grant.bib

@inproceedings{rodrigues2020scikit,
  author       = {Eduardo Rodrigues and Benjamin Krikler and Chris Burr and Dmitri Smirnov and Hans Dembinski and Henry Schreiner and Jaydeep Nandi and Jim Pivarski and Matthew Feickert and Matthieu Marinangeli and Nick Smith and Pratyush Das},
  title        = {The Scikit-HEP Project: Overview and Prospects},
  booktitle    = {EPJ Web of Conferences},
  volume       = {245},
  pages        = {06028},
  year         = {2020},
  publisher    = {EDP Sciences},
  doi          = {10.1051/epjconf/202024506028},
  url          = {https://doi.org/10.1051/epjconf/202024506028},
}

@inproceedings{belle2_core_software,
  author       = {The Belle II Collaboration},
  title        = {The Belle II Core Software (basf2): Simulation, Reconstruction, and Analysis Framework},
  booktitle    = {EPJ Web of Conferences},
  volume       = {295},
  pages        = {05018},
  year         = {2024},
  publisher    = {EDP Sciences},
  doi          = {10.1051/epjconf/202429505018},
  url          = {https://doi.org/10.1051/epjconf/202429505018}
}

@article{lhcb2022prompt,
  author       = {LHCb Collaboration},
  title        = {Measurement of prompt charged-particle production in $pp$ collisions at $\sqrt{s} = 13\,\mathrm{TeV}$},
  journal      = {Journal of High Energy Physics},
  volume       = {2022},
  number       = {1},
  pages        = {166},
  year         = {2022},
  doi          = {10.1007/JHEP01(2022)166},
  url          = {https://link.springer.com/article/10.1007/JHEP01(2022)166},
}

@article{rey2021pysal,
  author       = {Sergio J. Rey and Elijah Knaap},
  title        = {The PySAL Ecosystem: Philosophy and Implementation},
  journal      = {Center for Geospatial Sciences, University of California, Riverside},
  year         = {2021},
  url          = {https://cogs.sdsu.edu/publication/rey-2021-py-sal-ecosystem/}
}

@article{fan2018network,
  author       = {Fan, Y. and Zhu, X. and She, B. and Guo, W. and Guo, T.},
  title        = {Network-Constrained Spatio-Temporal Clustering Analysis of Traffic Collisions in Jianghan District of Wuhan, China},
  journal      = {PLOS ONE},
  volume       = {13},
  number       = {4},
  pages        = {e0195093},
  year         = {2018},
  doi          = {10.1371/journal.pone.0195093},
  url          = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195093}
}

@article{spiridon2017hamiltonian,
  author       = {Spiridon, L. and Minh, D. D.},
  title        = {Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling},
  journal      = {Journal of Chemical Theory and Computation},
  volume       = {13},
  number       = {10},
  pages        = {4649--4659},
  year         = {2017},
  doi          = {10.1021/acs.jctc.7b00625},
  url          = {https://pubs.acs.org/doi/10.1021/acs.jctc.7b00625}
}

@article{jakubska2018pickover,
  author       = {Jakubska-Busse, Anna and Janowicz, Mariusz W. and Ochnio, Leszek and Ashbourn, Julian M. A.},
  title        = {Pickover Biomorphs and Non-Standard Complex Numbers},
  journal      = {Chaos, Solitons \& Fractals},
  volume       = {113},
  pages        = {46--52},
  year         = {2018},
  doi          = {10.1016/j.chaos.2018.05.020},
  url          = {https://www.sciencedirect.com/science/article/pii/S0960077918302091}
}

@article{noorbakhsh2019pan,
  author       = {Javad Noorbakhsh and Saman Farahmand and Mehdi Soltanieh-ha and Sridevi Namburi and Kamran Zarringhalam and Jason Chuang},
  title        = {Pan-Cancer Classifications of Tumor Histological Images Using Deep Learning},
  journal      = {bioRxiv},
  year         = {2019},
  doi          = {10.1101/715656},
  url          = {https://www.biorxiv.org/content/10.1101/715656v1}
}

@misc{cdss2025datasciencemajor,
  author       = {{College of Computing, Data Science, and Society (CDSS)}},
  title        = {UC Berkeley Data Science Major Now Largest on Campus},
  year         = {2025},
  month        = {March},
  url          = {https://cdss.berkeley.edu/dsus/news/data-science-major-now-largest-campus}
}

@inproceedings{van_dusen2019accelerating,
  author       = {Eric Van Dusen and Anthony Suen and Alan Liang and Amal Bhatnagar},
  title        = {Accelerating the Advancement of Data Science Education},
  booktitle    = {Proceedings of the 18th Python in Science Conference (SciPy 2019)},
  pages        = {52--59},
  year         = {2019},
  month        = {July},
  publisher    = {SciPy},
  doi          = {10.25080/Majora-7ddc1dd1-000},
  url          = {https://doi.org/10.25080/Majora-7ddc1dd1-000}
}

@misc{meeseeksdev_github,
  author       = {Matthias Bussonnier and contributors},
  title        = {MeeseeksDev: Development deployment of MeeseeksBox (use at your own risk)},
  year         = {2017},
  howpublished = {\url{https://github.com/scientific-python/MeeseeksDev}},
  note         = {Version as of April 2025},
  institution  = {Scientific Python},
  url          = {https://github.com/scientific-python/MeeseeksDev}
}

@misc{sync_teams_action_github,
  author       = {Scientific Python Developers},
  title        = {sync-teams-action: Synchronize team membership and permissions for GitHub organizations},
  year         = {2023},
  howpublished = {\url{https://github.com/scientific-python/sync-teams-action}},
  note         = {Version as of April 2025},
  url          = {https://github.com/scientific-python/sync-teams-action}
}

@misc{alliedmarketresearch2023algorithmic,
  author       = {Allied Market Research},
  title        = {Algorithmic Trading Market Size, Share, Industry Analysis - 2032},
  year         = {2023},
  url          = {https://www.alliedmarketresearch.com/algorithmic-trading-market-A08567}
}

@misc{citadel_quant_interview,
  author       = {PyQuant News},
  title        = {A short interview with a front office quant at Citadel},
  year         = {2024},
  month        = {July},
  url          = {https://www.linkedin.com/posts/pyquant-news_a-short-interview-with-a-front-office-quant-activity-7219008634192621568-Gco4},
  note         = {LinkedIn post by PyQuant News, July 16, 2024}
}

@misc{citadel_interview_2025,
  author       = {Interview Query},
  title        = {Citadel LLC Data Scientist Interview Questions + Guide in 2025},
  year         = {2025},
  url          = {https://www.interviewquery.com/interview-guides/citadel-data-scientist},
  abstract     = {Details Python's role in Citadel's data science workflows, including machine learning pipelines and ETL processes.}
}

