Project.toml file for the required packages and install them in your local Julia environment.

Structure

  • scripts/Bayesian_ChangePointStudy main scripts to run the Bayesian inference for the models in the paper.
  • scripts/plot_scripts scripts to generate the figures in the paper.
  • src main Julia code used to build the ode models, adjoint sensitivity analysis, and Bayesian inference. Some of the code that calculates gradient information of the parameters are adapted from the SciMLSensitivity.jl with copyright Copyright (c) 2016-2020: ChrisRackauckas, Julia Computing.
  • data directory to save the generated simulation data and the raw data from covid-19-data.
  • test directory to run the tests for the correctness of reverse-mode AD and the gradient calculation of the parameters.

Owner

  • Name: Xiaoming Fu
  • Login: xiaomingfu2013
  • Kind: user
  • Company: Helmholtz-Zentrum Dresden-Rossendorf

Currently post-doc at the Center for Advanced Systems Understanding (CASUS) and the Helmholtz-Zentrum Dresden-Rossendorf (HZDR)

Citation (CITATION.bib) 

@article {Fu2024Simultaneous,
	author = {Xiaoming Fu and Kai Fan and Heinrich Zozmann and Lennart Sch{\"u}ler and Justin M. Calabrese},
	title = {Simultaneous Identification of Changepoints and Model Parameters in Switching Dynamical Systems},
	elocation-id = {2024.01.30.577909},
	year = {2024},
	doi = {10.1101/2024.01.30.577909},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2024/02/01/2024.01.30.577909},
	eprint = {https://www.biorxiv.org/content/early/2024/02/01/2024.01.30.577909.full.pdf},
	journal = {bioRxiv}
}

GitHub Events

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Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v3 composite
  • julia-actions/cache v1 composite
  • julia-actions/julia-buildpkg v1 composite
  • julia-actions/setup-julia v1 composite
scripts/plots_scripts/poetry.lock pypi
  • appnope 0.1.3
  • asttokens 2.4.1
  • cffi 1.16.0
  • colorama 0.4.6
  • comm 0.2.0
  • contourpy 1.2.0
  • cycler 0.12.1
  • debugpy 1.8.0
  • decorator 5.1.1
  • exceptiongroup 1.1.3
  • executing 2.0.1
  • fonttools 4.44.1
  • importlib-metadata 6.8.0
  • importlib-resources 6.1.1
  • ipykernel 6.26.0
  • ipython 8.17.2
  • jedi 0.19.1
  • joblib 1.3.2
  • jupyter-client 8.6.0
  • jupyter-core 5.5.0
  • kiwisolver 1.4.5
  • matplotlib 3.8.1
  • matplotlib-inline 0.1.6
  • nest-asyncio 1.5.8
  • numpy 1.26.2
  • packaging 23.2
  • pandas 2.1.3
  • parso 0.8.3
  • pexpect 4.8.0
  • pillow 10.1.0
  • platformdirs 4.0.0
  • prompt-toolkit 3.0.41
  • psutil 5.9.6
  • ptyprocess 0.7.0
  • pure-eval 0.2.2
  • pycparser 2.21
  • pygments 2.16.1
  • pyparsing 3.1.1
  • python-dateutil 2.8.2
  • pytz 2023.3.post1
  • pywin32 306
  • pyzmq 25.1.1
  • scikit-learn 1.3.2
  • scipy 1.11.3
  • seaborn 0.13.0
  • six 1.16.0
  • stack-data 0.6.3
  • threadpoolctl 3.2.0
  • tornado 6.3.3
  • traitlets 5.13.0
  • typing-extensions 4.8.0
  • tzdata 2023.3
  • wcwidth 0.2.10
  • zipp 3.17.0
scripts/plots_scripts/pyproject.toml pypi
  • ipykernel ^6.26.0 develop
  • matplotlib ^3.8.1
  • numpy ^1.26.2
  • pandas ^2.1.3
  • python >=3.9,<3.13
  • scikit-learn ^1.3.2
  • scipy ^1.11.3
  • seaborn ^0.13.0