IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-48559-9.html
   My bibliography  Save this article

Multispecies deep learning using citizen science data produces more informative plant community models

Author

Listed:
  • Philipp Brun

    (Swiss Federal Research Institute WSL)

  • Dirk N. Karger

    (Swiss Federal Research Institute WSL)

  • Damaris Zurell

    (University of Potsdam)

  • Patrice Descombes

    (département de botanique
    University of Lausanne)

  • Lucienne C. Witte

    (Swiss Federal Research Institute WSL)

  • Riccardo Lutio

    (ETH Zurich)

  • Jan Dirk Wegner

    (University of Zurich)

  • Niklaus E. Zimmermann

    (Swiss Federal Research Institute WSL)

Abstract

In the age of big data, scientific progress is fundamentally limited by our capacity to extract critical information. Here, we map fine-grained spatiotemporal distributions for thousands of species, using deep neural networks (DNNs) and ubiquitous citizen science data. Based on 6.7 M observations, we jointly model the distributions of 2477 plant species and species aggregates across Switzerland with an ensemble of DNNs built with different cost functions. We find that, compared to commonly-used approaches, multispecies DNNs predict species distributions and especially community composition more accurately. Moreover, their design allows investigation of understudied aspects of ecology. Including seasonal variations of observation probability explicitly allows approximating flowering phenology; reweighting predictions to mirror cover-abundance allows mapping potentially canopy-dominant tree species nationwide; and projecting DNNs into the future allows assessing how distributions, phenology, and dominance may change. Given their skill and their versatility, multispecies DNNs can refine our understanding of the distribution of plants and well-sampled taxa in general.

