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stnmf

A fast and versatile implementation of spike-triggered non-negative matrix factorization (STNMF) based on accelerated/fast HALS algorithms

https://github.com/gollischlab/stnmf_with_afhals

Science Score: 57.0%

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    DOI references
    Found 4 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary

Keywords

hals neuroscience nmf nnsvd-lrc primate receptive-field retina stnmf subunits
Last synced: 6 months ago · JSON representation ·

Repository

A fast and versatile implementation of spike-triggered non-negative matrix factorization (STNMF) based on accelerated/fast HALS algorithms

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Topics
hals neuroscience nmf nnsvd-lrc primate receptive-field retina stnmf subunits
Created almost 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

STNMF with AF-HALS

Build status Documentation status PyPI version DOI

A fast and versatile implementation of spike-triggered non-negative matrix factorization (STNMF) based on accelerated fast hierarchical alternating least squares (AF-HALS) algorithms.

This Python package allows fast inference of receptive-field subunits from the spiking responses of retinal ganglion cells including methods of hyperparameter tuning.

Described in the paper:

Zapp SJ, Khani MH, Schreyer HM, Sridhar S, Ramakrishna V, Krüppel S, Protti DA, Mietsch M, Karamanlis D, Gollisch T (2024). Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina. bioRxiv, 590506. https://doi.org/10.1101/2024.04.22.590506

Documentation

The documentation is available at https://stnmf.readthedocs.io.

Installation

Install using pip from command-line:

bash pip install stnmf

Contact

For feedback and bug reports, please use the Github issue tracker.

Owner

  • Name: Gollisch Lab
  • Login: gollischlab
  • Kind: user
  • Location: Göttingen, Germany
  • Company: University Medical Center Göttingen, Department of Ophthalmology

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "STNMF with AF-HALS"
url: "https://github.com/gollischlab/STNMF_with_AFHALS"
authors:
  - family-names: "Zapp"
    given-names: "Sören J."
    orcid: "https://orcid.org/0000-0003-0836-1663"
  - family-names: "Gollisch"
    given-names: "Tim"
    orcid: "https://orcid.org/0000-0003-3998-533X"
preferred-citation:
  type: article
  authors:
  - family-names: "Zapp"
    given-names: "Sören J."
    orcid: "https://orcid.org/0000-0003-0836-1663"
  - family-names: "Khani"
    given-names: "Mohammad H."
    orcid: "https://orcid.org/0000-0003-3123-7054"
  - family-names: "Schreyer"
    given-names: "Helene M."
  - family-names: "Sridhar"
    given-names: "Shashwat"
    orcid: "https://orcid.org/0000-0002-8837-8555"
  - family-names: "Ramakrishna"
    given-names: "Varsha"
    orcid: "https://orcid.org/0009-0002-1369-2600"
  - family-names: "Krüppel"
    given-names: "Steffen"
    orcid: "https://orcid.org/0000-0002-2773-6785"
  - family-names: "Mietsch"
    given-names: "Matthias"
    orcid: "https://orcid.org/0000-0002-3520-5394"
  - family-names: "Protti"
    given-names: "Dario A."
    orcid: "https://orcid.org/0000-0002-2554-6419"
  - family-names: "Karamanlis"
    given-names: "Dimokratis"
    orcid: "https://orcid.org/0000-0002-9469-5020"
  - family-names: "Gollisch"
    given-names: "Tim"
    orcid: "https://orcid.org/0000-0003-3998-533X"
  doi: 10.1101/2024.04.22.590506
  journal: bioRxiv
  month:
  start: 590506
  end:
  title: "Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina"
  issue:
  volume:
  year: 2024

GitHub Events

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  • Total packages: 1
  • Total downloads:
    • pypi 17 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
pypi.org: stnmf

Fast and versatile implementation of spike-triggered non-negative matrix factorization based on AF-HALS

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 17 Last month
Rankings
Dependent packages count: 10.0%
Average: 37.9%
Dependent repos count: 65.8%
Maintainers (1)
szapp
Last synced: 6 months ago

Dependencies

.github/workflows/pypi.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
docs/requirements.txt pypi
  • PyYAML ==6.0.1
  • requests ==2.31.0
  • sphinx ==7.2.6
  • sphinx-carousel ==1.2.0
  • sphinx-copybutton ==0.5.2
  • sphinx-design ==0.5.0
  • sphinx-rtd-theme ==2.0.0
pyproject.toml pypi