@misc{twosigma_pandas_2023,
  author       = {Two Sigma},
  title        = {pandas at a Crossroads: The Past, Present, and Future with Jeff Reback},
  year         = {2023},
  month        = {May},
  url          = {https://www.twosigma.com/articles/pandas-at-a-crossroads-the-past-present-and-future-with-jeff-reback/},
  abstract     = {Discusses pandas' use in financial trading systems and large-scale data processing at Two Sigma.}
}

@misc{twosigma_future_pandas,
  author       = {Jeff Reback},
  title        = {The Future of Pandas},
  year         = {2020},
  month        = {September},
  url          = {https://www.twosigma.com/articles/the-future-of-pandas/},
  abstract     = {Architecture overview for pandas' role in financial analytics at scale.}
}

@misc{cdss2025nwdse,
  author       = {{College of Computing, Data Science, and Society (CDSS)}},
  title        = {Expanding Access to Data Science Education Through Partnerships and Open-Source Resources},
  year         = {2025},
  month        = {March},
  url          = {https://cdss.berkeley.edu/dsus/nwdse}
}

@article{burt2018hierarchy,
  author       = {Burt, Jonathan B. and Demirtas, Murat and Eckner, William J. and Navejar, Nicholas M. and Ji, Joseph L. and Martin, William J. and Bernacchia, Alberto and Anticevic, Alan and Murray, John D.},
  title        = {Hierarchy of Transcriptomic Specialization Across Human Cortex Captured by Structural Neuroimaging Topography},
  journal      = {Nature Neuroscience},
  volume       = {21},
  number       = {9},
  pages        = {1251--1260},
  year         = {2018},
  doi          = {10.1038/s41593-018-0195-0},
  url          = {https://www.nature.com/articles/s41593-018-0195-0}
}

@inproceedings{hughes2014geovisualization,
  author       = {Hughes, C. and Naik, V. S. and Sengupta, R. and Saxena, D.},
  title        = {Geovisualization for Cluster Detection of Hepatitis A \& E Outbreaks in Ahmedabad, Gujarat, India},
  booktitle    = {Proceedings of the Third ACM SIGSPATIAL International Workshop on the Use of GIS in Public Health},
  pages        = {39--44},
  year         = {2014},
  publisher    = {ACM},
  doi          = {10.1145/2684108.2684117},
  url          = {https://dl.acm.org/doi/10.1145/2684108.2684117}
}

@misc{indico_cern_seminar_2020,
  author       = {Eduardo Rodrigues},
  title        = {HEP Data Analysis in Python Ecosystem and Community Efforts},
  howpublished = {Manchester HEP Seminar, All@Home},
  year         = {2020},
  month        = {December},
  day          = {4},
  url          = {https://indico.cern.ch/event/961730/attachments/2157295/3638863/2020-12-04_ManchesterSeminar.pdf}
}

@mastersthesis{hennig2023km3net,
  author       = {Lukas Hennig},
  title        = {Tau Neutrino Identification with Graph Neural Networks in KM3NeT/ORCA},
  school       = {Friedrich-Alexander-Universität Erlangen-Nürnberg},
  year         = {2023},
  month        = {June},
  address      = {Erlangen, Germany},
  url          = {https://ecap.nat.fau.de/wp-content/uploads/2023/06/2023-06_LukasHennig_MSc_ORCA_TauID_GNNs.pdf}
}

@article{Bockelman:2023gbj,
    author = "Bockelman, Brian and others",
    title = "{IRIS-HEP Strategic Plan for the Next Phase of Software Upgrades for HL-LHC Physics}",
    eprint = "2302.01317",
    archivePrefix = "arXiv",
    primaryClass = "hep-ex",
    reportNumber = "FERMILAB-PUB-23-068-PPD",
    month = "2",
    year = "2023"
}

@software{Pivarski_Awkward_Array_2018,
author = {Pivarski, Jim and Osborne, Ianna and Ifrim, Ioana and Schreiner, Henry and Hollands, Angus and Biswas, Anish and Das, Pratyush and Roy Choudhury, Santam and Smith, Nicholas and Goyal, Manasvi},
doi = {10.5281/zenodo.4341376},
month = {10},
title = {{Awkward Array}},
year = {2018}
}

@software{scikit-hep_uproot3_3_14_4,
  author       = {Jim Pivarski and Pratyush Das and Chris Burr and Dmitri Smirnov and Matthew Feickert and Tamas Gal and Luke Kreczko and Nicholas Smith and Noah Biederbeck and Oksana Shadura and Mason Proffitt and benkrikler and Hans Dembinski and Henry Schreiner and Jonas Rembser and Marcel R. and Chao Gu and Edoardo Rodrigues and JMSchoeffmann and Jonas Rübenach and Lukas Koch and Michele Peresano and Niclas Eich and Ruggero Turra},
  title        = {scikit-hep/uproot3: 3.14.4},
  version      = {3.14.4},
  publisher    = {Zenodo},
  year         = {2021},
  doi          = {10.5281/zenodo.4537826},
  url          = {https://zenodo.org/record/4537826}
}

@InProceedings{henry_schreiner-proc-scipy-2020,
  author    = { {H}enry {S}chreiner and {H}ans {D}embinski and {S}huo {L}iu and {J}im {P}ivarski },
  title     = { {B}oost-histogram: {H}igh-{P}erformance {H}istograms as {O}bjects },
  booktitle = { {P}roceedings of the 19th {P}ython in {S}cience {C}onference },
  pages     = { 63 - 69 },
  year      = { 2020 },
  editor    = { {M}eghann {A}garwal and {C}hris {C}alloway and {D}illon {N}iederhut and {D}avid {S}hupe },
  doi       = { 10.25080/Majora-342d178e-009 }
}

@software{scikit-hep_boost_histogram_1_5_2,
  author       = {Princeton University and
                  TU Dortmund and
                  The University of Manchester and
                  CERN and
                  UCL-ARC, UCL and
                  Amazon and
                  University of Wisconsin-Madison and
                  @sezane},
  title        = {scikit-hep/boost-histogram: Version 1.5.2},
  version      = {1.5.2},
  publisher    = {Zenodo},
  year         = {2025},
  doi          = {10.5281/zenodo.15098538},
  url          = {https://zenodo.org/record/15098538}
}

@software{vector_v0_10_0,
  author       = {Princeton University and University of Delhi},
  title        = {Vector: A Python library for 2D, 3D, and Lorentz vectors},
  version      = {v0.10.0},
  publisher    = {Zenodo},
  year         = {2022},
  doi          = {10.5281/zenodo.7054478},
  url          = {https://zenodo.org/record/7054478}
}

