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CITATION.cff

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given-names: Bence
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orcid: "https://orcid.org/0000-0003-0849-7480"
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- family-names: Biswas
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given-name: Arnab
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given-names: Arnab
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- family-names: Broderick
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given-names: William F.
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orcid: "https://orcid.org/0000-0002-8999-9003"
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orcid: "https://orcid.org/0000-0003-4681-0538"
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- family-names: Lewis
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given-names: Caitlin
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orcid: 0000-0002-3317-0722
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orcid: https://orcid.org/0000-0002-3317-0722
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- family-names: Maura
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given-names: Camila
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orcid: https://orcid.org/0000-0002-1304-5641
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- family-names: Crespo
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- family-names: Crespo Darriba
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given-names: Pablo
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- family-names: Viejo
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given-names: Guillaume
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given-names: Pranati
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- family-names: Thomson
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given-names: Eric
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orcid: https://orcid.org/0000-0002-7118-2249
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- family-names: Williams
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given-names: Alex
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orcid: "https://orcid.org/0000-0001-5853-103X"

README.md

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[![codecov](https://codecov.io/gh/flatironinstitute/nemos/graph/badge.svg?token=vvtrcTFNeu)](https://codecov.io/gh/flatironinstitute/nemos)
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[![Documentation Status](https://readthedocs.org/projects/nemos/badge/?version=latest)](https://nemos.readthedocs.io/en/latest/?badge=latest)
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[![nemos CI](https://github.com/flatironinstitute/nemos/actions/workflows/ci.yml/badge.svg)](https://github.com/flatironinstitute/nemos/actions/workflows/ci.yml)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17553287.svg)](https://doi.org/10.5281/zenodo.17553287)
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NeMoS (Neural ModelS) is a statistical modeling framework optimized for systems neuroscience and powered by [JAX](https://jax.readthedocs.io/en/latest/).
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In all cases, we request that you respect our [code of
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conduct](CODE_OF_CONDUCT.md).
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## Citing us
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If you use NeMoS in a published academic article or presentation, please
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cite the code by the DOI. You can click on
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`Cite this repository` on the right side of the GitHub page to get a copyable
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citation for the code, or use the following:
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- Code: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17553287.svg)](https://doi.org/10.5281/zenodo.17553287)
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See the [citation
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guide](https://docs.plenoptic.org/docs/branch/main/citation.html) for more
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details, including citations for the different synthesis methods and
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computational moels included in plenoptic.
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## Support
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This package is supported by:

docs/citation.md

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(citation-doc)=
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# Citation Guide and Bibliography
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If you use NeMoS in a published academic article or presentation, please cite the code by the DOI. You can use the following:
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- Code: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17553287.svg)](https://doi.org/10.5281/zenodo.17553287)
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Additionally, it may be a good idea to cite the following paper(s) depending on which component you use:
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- {class}`GLM <nemos.glm.GLM>` or {class}`PopulationGLM <nemos.glm.PopulationGLM>`: {cite:alp}`nelder1972generalized`.
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- {class}`BSplineEval <nemos.basis.BSplineEval>` or {class}`BSplineConv <nemos.basis.BSplineConv>`: {cite:alp}`de1972calculating,cox1972numerical`.
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- {class}`MSplineEval <nemos.basis.MSplineEval>` or {class}`MSplineConv <nemos.basis.MSplineConv>`: {cite:alp}`ramsay1988monotone`.
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- {class}`RaisedCosineLinearEval <nemos.basis.RaisedCosineLinearEval>` or {class}`RaisedCosineLogEval <nemos.basis.RaisedCosineLogEval>` or {class}`RaisedCosineLinearConv <nemos.basis.RaisedCosineLinearConv>` or {class}`RaisedCosineLogConv <nemos.basis.RaisedCosineLogConv>`: {cite:alp}`pillow2005prediction`.
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- {class}`ElasticNet <nemos.regularizer.ElasticNet>`: {cite:alp}`zou2005regularization`.
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- {class}`GroupLasso <nemos.regularizer.GroupLasso>`: {cite:alp}`yuan2006model`.
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- {class}`Lasso <nemos.regularizer.Lasso>`: {cite:alp}`tibshirani1996regression`.
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- {class}`Ridge <nemos.regularizer.Ridge>`: {cite:alp}`hoerl1970ridge1,hoerl1970ridge2`.
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## Bibliography
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```{bibliography} references.bib
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:style: plain
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```

