Publications

Journal and conference publications

No Publication References Years Types
1
Avavi, A. (2023). Expert Finding for Citizen Science. In Artificial Intelligence Research and Development: Proceedings of the 25th International Conference of the Catalan Association for Artificial Intelligence (Vol. 375, p. 59). SAGE Publications Limited.
2023
Conference proceedings
2
Bonnet P, Affouard A, Lombardo J-C, Chouet M, Gresse H, Hequet V, Palard R, Fromholtz M, Espitalier V, Goëau H, Deneu B, Botella C, Estopinan J, Leblanc C, Servajean M, Munoz F, Joly A. (2023) Synergizing Digital, Biological, and Participatory Sciences for Global Plant Species Identification: Enabling access to a worldwide identification service. Biodiversity Information Science and Standards 7: e112545.
2023
Conference proceedings
3
Botella, C., Deneu, B., Marcos, D., Servajean, M., Estopinan, J., Larcher, T., ... & Joly, A. (2023). The GeoLifeCLEF 2023 Dataset to evaluate plant species distribution models at high spatial resolution across Europe. arXiv preprint arXiv:2308.05121.
2023
Data paper
4
Ceccaroni, L., Oliver, J. L., Roger, E., Bibby, J., Flemons, P., Michael, K., & Joly, A. (2023). Advancing the productivity of science with citizen science and artificial intelligence, in OECD (2023), Artificial Intelligence in Science: Challenges, Opportunities and the Future of Research, OECD Publishing, Paris,
2023
Journal
5
Goëau, H., Bonnet, P., & Joly, A. (2025). Overview of PlantCLEF 2023: image-based plant identification at global scale. CLEF 2023 Conference and Labs of the Evaluation Forum, September 18 to 21, 2023, Thessaloniki, Greece.
2023
Conference proceedings
6
Joly, A., Botella, C., Picek, L., Kahl, S., Goëau, H., Deneu, B., ... & Müller, H. (2023). Overview of LifeCLEF 2023: evaluation of ai models for the identification and prediction of birds, plants, snakes and fungi. In International Conference of the Cross-Language Evaluation Forum for European Languages (pp. 416-439). Cham: Springer Nature Switzerland.
2023
Conference proceedings
7
Komander, B., Cerquides, J., & Piera, J. (2023). Developing and Validating Tools for the Automated Analysis and Enhancement of Online Discussions. In HHAI 2023: Augmenting Human Intellect (pp. 433-435). IOS Press.
2023
Conference proceedings
8
Lukowicz, P. (2023). Developing and Validating Tools for the Automated Analysis and Enhancement of Online Discussions. In HHAI 2023: Augmenting Human Intellect: Proceedings of the Second International Conference on Hybrid Human-Artificial Intelligence (Vol. 368, p. 433). IOS Press.
2023
Conference proceedings
9
Sanz, I. (2023). Expert Finding for Citizen Science. In Artificial Intelligence Research and Development: Proceedings of the 25th International Conference of the Catalan Association for Artificial Intelligence (Vol. 375, p. 59). IOS Press.
2023
Conference proceedings
10
Díaz-Calafat, J., Jaume-Ramis, S., Soacha, K., Álvarez, A., & Piera, J. (2024). Revealing biases in insect observations: A comparative analysis between academic and citizen science data. Plos one, 19(7), e0305757.
2024
Journal
11
Estopinan, J., Bonnet, P., Servajean, M., Munoz, F., & Joly, A. (2024). Modelling Species Distributions with Deep Learning to Predict Plant Extinction Risk and Assess Climate Change Impacts. arXiv preprint arXiv:2401.05470.
2024
Pre-print
12
Estopinan, J., Servajean, M., Bonnet, P., Joly, A., & Munoz, F. (2024). Mapping global orchid assemblages with deep learning provides novel conservation insights. Ecological Informatics, 81, 102627.
2024
Journal
13
Ghani, B., Kalkman, V. J., Planqué, B., Vellinga, W. P., Gill, L., & Stowell, D. (2024). Generalization in birdsong classification: impact of transfer learning methods and dataset characteristics. arXiv preprint arXiv:2409.15383.
2024
Pre-print
14
Goeau, H., Espitalier, V., Bonnet, P., & Joly, A. (2025). Overview of PlantCLEF 2024: multi-species plant identification in vegetation plot images. CLEF 2024 Conference and Labs of the Evaluation Forum, September 09 to 12, 2024, Grenoble, France.
2024
Conference proceedings
15
Joly, A., Picek, L., Kahl, S., Goëau, H., Espitalier, V., Botella, C., ... & Müller, H. (2024). Overview of LifeCLEF 2024: Challenges on species distribution prediction and identification. In International Conference of the Cross-Language Evaluation Forum for European Languages (pp. 183-207). Cham: Springer Nature Switzerland.
2024
Pre-print
16
Larcher, T., Picek, L., Deneu, B., Lorieul, T., Servajean, M., & Joly, A. (2024). Malpolon: a framework for deep species distribution modeling. arXiv preprint arXiv:2409.18102.