@article{PhysRevD.110.030001,
  title = {Review of Particle Physics},
  author = {Navas, S. and Amsler, C. and Gutsche, T. and Hanhart, C. and Hern\'andez-Rey, J. J. and Louren\ifmmode \mbox{\c{c}}\else \c{c}\fi{}o, C. and Masoni, A. and Mikhasenko, M. and Mitchell, R. E. and Patrignani, C. and Schwanda, C. and Spanier, S. and Venanzoni, G. and Yuan, C. Z. and Agashe, K. and Aielli, G. and Allanach, B. C. and Alvarez-Mu\~niz, J. and Antonelli, M. and Aschenauer, E. C. and Asner, D. M. and Assamagan, K. and Baer, H. and Banerjee, Sw. and Barnett, R. M. and Baudis, L. and Bauer, C. W. and Beatty, J. J. and Beringer, J. and Bettini, A. and Biebel, O. and Black, K. M. and Blucher, E. and Bonventre, R. and Briere, R. A. and Buckley, A. and Burkert, V. D. and Bychkov, M. A. and Cahn, R. N. and Cao, Z. and Carena, M. and Casarosa, G. and Ceccucci, A. and Cerri, A. and Chivukula, R. S. and Cowan, G. and Cranmer, K. and Crede, V. and Cremonesi, O. and D'Ambrosio, G. and Damour, T. and de Florian, D. and de Gouv\^ea, A. and DeGrand, T. and Demers, S. and Demiragli, Z. and Dobrescu, B. A. and D'Onofrio, M. and Doser, M. and Dreiner, H. K. and Eerola, P. and Egede, U. and Eidelman, S. and El-Khadra, A. X. and Ellis, J. and Eno, S. C. and Erler, J. and Ezhela, V. V. and Fava, A. and Fetscher, W. and Fields, B. D. and Freitas, A. and Gallagher, H. and Gershon, T. and Gershtein, Y. and Gherghetta, T. and Gonzalez-Garcia, M. C. and Goodman, M. and Grab, C. and Gritsan, A. V. and Grojean, C. and Groom, D. E. and Gr\"unewald, M. and Gurtu, A. and Haber, H. E. and Hamel, M. and Hashimoto, S. and Hayato, Y. and Hebecker, A. and Heinemeyer, S. and Hikasa, K. and Hisano, J. and H\"ocker, A. and Holder, J. and Hsu, L. and Huston, J. and Hyodo, T. and Ianni, Al. and Kado, M. and Karliner, M. and Katz, U. F. and Kenzie, M. and Khoze, V. A. and Klein, S. R. and Krauss, F. and Kreps, M. and Kri\ifmmode \check{z}\else \v{z}\fi{}an, P. and Krusche, B. and Kwon, Y. and Lahav, O. and Lellouch, L. P. and Lesgourgues, J. and Liddle, A. R. and Ligeti, Z. and Lin, C.-J. and Lippmann, C. and Liss, T. M. and Lister, A. and Littenberg, L. and Lugovsky, K. S. and Lugovsky, S. B. and Lusiani, A. and Makida, Y. and Maltoni, F. and Manohar, A. V. and Marciano, W. J. and Matthews, J. and Mei\ss{}ner, U.-G. and Melzer-Pellmann, I.-A. and Mertsch, P. and Miller, D. J. and Milstead, D. and M\"onig, K. and Molaro, P. and Moortgat, F. and Moskovic, M. and Nagata, N. and Nakamura, K. and Narain, M. and Nason, P. and Nelles, A. and Neubert, M. and Nir, Y. and O'Connell, H. B. and O'Hare, C. A. J. and Olive, K. A. and Peacock, J. A. and Pianori, E. and Pich, A. and Piepke, A. and Pietropaolo, F. and Pomarol, A. and Pordes, S. and Profumo, S. and Quadt, A. and Rabbertz, K. and Rademacker, J. and Raffelt, G. and Ramsey-Musolf, M. and Richardson, P. and Ringwald, A. and Robinson, D. J. and Roesler, S. and Rolli, S. and Romaniouk, A. and Rosenberg, L. J and Rosner, J. L. and Rybka, G. and Ryskin, M. G. and Ryutin, R. A. and Safdi, B. and Sakai, Y. and Sarkar, S. and Sauli, F. and Schneider, O. and Sch\"onert, S. and Scholberg, K. and Schwartz, A. J. and Schwiening, J. and Scott, D. and Sefkow, F. and Seljak, U. and Sharma, V. and Sharpe, S. R. and Shiltsev, V. and Signorelli, G. and Silari, M. and Simon, F. and Sj\"ostrand, T. and Skands, P. and Skwarnicki, T. and Smoot, G. F. and Soffer, A. and Sozzi, M. S. and Spiering, C. and Stahl, A. and Sumino, Y. and Takahashi, F. and Tanabashi, M. and Tanaka, J. and Ta\ifmmode \check{s}\else \v{s}\fi{}evsk\'y, M. and Terao, K. and Terashi, K. and Terning, J. and Thoma, U. and Thorne, R. S. and Tiator, L. and Titov, M. and Tovey, D. R. and Trabelsi, K. and Urquijo, P. and Valencia, G. and Van de Water, R. and Varelas, N. and Verde, L. and Vivarelli, I. and Vogel, P. and Vogelsang, W. and Vorobyev, V. and Wakely, S. P. and Walkowiak, W. and Walter, C. W. and Wands, D. and Weinberg, D. H. and Weinberg, E. J. and Wermes, N. and White, M. and Wiencke, L. R. and Willocq, S. and Woody, C. L. and Workman, R. L. and Yao, W.-M. and Yokoyama, M. and Yoshida, R. and Zanderighi, G. and Zeller, G. P. and Zhu, R.-Y. and Zhu, S.-L. and Zimmermann, F. and Zyla, P. A. and Anderson, J. and Kramer, M. and Schaffner, P. and Zheng, W.},
  collaboration = {Particle Data Group Collaboration},
  journal = {Phys. Rev. D},
  volume = {110},
  issue = {3},
  pages = {030001},
  numpages = {5},
  year = {2024},
  month = {Aug},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevD.110.030001},
  url = {https://link.aps.org/doi/10.1103/PhysRevD.110.030001}
}

@article{Rodrigues:2020syo,
    author = "Rodrigues, Eduardo and others",
    editor = "Doglioni, C. and Kim, D. and Stewart, G. A. and Silvestris, L. and Jackson, P. and Kamleh, W.",
    title = "{The Scikit HEP Project -- overview and prospects}",
    eprint = "2007.03577",
    archivePrefix = "arXiv",
    primaryClass = "physics.comp-ph",
    doi = "10.1051/epjconf/202024506028",
    journal = "EPJ Web Conf.",
    volume = "245",
    pages = "06028",
    year = "2020"
}

@software{scikit_hep_particle_v0_25_3,
  author       = {University of Liverpool and Princeton University},
  title        = {scikit-hep/particle: Release 0.25.3},
  version      = {v0.25.3},
  publisher    = {Zenodo},
  year         = {2025},
  doi          = {10.5281/zenodo.15132783},
  url          = {https://zenodo.org/record/15132783},
  abstract     = {PDG particle data and identification codes.}
}

@misc{pysal_github,
  author       = {PySAL Development Team},
  title        = {PySAL: Python Spatial Analysis Library Meta-Package},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/pysal/pysal},
  abstract     = {PySAL is an open-source cross-platform library for geospatial data science, focusing on geospatial vector data. It supports tasks such as spatial cluster detection, regression modeling, econometrics, and exploratory spatio-temporal data analysis.},
  note         = {Available at \url{https://github.com/pysal/pysal}}
}