docs/conf.py

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'sphinx_design', # For layout components
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'myst_nb',
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'sphinx_contributors',
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"sphinxcontrib.bibtex",
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'sphinx_code_tabs',
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'sphinx.ext.mathjax',
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'sphinx_autodoc_typehints',
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napoleon_use_param = True
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napoleon_use_rtype = True
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# SPHINXCONTRIB-BIBTEX
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bibtex_bibfiles = ["references.bib"]
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bibtex_reference_style = "author_year"
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autodoc_typehints = "description" # Use "description" to place hints in the description
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autodoc_type_aliases = {
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"ArrayLike": "ArrayLike",

docs/index.md

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Tutorials <tutorials/README>
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Getting Help <getting_help>
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API Reference <api_reference>
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Citation Guide <citation>
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For Developers <developers_notes/README>
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```
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Open source, [licensed under MIT](https://github.com/flatironinstitute/nemos/blob/main/LICENSE).
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## <span class="iconify" data-icon="mdi:lead-pencil" style="width: 1em"></span> __Cite Us__
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## Support
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If you use NeMoS in academic work, please cite the software. See the [](citation-doc) for more details.
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## __Support__
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This package is supported by:
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docs/references.bib

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@article{pillow2005prediction,
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title={Prediction and decoding of retinal ganglion cell responses with a probabilistic spiking model},
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author={Pillow, Jonathan W and Paninski, Liam and Uzzell, Valerie J and Simoncelli, Eero P and Chichilnisky, EJ},
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journal={Journal of Neuroscience},
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volume={25},
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number={47},
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pages={11003--11013},
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year={2005},
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publisher={Society for Neuroscience}
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}
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@article{nelder1972generalized,
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title={Generalized linear models},
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author={Nelder, John Ashworth and Wedderburn, Robert WM},
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journal={Journal of the Royal Statistical Society Series A: Statistics in Society},
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volume={135},
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number={3},
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pages={370--384},
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year={1972},
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publisher={Oxford University Press}
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}
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@article{tibshirani1996regression,
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title={Regression shrinkage and selection via the lasso},
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author={Tibshirani, Robert},
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journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
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volume={58},
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number={1},
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pages={267--288},
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year={1996},
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publisher={Oxford University Press}
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}
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@article{yuan2006model,
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title={Model selection and estimation in regression with grouped variables},
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author={Yuan, Ming and Lin, Yi},
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journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
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volume={68},
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number={1},
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pages={49--67},
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year={2006},
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publisher={Oxford University Press}
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}
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@article{hoerl1970ridge1,
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title={Ridge regression: Biased estimation for nonorthogonal problems},
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author={Hoerl, Arthur E and Kennard, Robert W},
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journal={Technometrics},
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volume={12},
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number={1},
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pages={55--67},
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year={1970},
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publisher={Taylor \& Francis}
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}
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@article{hoerl1970ridge2,
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title={Ridge regression: applications to nonorthogonal problems},
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author={Hoerl, Arthur E and Kennard, Robert W},
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journal={Technometrics},
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volume={12},
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number={1},
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pages={69--82},
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year={1970},
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publisher={Taylor \& Francis}
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}
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@article{de1972calculating,
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title={On calculating with B-splines},
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author={De Boor, Carl},
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journal={Journal of Approximation theory},
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volume={6},
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number={1},
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pages={50--62},
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year={1972},
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publisher={Academic Press}
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}
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@article{cox1972numerical,
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title={The numerical evaluation of B-splines},
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author={Cox, Maurice G},
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journal={IMA Journal of Applied mathematics},
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volume={10},
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number={2},
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pages={134--149},
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year={1972},
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publisher={Oxford University Press}
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}
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@article{ramsay1988monotone,
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title={Monotone regression splines in action},
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author={Ramsay, James O},
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journal={Statistical science},
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pages={425--441},
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year={1988},
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publisher={JSTOR}
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}
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@article{zou2005regularization,
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title={Regularization and variable selection via the elastic net},
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author={Zou, Hui and Hastie, Trevor},
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journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
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volume={67},
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number={2},
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pages={301--320},
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year={2005},
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publisher={Oxford University Press}
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}

pyproject.toml

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"sphinx-design",
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"sphinx-issues",
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"sphinxcontrib-apidoc",
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"sphinxcontrib-bibtex",
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"sphinxemoji",

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