Suggested Citation

  • Philipp Brun & Dirk N. Karger & Damaris Zurell & Patrice Descombes & Lucienne C. Witte & Riccardo Lutio & Jan Dirk Wegner & Niklaus E. Zimmermann, 2024. "Multispecies deep learning using citizen science data produces more informative plant community models," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48559-9
    DOI: 10.1038/s41467-024-48559-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-48559-9
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-48559-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Gneiting, Tilmann & Raftery, Adrian E., 2007. "Strictly Proper Scoring Rules, Prediction, and Estimation," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 359-378, March.
    2. Christophe Botella & Alexis Joly & Pascal Monestiez & Pierre Bonnet & François Munoz, 2020. "Bias in presence-only niche models related to sampling effort and species niches: Lessons for background point selection," PLOS ONE, Public Library of Science, vol. 15(5), pages 1-18, May.
    3. Gregory Giuliani & Denisa Rodila & Nathan Külling & Ramona Maggini & Anthony Lehmann, 2022. "Downscaling Switzerland Land Use/Land Cover Data Using Nearest Neighbors and an Expert System," Land, MDPI, vol. 11(5), pages 1-21, April.
    4. Benjamin Deneu & Maximilien Servajean & Pierre Bonnet & Christophe Botella & François Munoz & Alexis Joly, 2021. "Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment," PLOS Computational Biology, Public Library of Science, vol. 17(4), pages 1-21, April.
    5. Detlef Vuuren & Jae Edmonds & Mikiko Kainuma & Keywan Riahi & Allison Thomson & Kathy Hibbard & George Hurtt & Tom Kram & Volker Krey & Jean-Francois Lamarque & Toshihiko Masui & Malte Meinshausen & N, 2011. "The representative concentration pathways: an overview," Climatic Change, Springer, vol. 109(1), pages 5-31, November.
    6. Charles R. Harris & K. Jarrod Millman & Stéfan J. Walt & Ralf Gommers & Pauli Virtanen & David Cournapeau & Eric Wieser & Julian Taylor & Sebastian Berg & Nathaniel J. Smith & Robert Kern & Matti Picu, 2020. "Array programming with NumPy," Nature, Nature, vol. 585(7825), pages 357-362, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Parinaz Rashidi & Sopan D. Patil & Aafke M. Schipper & Rob Alkemade & Isabel Rosa, 2023. "Downscaling Global Land-Use Scenario Data to the National Level: A Case Study for Belgium," Land, MDPI, vol. 12(9), pages 1-19, September.
    2. Tan Wang & L. Jeff Hong, 2023. "Large-Scale Inventory Optimization: A Recurrent Neural Networks–Inspired Simulation Approach," INFORMS Journal on Computing, INFORMS, vol. 35(1), pages 196-215, January.
    3. Azar, Pablo D. & Micali, Silvio, 2018. "Computational principal agent problems," Theoretical Economics, Econometric Society, vol. 13(2), May.
    4. Léon Faure & Bastien Mollet & Wolfram Liebermeister & Jean-Loup Faulon, 2023. "A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Angelica Gianfreda & Francesco Ravazzolo & Luca Rossini, 2023. "Large Time‐Varying Volatility Models for Hourly Electricity Prices," Oxford Bulletin of Economics and Statistics, Department of Economics, University of Oxford, vol. 85(3), pages 545-573, June.
    6. Claudia Quinteros-Cartaya & Guillermo Solorio-Magaña & Francisco Javier Núñez-Cornú & Felipe de Jesús Escalona-Alcázar & Diana Núñez, 2023. "Microearthquakes in the Guadalajara Metropolitan Zone, Mexico: evidence from buried active faults in Tesistán Valley, Zapopan," Natural Hazards: Journal of the International Society for the Prevention and Mitigation of Natural Hazards, Springer;International Society for the Prevention and Mitigation of Natural Hazards, vol. 116(3), pages 2797-2818, April.
    7. Tobias Fissler & Yannick Hoga, 2024. "How to Compare Copula Forecasts?," Papers 2410.04165, arXiv.org.
    8. Davide Pettenuzzo & Francesco Ravazzolo, 2016. "Optimal Portfolio Choice Under Decision‐Based Model Combinations," Journal of Applied Econometrics, John Wiley & Sons, Ltd., vol. 31(7), pages 1312-1332, November.
    9. Gupta, Rishabh & Mishra, Ashok, 2019. "Climate change induced impact and uncertainty of rice yield of agro-ecological zones of India," Agricultural Systems, Elsevier, vol. 173(C), pages 1-11.
    10. Rubio, F.J. & Steel, M.F.J., 2011. "Inference for grouped data with a truncated skew-Laplace distribution," Computational Statistics & Data Analysis, Elsevier, vol. 55(12), pages 3218-3231, December.
    11. Voisin, Nathalie & Dyreson, Ana & Fu, Tao & O'Connell, Matt & Turner, Sean W.D. & Zhou, Tian & Macknick, Jordan, 2020. "Impact of climate change on water availability and its propagation through the Western U.S. power grid," Applied Energy, Elsevier, vol. 276(C).
    12. Furqan Dar & Samuel R. Cohen & Diana M. Mitrea & Aaron H. Phillips & Gergely Nagy & Wellington C. Leite & Christopher B. Stanley & Jeong-Mo Choi & Richard W. Kriwacki & Rohit V. Pappu, 2024. "Biomolecular condensates form spatially inhomogeneous network fluids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    13. Hwang, Eunju, 2022. "Prediction intervals of the COVID-19 cases by HAR models with growth rates and vaccination rates in top eight affected countries: Bootstrap improvement," Chaos, Solitons & Fractals, Elsevier, vol. 155(C).
    14. R de Fondeville & A C Davison, 2018. "High-dimensional peaks-over-threshold inference," Biometrika, Biometrika Trust, vol. 105(3), pages 575-592.
    15. Armantier, Olivier & Treich, Nicolas, 2013. "Eliciting beliefs: Proper scoring rules, incentives, stakes and hedging," European Economic Review, Elsevier, vol. 62(C), pages 17-40.
    16. Domenico Piccolo & Rosaria Simone, 2019. "The class of cub models: statistical foundations, inferential issues and empirical evidence," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 28(3), pages 389-435, September.
    17. Finn Lindgren, 2015. "Comments on: Comparing and selecting spatial predictors using local criteria," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 24(1), pages 35-44, March.
    18. Chuliá, Helena & Garrón, Ignacio & Uribe, Jorge M., 2024. "Daily growth at risk: Financial or real drivers? The answer is not always the same," International Journal of Forecasting, Elsevier, vol. 40(2), pages 762-776.
    19. Nina Tiel & Fabian Fopp & Philipp Brun & Johan Hoogen & Dirk Nikolaus Karger & Cecilia M. Casadei & Lisha Lyu & Devis Tuia & Niklaus E. Zimmermann & Thomas W. Crowther & Loïc Pellissier, 2024. "Regional uniqueness of tree species composition and response to forest loss and climate change," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    20. Laura Liu & Hyungsik Roger Moon & Frank Schorfheide, 2023. "Forecasting with a panel Tobit model," Quantitative Economics, Econometric Society, vol. 14(1), pages 117-159, January.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48559-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.