@misc{scikit_hep_github,
  author       = {Scikit-HEP Development Team},
  title        = {Scikit-HEP: Metapackage for Particle Physics Data Analysis},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/scikit-hep/scikit-hep},
  abstract     = {Scikit-HEP is a community-driven project providing an ecosystem of Python tools for data analysis in high-energy physics. It includes packages for histogramming, fitting, vector manipulation, particle properties, and interoperability with the broader scientific Python ecosystem. The project aims to improve discoverability, interoperability, and sustainability of HEP tools.},
  note         = {Available at \url{https://github.com/scikit-hep/scikit-hep}}
}

@misc{lazy_loader_github,
  author       = {Scientific Python Development Team},
  title        = {lazy-loader: Populate library namespace lazily},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/scientific-python/lazy-loader},
  abstract     = {lazy-loader is a lightweight Python library that enables lazy loading of submodules and functions to optimize memory usage and reduce import times. It is designed to improve performance and efficiency in scientific Python libraries by loading components only when they are accessed.},
  note         = {Available at \url{https://github.com/scientific-python/lazy-loader}}
}

@misc{scientific_python_cookie_github,
  author       = {Scientific Python Development Team},
  title        = {Cookie: A Copier/Cookiecutter Template for Scientific Python Projects},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/scientific-python/cookie},
  abstract     = {Cookie is a template generator for new Python projects based on the Scientific Python Developer Guide. It supports multiple build backends, optional VCS versioning, and integration with tools like GitHub Actions, pre-commit, and nox. It ensures adherence to PyPA best practices and promotes consistency across scientific Python projects.},
  note         = {Available at \url{https://github.com/scientific-python/cookie}}
}

@misc{pytest_doctestplus_github,
  author       = {Scientific Python Development Team},
  title        = {pytest-doctestplus: Advanced Doctest Support for Pytest},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/scientific-python/pytest-doctestplus},
  abstract     = {pytest-doctestplus is a plugin for the pytest framework that enhances doctest capabilities. It supports testing Python code snippets in docstrings and standalone documentation files, including reStructuredText (.rst), markdown (.md), and TeX (.tex). Features include floating-point comparison, skipping tests, handling remote data, and fixing existing docstrings, making it a valuable tool for ensuring accurate and robust documentation in scientific Python projects.},
  note         = {Available at \url{https://github.com/scientific-python/pytest-doctestplus}}
}

@misc{spin_github,
  author       = {Scientific Python Development Team},
  title        = {Spin: Developer Tool for Scientific Python Libraries},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/scientific-python/spin},
  abstract     = {Spin is a developer tool that simplifies and abstracts common command-line tasks for scientific Python projects. It provides an extendable interface for build, test, and installation workflows, particularly useful for projects migrating to Meson after the deprecation of distutils. Spin enhances productivity and consistency across ecosystem libraries by offering customizable commands and auto-completion features.},
  note         = {Available at \url{https://github.com/scientific-python/spin}}
}

@misc{repo_review_github,
  author       = {Scientific Python Development Team},
  title        = {repo-review: Framework for Repository Compliance Checks},
  year         = {2025},
  publisher    = {GitHub},
  url          = {https://github.com/scientific-python/repo-review},
  abstract     = {repo-review is a framework designed to evaluate repositories against the Scientific Python Development Guide. It performs automated checks for compliance with best practices in areas such as packaging, documentation, and configuration. By identifying potential issues and providing actionable recommendations, repo-review enhances the quality, consistency, and security of scientific Python projects.},
  note         = {Available at \url{https://github.com/scientific-python/repo-review}}
}

@software{zarr_python_v2_18_7,
  author       = {Alistair Miles and
                  Joe Hamman and
                  Dimitri Papadopoulos Orfanos and
                  David Stansby and
                  M Bussonnier and
                  Josh Moore and
                  Davis Bennett and
                  Norman Rzepka and
                  Deepak Cherian and
                  Sanket Verma and
                  James Bourbeau and
                  Andrew Fulton and
                  Ryan Abernathey and
                  Gregory Lee and
                  Hannes Spitz and
                  Mads R. B. Kristensen and
                  Max Jones and
                  Zain Patel and
                  Saransh Chopra and
                  Matthew Rocklin and
                  Martin Durant and
                  Juan Nunez-Iglesias and
                  Raphael Dussin},
  title        = {zarr-developers/zarr-python: v2.18.7},
  version      = {v2.18.7},
  publisher    = {Zenodo},
  year         = {2025},
  doi          = {10.5281/zenodo.15180703},
  url          = {https://zenodo.org/record/15180703},
  abstract     = {Zarr is a Python library for scalable, chunked, compressed, N-dimensional arrays. This release includes fixes for compatibility with updated dependencies, ensuring stability in zarr-python v2.}
}

@misc{gitstar_ranking,
  author       = {K0kubun},
  title        = {Gitstar Ranking: GitHub Star Ranking for Users, Organizations, and Repositories},
  year         = {2025},
  publisher    = {Gitstar Ranking},
  url          = {https://gitstar-ranking.com},
  abstract     = {Gitstar Ranking is a free and open-source platform that uses GitHub's API to provide rankings for users, organizations, and repositories based on GitHub stars. It offers insights into the most popular contributors and projects in the GitHub ecosystem.},
  note         = {Available at \url{https://gitstar-ranking.com}}
}

@article{Beyreuther2010,
  author    = {Moritz Beyreuther and Robert Barsch and Lion Krischer and Tobias Megies and Yannik Behr and Joachim Wassermann},
  title     = {ObsPy: A Python Toolbox for Seismology},
  journal   = {Seismological Research Letters},
  volume    = {81},
  number    = {3},
  pages     = {530--533},
  year      = {2010},
  doi       = {10.1785/gssrl.81.3.530}
}

@article{Megies2011,
  author    = {Tobias Megies and Moritz Beyreuther and Robert Barsch and Lion Krischer and Joachim Wassermann},
  title     = {ObsPy – What can it do for data centers and observatories?},
  journal   = {Annals Of Geophysics},
  volume    = {54},
  number    = {1},
  pages     = {47--58},
  year      = {2011},
  doi       = {10.4401/ag-4838}
}

@article{Krischer2015,
  author    = {Lion Krischer and Tobias Megies and Robert Barsch and Moritz Beyreuther and Thomas Lecocq and Corentin Caudron and Joachim Wassermann},
  title     = {ObsPy: a bridge for seismology into the scientific Python ecosystem},
  journal   = {Computational Science \& Discovery},
  volume    = {8},
  number    = {1},
  pages     = {014003},
  year      = {2015},
  doi       = {10.1088/1749-4699/8/1/014003}
}

@article{astropy:2022,
  title={The Astropy Project: sustaining and growing a community-oriented open-source project and the latest major release (v5. 0) of the core package},
  author={Astropy Collaboration and others},
  journal={Astrophysical Journal},
  volume={935},
  number={2},
  pages={167},
  year={2022},
  publisher={American Astronomical Society}
}


