Spike-triggered non-negative matrix factorization

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, S. J., Khani, M. H., Schreyer, H. M., Sridhar, S., Ramakrishna, V., Krüppel, S., Mietsch, M., Protti, D. A., 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

The package provides code to recover spatial subunits from a spike-triggered stimulus ensemble using matrix factorization to solve

\(\mathbf{V} \approx \mathbf{W} \mathbf{H} \,,\)

with a non-negativity constraint on \(\mathbf{W}\). Here \(\mathbf{V}\) is the effective spike-triggered stimulus ensemble (STE), an (n, m) array_like consisting of n pixels and m spikes and \(\mathbf{W}\) is an (n, r) array_like containing the recovered spatial modules with the corresponding weights \(\mathbf{H}\) as (r, m) array_like.

Citation

If you use this software, please cite it as below.

Zapp, S. J., Khani, M. H., Schreyer, H. M., Sridhar, S., Ramakrishna, V., Krüppel, S., Mietsch, M., Protti, D. A., 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
@article{Zapp_2024,
     title = {Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina},
     url = {http://dx.doi.org/10.1101/2024.04.22.590506},
     DOI = {10.1101/2024.04.22.590506},
     publisher = {Cold Spring Harbor Laboratory},
     author = {Zapp, S{\\"{o}}ren J. and Khani, Mohammad H. and Schreyer, Helene M. and Sridhar, Shashwat and Ramakrishna, Varsha and Kr{\\"{u}}ppel, Steffen and Mietsch, Matthias and Protti, Dario A. and Karamanlis, Dimokratis and Gollisch, Tim},
     year = {2024},
     month = apr,
     journal = {bioRxiv},
     pages = {590506} 
}

TY  - GENERIC
DO  - 10.1101/2024.04.22.590506
UR  - http://dx.doi.org/10.1101/2024.04.22.590506
TI  - Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina
AU  - Zapp, Sören J.
AU  - Khani, Mohammad H.
AU  - Schreyer, Helene M.
AU  - Sridhar, Shashwat
AU  - Ramakrishna, Varsha
AU  - Krüppel, Steffen
AU  - Mietsch, Matthias
AU  - Protti, Dario A.
AU  - Karamanlis, Dimokratis
AU  - Gollisch, Tim
PY  - 2024
DA  - 2024/04/25
PB  - Cold Spring Harbor Laboratory
JF  - bioRxiv
SP  - 590506
ER  -

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

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