2024
Pre-print
17
Leblanc, C., Bonnet, P., Servajean, M., Chytrý, M., Aćić, S., Argagnon, O., ... & Joly, A. (2024). A deep‐learning framework for enhancing habitat identification based on species composition. Applied vegetation science, 27(3), e12802.
2024
Journal
18
Lefort, T., Affouard, A., Charlier, B., Lombardo, J. C., Chouet, M., Goëau, H., ... & Joly, A. (2024). Cooperative learning of Pl@ntNet's Artificial Intelligence algorithm: how does it work and how can we improve it?. Methods in Ecology and Evolution. 00, 1–12.
2024
Journal
19
Macau, A. M., Rodriguez-Soto, M., López-Sánchez, M., Aguilar, J. A. R., Marchesini, E., & Farinelli, A (2024). An approximate process for designing ethical environments with multi-agent reinforcement learning. In The Sixteenth Workshop on Adaptive and Learning Agents. Auckland, New Zealand.
2024
Conference proceedings
20
Pernat, N., Memedemin, D., August, T., Preda, C., Reyserhove, L., Schirmel, J., & Groom, Q. (2024). Extracting secondary data from citizen science images reveals host flower preferences of the Mexican grass‐carrying wasp Isodontia mexicana in its native and introduced ranges. Ecology and Evolution, 14(6), e11537.
2024
Journal
21
Picek, L., Botella, C., Servajean, M., Leblanc, C., Palard, R., Larcher, T., ... & Joly, A. (2024). Geoplant: Spatial plant species prediction dataset. Advances in Neural Information Processing Systems, 37, 126653-126676.
2024
Conference proceedings
22
Porcher E, Bonnet P, Damgaard C, De Frenne P, Deguines N, Ehlers B K., Frei J, García M B., Gros C, Jandt U, Joly A, Martin G, Michez D, Pescott O L., Roth T, Waller D. (2024). Can we harmonize the monitoring of plants and pollinators?. New Phytologist, 244 (1) : 39-42.
2024
Journal
23
Priebe, D., Ghani, B., & Stowell, D. (2024). Efficient speech detection in environmental audio using acoustic recognition and knowledge distillation. Sensors, 24(7), 2046.
2024
Journal
24
Rodríguez Soto, M., Rodriguez-Aguilar, J. A., & Lopez-Sanchez, M. (2024). An analytical study of utility functions in multi-objective reinforcement learning. Advances in Neural Information Processing Systems, 37, 77726-77747.
2024
Conference proceedings
25
Rodríguez-Farrés, P., Ballester, R., Ansótegui, C., Levy, J., Cerquides, J. (2024). Implementing 3-SAT Gadgets for Quantum Annealers with Random Instances. In: Franco, L., de Mulatier, C., Paszynski, M., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M.A. (eds) Computational Science – ICCS 2024. ICCS 2024. Lecture Notes in Computer Science, vol 14837. Springer, Cham.
2024
Conference proceedings
26
Bourel, B., Joly, A., Servajean, M., Bettinger, S., Sanabria‐Fernández, J. A., & Mouillot, D. (2025). From Presence‐Only to Abundance Species Distribution Models Using Transfer Learning. Ecology Letters, 28(7), e70177.
2024
Journal
27
Espitalier, V., Lombardo, J. C., Goëau, H., Botella, C., Høye, T. T., Dyrmann, M., ... & Joly, A. (2025). Adapting a global plant identification model to detect invasive alien plant species in high-resolution road side images. Ecological Informatics, Vol. 89, 103129.
2025
Journal
28
Faiß, M., Ghani, B., & Stowell, D. (2025). InsectSet459: an open dataset of insect sounds for bioacoustic machine learning. arXiv preprint arXiv:2503.15074.
2025
Data paper
29
Gil‐Gonzalez, S., Velasco‐Regúlez, B., Cerquides, J., Hinarejos, P., Monllau, J. C., & Pelfort, X. (2025). Antibiotic‐loaded bone cement is associated with a reduction of the risk of revision of total knee arthroplasty: Analysis of the Catalan Arthroplasty Register. Knee Surgery, Sports Traumatology, Arthroscopy, 33(1), 354-363.
2025
Journal
30
Leblanc, C., Bonnet, P., Servajean, M., Thuiller, W., Chytrý, M., Aćić, S., ... & Joly, A. (2025). Learning the syntax of plant assemblages. Nature Plants 11, 2026–2040.
2025
Journal
31
Leblanc, C., Picek, L., Palard, R., Deneu, B., Servajean, M., Bonnet, P., & Joly, A. (2025). Mapping biodiversity at very-high resolution in Europe. In Proceedings of the Computer Vision and Pattern Recognition Conference (pp. 2349-2358).