@misc{yaglm-github,
  author = {},
  title = {\texttt{YAGLM}},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/yaglm/yaglm}},
}

@misc{islp-github,
  author = {},
  title = {\texttt{ISLP}},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/intro-stat-learning/ISLP}},
}

@online{SPP,
author = {{Scientific Python Team}},
title = {{Scientific Python Project Homepage}},
url = {https://scientific-python.org/},
}

@online{specs,
author = {{SPEC Steering Committee}},
title = {{Scientific Python Ecosystem Coordination}},
url = {https://scientific-python.org/specs},
}

@online{spec6,
author = {{Stéfan van der Walt, Jarrod Millman, Pamphile Roy, Lars Grüter}},
title = {{SPEC 6 — Keys to the Castle}},
url = {https://scientific-python.org/specs/spec-0006/},
}

@online{spec8,
author = {{Matthew Feickert, Pamphile Roy, Juanita Gomez, Seth Larson, Lars Grüter, Jarrod Millman}},
title = {{SPEC 8 — Securing the Release Process}},
url = {https://scientific-python.org/specs/spec-0008/},
}

@online{numfocus,
title = {{NumFOCUS}},
url = {https://numfocus.org},
}

@online{Octoverse2024,
author = {{GitHub}},
title = {Octoverse 2024: The state of open source and AI},
year = {2024},
url = {https://github.blog/news-insights/octoverse/octoverse-2024/},
urldate = {2024-11-21},
organization = {GitHub}
}

@conference{Kluyver2016jupyter,
Title = {Jupyter Notebooks -- a publishing format for reproducible computational workflows},
Author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol Willing},
Booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
Editor = {F. Loizides and B. Schmidt},
Organization = {IOS Press},
Pages = {87 - 90},
Year = {2016}
} 

@article{harris2020array,
 title         = {Array programming with {NumPy}},
 author        = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
                 van der Walt and Ralf Gommers and Pauli Virtanen and David
                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
                 Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
                 R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
                 G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
                 Travis E. Oliphant},
 year          = {2020},
 month         = sep,
 journal       = {Nature},
 volume        = {585},
 number        = {7825},
 pages         = {357--362},
 doi           = {10.1038/s41586-020-2649-2},
 publisher     = {Springer Science and Business Media {LLC}},
 url           = {https://doi.org/10.1038/s41586-020-2649-2}
}

@article{virtanen2020scipy,
  author =        {Virtanen, P. and Gommers, R. and Oliphant, T. E. and
                   Haberland, M. and Reddy, T. and Cournapeau, D. and
                   Burovski, E. and Peterson, P. and Weckesser, W. and
                   Bright, J. and van der Walt, S. J. and Brett, M. and
                   Wilson, J. and K. J. Millman and Mayorov, N. and
                   Nelson, A. R. J. and Jones, E. and Kern, R. and
                   Larson, E. and Carey, C. J. and Polat, \.{I}. and
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  journal =       {Nature Methods},
  pages =         {261--272},
  title =         {{SciPy} 1.0---Fundamental Algorithms for Scientific
                   Computing in {Python}},
  volume =        {17},
  year =          {2020},
}

@article{hunter2007matplotlib,
  author =        {Hunter, John D},
  journal =       {Computing in Science \& Engineering},
  number =        {3},
  pages =         {90--95},
  publisher =     {IEEE},
  title =         {Matplotlib: A {2D} graphics environment},
  volume =        {9},
  year =          {2007},
  url =           {https://doi.org/10.1109/MCSE.2007.55},
}

@inproceedings{mckinney-proc-scipy-2010,
  author =        {Wes McKinney},
  booktitle =     {Proceedings of the 9th Python in Science Conference},
  editor =        {St\'efan van der Walt and Jarrod Millman},
  pages =         {51--56},
  title =         {Data Structures for Statistical Computing in
                   {Python}},
  year =          {2010},
}

@article{pedregosa2011scikit,
  author =        {Pedregosa, Fabian and Varoquaux, Ga{\"e}l and
                   Gramfort, Alexandre and Michel, Vincent and
                   Thirion, Bertrand and Grisel, Olivier and
                   Blondel, Mathieu and Prettenhofer, Peter and
                   Weiss, Ron and Dubourg, Vincent and Weiss, Ron and
                   Dubourg, Vincent and Vanderplas, Jake and
                   Passos, Alexandre and Cournapeau, David and
                   Brucher, Matthieu and Perrot, Matthieu and
                   Duchesnay, {\'E}douard},
  journal =       {Journal of Machine Learning Research},
  number =        {Oct},
  pages =         {2825--2830},
  title =         {Scikit-learn: Machine Learning in {P}ython},
  volume =        {12},
  year =          {2011},
  url =           {http://www.jmlr.org/papers/volume12/pedregosa11a/
                   pedregosa11a.pdf},
}

@article{vanderwalt2014scikit,
  author =        {van der Walt, St{\'e}fan and
                   Sch{\"o}nberger, Johannes L and Nunez-Iglesias, Juan and
                   Boulogne, Fran{\c{c}}ois and Warner, Joshua D and
                   Yager, Neil and Gouillart, Emmanuelle and Yu, Tony and
                   {the scikit-image contributors}},
  journal =       {PeerJ},
  pages =         {e453},
  publisher =     {PeerJ Inc.},
  title =         {{scikit-image}: image processing in {P}ython},
  volume =        {2},
  year =          {2014},
  url =           {https://doi.org/10.7717/peerj.453},
}

@article{vanderwalt2011numpy,
  author =        {van der Walt, St{\'e}fan and Colbert, S Chris and
                   Varoquaux, Ga{\"e}l},
  journal =       {Computing in Science \& Engineering},
  number =        {2},
  pages =         {22--30},
  publisher =     {IEEE},
  title =         {The {NumPy} array: a structure for efficient
                   numerical computation},
  volume =        {13},
  year =          {2011},
  url =           {https://doi.org/10.1109/MCSE.2011.37},
}

@article{perez2007ipython,
  author =        {P{\'e}rez, Fernando and Granger, Brian E},
  journal =       {Computing in Science \& Engineering},
  number =        {3},
  pages =         {21--29},
  publisher =     {IEEE},
  title =         {{IP}ython: a system for interactive scientific
                   computing},
  volume =        {9},
  year =          {2007},
  url =           {https://doi.org/10.1109/MCSE.2007.53},
}

@article{perez2011python,
  title={Python: an ecosystem for scientific computing},
  author={Perez, Fernando and Granger, Brian E and Hunter, John D},
  journal={Computing in Science \& Engineering},
  volume={13},
  number={2},
  pages={13--21},
  year={2011},
  publisher={IEEE}
}

@article{coats2019aim,
title={The AIM Initiative: A Strategy for Augmenting Intelligence using Machines},
author={Coats, Daniel R},
journal={Office of the Director of National Intelligence},
year={2019}
}

@techreport{ravich2020seab,
title={SEAB Artificial Intelligence and Machine Learning Working Group},
author={Ravich, Samantha and Rosenbaum, Thomas},
institution={U.S. Department of Energy},
year={2020}
}

@inproceedings{dantas2024asapy,
  title={AsaPy: A Python Library for Aerospace Simulation Analysis},
  author={Dantas, Joao PA and Silva, Samara R and Gomes, Vitor CF and Costa, Andre N and Samersla, Adrisson R and Geraldo, Diego and Maximo, Marcos ROA and Yoneyama, Takashi},
  booktitle={Proceedings of the 38th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation},
  pages={15--24},
  year={2024}
}

@article{kaspersky2024xz,
title={XZ backdoor story Part 2: Assessing the Y, and How, of the XZ Utils incident (social engineering)},
author={Global Research \& Analysis Team, Kaspersky},
journal={Securelist},
year={2024},
month={April}
}
@article{newman2024mystery,
title={The Mystery of 'Jia Tan,' the XZ Backdoor Mastermind},
author={Andy Greenberg, Andy and Burgess, Matt},
journal={WIRED},
year={2024},
month={April}
}

@article{hey2020machine,
  title={Machine learning and big scientific data},
  author={Hey, Tony and Butler, Keith and Jackson, Sam and Thiyagalingam, Jeyarajan},
  journal={Philosophical Transactions of the Royal Society A},
  volume={378},
  number={2166},
  pages={20190054},
  year={2020},
  publisher={The Royal Society Publishing}
}

@article{raschka2020machine,
  title={Machine learning in python: Main developments and technology trends in data science, machine learning, and artificial intelligence},
  author={Raschka, Sebastian and Patterson, Joshua and Nolet, Corey},
  journal={Information},
  volume={11},
  number={4},
  pages={193},
  year={2020},
  publisher={MDPI}
}

@incollection{igual2024introduction,
  title={Introduction to data science},
  author={Igual, Laura and Segu{\'\i}, Santi},
  booktitle={Introduction to Data Science: A Python Approach to Concepts, Techniques and Applications},
  pages={1--4},
  year={2024},
  publisher={Springer}
}

@book{lin2022introduction,
  title={An introduction to Python programming for scientists and engineers},
  author={Lin, Johnny Wei-Bing and Aizenman, Hannah and Espinel, Erin Manette Cartas and Gunnerson, Kim and Liu, Joanne},
  year={2022},
  publisher={Cambridge University Press}
}

@techreport{andreuzzi2021improving,
  title={Improving throughput of CERN’s multi-language distributed online data processing platform},
  author={Andreuzzi, Francesco},
  year={2021}
}

@techreport{elvira2022future,
  title={The Future of High Energy Physics Software and Computing (V2. 1)},
  author={Elvira, V Daniel and Gottlieb, Steven and Gutsche, Oliver and Nachman, Benjamin},
  year={2022},
  institution={Fermi National Accelerator Laboratory (FNAL), Batavia, IL (United States)}
}

@incollection{gurovich2021visual,
  title={Visual and Near-infrared Astronomy},
  author={Gurovich, Sebastian and Payne, Jeffrey L and Filipovi{\'c}, Miroslav D},
  booktitle={Multimessenger Astronomy in Practice},
  pages={4--1},
  year={2021},
  publisher={IOP Publishing Bristol, UK}
}

@inproceedings{kamatar2023lazy,
  title={Lazy python dependency management in large-scale systems},
  author={Kamatar, Alok and Sakarvadia, Mansi and Hayot-Sasson, Valerie and Chard, Kyle and Foster, Ian},
  booktitle={2023 IEEE 19th International Conference on e-Science (e-Science)},
  pages={1--10},
  year={2023},
  organization={IEEE}
}

@misc{pypi2024ultralytics,
title={Supply-chain attack analysis: Ultralytics},
author={{Larson, Seth}},
publisher={{Python Package Index}},
year={2024},
month={December},
day={11}
}

@misc{checkmarx2024python,
title={Over 170K Users Affected by Attack Using Fake Python Infrastructure},
author={{Checkmarx Research Team}},
year={2024},
month={March}
}

@article{dux2024lightcurver,
  title={lightcurver: A Python Pipeline for Precise Photometry of Multiple-Epoch Wide-Field Images},
  author={Dux, Fr{\'e}d{\'e}ric},
  journal={arXiv preprint arXiv:2410.13625},
  year={2024}
}



@book{hilpisch2020python,
  title={Python for Algorithmic Trading},
  author={Hilpisch, Yves},
  year={2020},
  publisher={O'Reilly Media}
}

@book{chityala2020image,
  title={Image processing and acquisition using Python},
  author={Chityala, Ravishankar and Pudipeddi, Sridevi},
  year={2020},
  publisher={Chapman and Hall/CRC}
}

@article{imangaliyev2015personalized,
  title={Personalized microbial network inference via co-regularized spectral clustering},
  author={Imangaliyev, Sultan and Keijser, Bart and Crielaard, Wim and Tsivtsivadze, Evgeni},
  journal={Methods},
  volume={83},
  pages={28--35},
  year={2015},
  publisher={Elsevier}
}

@inproceedings{mane2024human,
  title={Human Disease Prediction Using Machine Learning},
  author={Mane, Vijay and Jadhav, Mohinee and Kadam, Ishita},
  booktitle={2024 International Conference on Emerging Smart Computing and Informatics (ESCI)},
  pages={1--6},
  year={2024},
  organization={IEEE}
}

@article{devi2023paper,
  title={Paper quality enhancement and model prediction using machine learning techniques},
  author={Devi, T Kalavathi and Priyanka, EB and Sakthivel, P},
  journal={Results in Engineering},
  volume={17},
  pages={100950},
  year={2023},
  publisher={Elsevier}
}

@article{laky2023using,
  title={Using PharmaPy with Jupyter Notebook to teach digital design in pharmaceutical manufacturing},
  author={Laky, Daniel J and Casas-Orozco, Daniel and Abdi, Mesfin and Feng, Xin and Wood, Erin and Reklaitis, Gintaras V and Nagy, Zoltan K},
  journal={Computer applications in engineering education},
  volume={31},
  number={6},
  pages={1662--1677},
  year={2023},
  publisher={Wiley Online Library}
}

@inproceedings{paffenroth2015python,
  title={Python in Data Science Research and Education.},
  author={Paffenroth, Randy C and Kong, Xiangnan},
  booktitle={SciPy},
  pages={164--170},
  year={2015}
}

@article{mantusov2021python,
  title={Python language in the development of computational competencies in humanities education},
  author={Mantusov, Anatoly B and Dorzhinova, Zamira B and others},
  journal={European Proceedings of Social and Behavioural Sciences},
  year={2021},
  publisher={European Publisher}
}

@article{bati2022integration,
  title={Integration of Python into Science Teacher Education, Developing Computational Problem Solving and Using Information and Communication Technologies Competencies of Pre-service Science Teachers},
  author={Bati, Kaan},
  journal={Informatics in Education-An International Journal},
  volume={21},
  number={2},
  pages={235--251},
  year={2022},
  publisher={Vilniaus Universiteto Leidykla}
}

@inproceedings{zhang2019applying,
  title={Applying python in brain science education},
  author={Zhang, Xiaofei and Huang, Jiajin and Yang, Yang and He, Xiang and Liu, Ruohao and Zhong, Ning},
  booktitle={2019 International Joint Conference on Information, Media and Engineering (IJCIME)},
  pages={396--400},
  year={2019},
  organization={IEEE}
}

@manual{r2023r,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2023},
  url = {https://www.R-project.org/},
}

@inproceedings{hagberg2008,
  address =       {Pasadena, CA USA},
  author =        {Aric A. Hagberg and Daniel A. Schult and
                   Pieter J. Swart},
  booktitle =     {Proceedings of the 7th Python in Science Conference},
  editor =        {Ga\"el Varoquaux and Travis Vaught and
                   K. Jarrod Millman},
  pages =         {11--15},
  title =         {Exploring Network Structure, Dynamics, and Function
                   using {NetworkX}},
  year =          {2008},
}

@article{astropy:2013,
  author =        {{Astropy Collaboration} and {Robitaille}, T.~P. and
                   {Tollerud}, E.~J. and {Greenfield}, P. and
                   {Droettboom}, M. and {Bray}, E. and {Aldcroft}, T. and
                   {Davis}, M. and {Ginsburg}, A. and
                   {Price-Whelan}, A.~M. and {Kerzendorf}, W.~E. and
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                   {Pierfederici}, F. and {Pontzen}, A. and {Ptak}, A. and
                   {Refsdal}, B. and {Servillat}, M. and
                   {Streicher}, O.},
  journal =       {Astronomy \& Astrophysics},
  month =         oct,
  pages =         {A33},
  title =         {{Astropy: A community Python package for astronomy}},
  volume =        {558},
  year =          {2013},
  doi =           {10.1051/0004-6361/201322068},
  eid =           {A33},
}


@article{astropy:2018,
  author =        {{Price-Whelan}, A.~M. and {Sip{\H{o}}cz}, B.~M. and
                   {G{\"u}nther}, H.~M. and {Lim}, P.~L. and
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  journal =       {The Astronomical Journal},
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@article{millman2007analysis,
  author =        {Millman, K Jarrod and Brett, Matthew},
  journal =       {Computing in Science \& Engineering},
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@article{price2018astropy,
  title={The Astropy Project: Building an open-science project and status of the v2. 0 core package},
  author={Price-Whelan, Adrian M and Sip{\H{o}}cz, BM and G{\"u}nther, HM and Lim, PL and Crawford, SM and Conseil, S and Shupe, DL and Craig, MW and Dencheva, N and Ginsburg, A and others},
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@book{james2013introduction,
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@InProceedings{pmlr-v80-massias18a,
  title     = {Celer: a Fast Solver for the Lasso with Dual Extrapolation},
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  booktitle = {Proceedings of the 35th International Conference on Machine Learning},
  pages     = {3321--3330},
  year      = {2018},
  volume    = {80},
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@article{millman2011python,
  title={Python for scientists and engineers},
  author={Millman, K Jarrod and Aivazis, Michael},
  journal={Computing in science \& engineering},
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  pages={9--12},
  year={2011},
  publisher={IEEE}
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@article{millman2014developing,
  author =        {Millman, K Jarrod and P{\'e}rez, Fernando},
  journal =       {Implementing Reproducible Research. CRC Press, Boca
                   Raton, FL},
  pages =         {149--183},
  title =         {Developing open-source scientific practice},
  year =          {2014},
  url =           {http://www.jarrodmillman.com/publications/millman2014developing.pdf},
}

@article{wilson-software-carpentry,
  author =        {Greg Wilson},
  journal =       {Computing in Science \& Engineering},
  month =         {November--December},
  title =         {Software Carpentry: Getting Scientists to Write
                   Better Code by Making Them More Productive},
  year =          {2006},
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@article{millman2018teaching,
  author =        {Millman, K Jarrod and Brett, Matthew and
                   Barnowski, Ross and Poline, Jean-Baptiste},
  journal =       {Frontiers in Neuroscience},
  pages =         {727},
  publisher =     {Frontiers},
  title =         {Teaching computational reproducibility for
                   neuroimaging},
  volume =        {12},
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@article{hoyer2017xarray,
  author =        {Hoyer, S. and J. Hamman},
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                   {Python}},
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  url =           {http://doi.org/10.5334/jors.148},
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@article{ihaka1996r,
  author =        {Ihaka, Ross and Gentleman, Robert},
  journal =       {Journal of Computational and Graphical Statistics},
  number =        {3},
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  publisher =     {Taylor \& Francis Group},
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@book{james2023introduction,
  title="An {I}ntroduction to {S}tatistical {L}earning: with {A}pplications in {P}ython",
  author="James, Gareth and Witten, Daniela and Hastie, Trevor and Tibshirani, Robert and Taylor, Jonathan",
  publisher="Springer Publication",
  year=2023,
  url="https://link.springer.com/book/10.1007/978-3-031-38747-0",
  doi="10.1007/978-3-031-38747-0",
  series="{S}pringer {T}exts in {S}tatistics"
}

@inproceedings{nbi0,
  author    = "Zhang, Keming and Jayasinghe, Tharindu and Bloom, Joshua",
  title     = "Stellar Spectra Fitting with Amortized Neural Posterior Estimation and nbi",
  year      = 2016,
  maintitle = "Fortieth International Conference on Machine Learning (ICML 2023)",
  booktitle = "Workshop on Machine Learning for Astrophysics"
}

@inproceedings{nbi1,
  author    = "Zhang, Keming and Bloom, Joshua and Hernitschek, Nina",
  title     = "nbi: the Astronomer’s Package for Neural Posterior Estimation",
  year      = 2023,
  maintitle = "Fortieth International Conference on Machine Learning (ICML 2023)",
  booktitle = "Workshop on Machine Learning for Astrophysics"
}

@inproceedings{nbi2,
  author    = "Zhang, Keming and Gaudi Scott B. and Bloom, Joshua",
  title     = "A Ubiquitous Unifying Degeneracy in 2-body Microlensing Systems",
  year      = 2022,
  maintitle = "Bulletin of the American Astronomical Society"
}

@inproceedings{nbi3,
  author    = "Blaum, Jacqueline and Bloom, Joshua",
  title     = "Stellar Insights at Scale with Likelihood-Free Inference",
  year      = 2022,
  maintitle = "American Astronomical Society Meeting Abstracts"
}

@article{carmichael2021yaglm,
  title={yaglm: a Python package for fitting and tuning generalized linear models that supports structured, adaptive and non-convex penalties},
  author={Carmichael, Iain and Keefe, Thomas and Giertych, Naomi and Williams, Jonathan P},
  journal={arXiv preprint arXiv:2110.05567},
  year={2021}
}



@article{carmichael2021joint,
  title={Joint and individual analysis of breast cancer histologic images and genomic covariates},
  author={Carmichael, Iain and Calhoun, Benjamin C and Hoadley, Katherine A and Troester, Melissa A and Geradts, Joseph and Couture, Heather D and Olsson, Linnea and Perou, Charles M and Niethammer, Marc and Hannig, Jan and others},
  journal={The annals of applied statistics},
  volume={15},
  number={4},
  pages={1697},
  year={2021},
  publisher={NIH Public Access}
}

@article{carmichael2020learning,
  title={Learning sparsity and block diagonal structure in multi-view mixture models},
  author={Carmichael, Iain},
  journal={arXiv preprint arXiv:2012.15313},
  year={2020}
}


@article{perry2021mvlearn,
  title={mvlearn: Multiview machine learning in python},
  author={Perry, Ronan and Mischler, Gavin and Guo, Richard and Lee, Theodore and Chang, Alexander and Koul, Arman and Franz, Cameron and Richard, Hugo and Carmichael, Iain and Ablin, Pierre and others},
  journal={The Journal of Machine Learning Research},
  volume={22},
  number={1},
  pages={4938--4944},
  year={2021},
  publisher={JMLRORG}
}

@article{scikit-learn,
 title={Scikit-learn: Machine Learning in {P}ython},
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         and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
         and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
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@inproceedings{sklearn_api,
  author    = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
               Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
               Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
               and Jaques Grobler and Robert Layton and Jake VanderPlas and
               Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
  title     = {{API} design for machine learning software: experiences from the scikit-learn
               project},
  booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
  year      = {2013},
  pages = {108--122},
}

@article{carmichael2021folded,
  title={The folded concave Laplacian spectral penalty learns block diagonal sparsity patterns with the strong oracle property},
  author={Carmichael, Iain},
  journal={arXiv preprint arXiv:2107.03494},
  year={2021}
}

@article{gentleman2004bioconductor,
  title={Bioconductor: open software development for computational biology and bioinformatics},
  author={Gentleman, Robert C and Carey, Vincent J and Bates, Douglas M and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and others},
  journal={Genome biology},
  volume={5},
  number={10},
  pages={1--16},
  year={2004},
  publisher={BioMed Central}
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@article{wickham2019welcome,
  title={Welcome to the  {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and
    Winston Chang and Lucy D'Agostino McGowan and Romain François and
    Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester
    and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan
    Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson
    and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and
    Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  journal={Journal of open source software},
  volume={4},
  number={43},
  pages={1686},
  year={2019},
  doi = {10.21105/joss.01686},
}

@article{carmichael2021geometric,
  title={Geometric insights into support vector machine behavior using the KKT conditions},
  author={Carmichael, Iain and Marron, JS},
  journal={Electronic Journal of Statistics},
  volume={15},
  number={2},
  pages={6311--6343},
  year={2021},
  publisher={The Institute of Mathematical Statistics and the Bernoulli Society}
}

@article{rodrigues2020syo,
    author = "Rodrigues, Eduardo and others",
    editor = "Doglioni, C. and Kim, D. and Stewart, G. A. and Silvestris, L. and Jackson, P. and Kamleh, W.",
    title = "{The Scikit HEP Project -- overview and prospects}",
    eprint = "2007.03577",
    archivePrefix = "arXiv",
    primaryClass = "physics.comp-ph",
    doi = "10.1051/epjconf/202024506028",
    journal = "EPJ Web Conf.",
    volume = "245",
    pages = "06028",
    year = "2020"
}

@article{gazzola2023s,
  title={What’s in a Name? Terminology Preferences Among Patients Receiving Methadone Treatment},
  author={Gazzola, Marina Gaeta and Maclean, Emma and Beitel, Mark and Carmichael, Iain D and Cammack, Katharine M and Eggert, Kathryn F and Roehrich, Teresa and Madden, Lynn M and Jegede, Oluwole and Zheng, Xiaoying and others},
  journal={Journal of General Internal Medicine},
  volume={38},
  number={3},
  pages={653--660},
  year={2023},
  publisher={Springer}
}

@article{gazzola2022cohort,
  title={A cohort study examining the relationship among housing status, patient characteristics, and retention among individuals enrolled in low-barrier-to-treatment-access methadone maintenance treatment},
  author={Gazzola, Marina Gaeta and Carmichael, Iain D and Madden, Lynn M and Dasgupta, Nabarun and Beitel, Mark and Zheng, Xiaoying and Eggert, Kathryn F and Farnum, Scott O and Barry, Declan T},
  journal={Journal of substance abuse treatment},
  volume={138},
  pages={108753},
  year={2022},
  publisher={Elsevier}
}

# Cites Scikit-HEP tooling
@article{Jung:2025oqh,
    author = "Jung, Philipp Alexander",
    collaboration = "CMS",
    title = "{b-hive: a modern start-to-finish flavor tagging framework}",
    doi = "10.22323/1.478.0275",
    journal = "PoS",
    volume = "LHCP2024",
    pages = "275",
    year = "2025"
}

# Talks about needing to support 'Python ecosystem for analysis' for the HL-LHC computing model
@article{Albin:2023szc,
    author = "Albin, Sam and Attebury, Garhan and Bloom, Kenneth and Bockelman, Brian and Lundstedt, Carl and Shadura, Oksana and Thiltges, John",
    title = "{Coffea-Casa: Building composable analysis facilities for the HL-LHC}",
    eprint = "2312.11485",
    archivePrefix = "arXiv",
    primaryClass = "cs.DC",
    doi = "10.1051/epjconf/202429507009",
    journal = "EPJ Web Conf.",
    volume = "295",
    pages = "07009",
    year = "2024"
}

# Technical computing report from ATLAS for the HL-LHC with discussion of using Scientific Python
@techreport{CERN-LHCC-2022-005,
      author        = "ATLAS Collaboration",
      title         = "{ATLAS Software and Computing HL-LHC Roadmap}",
      institution   = "CERN",
      reportNumber  = "CERN-LHCC-2022-005, LHCC-G-182",
      address       = "Geneva",
      year          = "2022",
      url           = "https://cds.cern.ch/record/2802918",
}

# Report for all 4 major LHC epxeiments that includes Scikit-HEP for HL-LHC
@article{Shope:2025ukx,
    author = "Shope, David Richard",
    collaboration = "ALICE, ATLAS, CMS, LHCb",
    title = "{Software Upgrades for the High-Luminosity LHC}",
    doi = "10.22323/1.478.0193",
    journal = "PoS",
    volume = "LHCP2024",
    pages = "193",
    year = "2025"
}

@article{pyhf_joss,
  doi = {10.21105/joss.02823},
  url = {https://doi.org/10.21105/joss.02823},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {58},
  pages = {2823},
  author = {Lukas Heinrich and Matthew Feickert and Giordon Stark and Kyle Cranmer},
  title = {pyhf: pure-Python implementation of HistFactory statistical models},
  journal = {Journal of Open Source Software}
}