2025
Conference proceedings
32
Marcos, D., van de Vlasakker, R., Athanasiadis, I. N., Bonnet, P., Goëau, H., Joly, A., ... & Panousis, K. P. (2025). Fully automatic extraction of morphological traits from the web: Utopia or reality? Applications in Plant Sciences 13(3): e70005.
2025
Journal
33
Martellucci, G., Goeau, H., Bonnet, P., Vinatier, F., & Joly, A. (2025). Overview of PlantCLEF 2025: Multi-species plant identification in vegetation quadrat images. CLEF 2025 Conference and Labs of the Evaluation Forum, September 09 to 12, 2024, Madrid, Spain.
2025
Conference proceedings
34
Pardo, D., Mulayim, M. O., & Castillo, M. (2025). Decoding Cheese Ripening: A Deep Learning Approach to Non-Invasive Monitoring. In Artificial Intelligence Research and Development, IOS Press.
2025
Conference proceedings
35
Picek, L., Kahl, S., Goëau, H., Adam, L., Larcher, T., Leblanc, C., ... & Joly, A. (2025). Overview of LifeCLEF 2025: Challenges on species presence prediction and identification, and individual animal identification. In International Conference of the Cross-Language Evaluation Forum for European Languages (pp. 338-362). Cham: Springer Nature Switzerland.
2025
Conference proceedings
36
Soacha-Godoy, K., López-Borrull, A., Serrano, F., & Piera, J. (2025). The Backbone of Participatory Science: Reframing Citizen Observatories as Research Infrastructures. Sustainability, 17(10), 4608.
2025
Journal
37
Soacha-Godoy, K., Prakash, P., Álvarez, A., Tejada, A.G., LópezBorrull, A., Salvador, X., Rodero, C., Torres, D., Rodero, I., Ayure, M. and Piera, J. (2025). Research Infrastructures in Citizen Science: State of Knowledge and Taxonomic Framework as a Pathway to Sustainability. Citizen Science: Theory and Practice, 10(1): 21, pp. 1–17.
2025
Journal
38
Kefalas, G., Lorilla, R. S., Boutsios, S., Bormpoudakis, D., Bonnet, P., Demertzi, A., Liquete, C., Vogiatzakis, I. Ν., Tzanopoulos, J., Upton, J., Howland, E., Bingham, H., Apostolopoulou, K., Burgess, N., & Drakou, E. G. (2026). Spatial identification of areas suitable for other effective area-based conservation measures in the European Union. Conservation Biology, e70263. https://doi.org/10.1111/cobi.70263
2026
Journal
39
R.S. LORILLA, G. KEFALAS, J. DUCRETTET, A. STRITIH, S. BOUTSIOS, L. SIRVENT, R. PALARD, A. JOLY, P. BONNET, E.G. DRAKOU, Co-developing ecosystem services indicators for sustainable local decision-making, Environmental and Sustainability Indicators, 2026.
2026
Journal

Technical Publications

No Partner(s) Title Publication Platform
1
CIRAD-INRIA
Couverture de toutes les flores du monde & nouvelle identification IA
Pl@ntNet website
2
CIRAD-INRIA
Pl@ntNet FAQ
Web version of Pl@ntNet identification tool
3
CIRAD-INRIA
Pl@ntNet FAQ
Web version of Pl@ntNet identification tool
4
CIRAD-INRIA
Covering all countries floras & new identification AI
Pl@ntNet website
5
INRIA
Malpolon public documentation
Plantnet.github.io
6
CIRAD-INRIA
Comprendre Pl@ntNet
Pl@ntNet website
7
CIRAD-INRIA
Understanding Pl@ntNet
Pl@ntNet website
8
CIRAD-INRIA
Update of the Pl@ntNet API documentation
My.pl@ntnet
9
CIRAD-INRIA
ARISE Machine prediction API - technical documentation
GUARDEN website
10
NATURALIS
AvesEcho v0.1 model and scripts documentation
GitLab
11
CIRAD-INRIA
Introduction to the technical developments on the Pl@ntNet platform to enable the use of two new international standards (World Checklist of Vascular Plants-WCVP from Kew Gardens, and World Geographical Scheme for Recording Plant Distributions-WGSRPD from TDWG), for the identification of plant communities within different regions of biogeographical interest in Europe
Pl@ntNet website
12
CIRAD-INRIA
Introduction to the technical developments on the Pl@ntNet platform to enable the use of two new international standards (World Checklist of Vascular Plants-WCVP from Kew Gardens, and World Geographical Scheme for Recording Plant Distributions-WGSRPD from TDWG), for the identification of plant communities within different regions of biogeographical interest in Europe
Pl@ntNet website
13
CIRAD-INRIA
Frequently asked questions (FAQ) of the Pl@ntNet platform, dedicated to clarify its use (for web or mobile version) for production of validated plant observations used to train deep learning model developed within task 3.1.
Web version of Pl@ntNet identification tool
14
CIRAD-INRIA
Frequently asked questions (FAQ) of the Pl@ntNet platform, dedicated to clarify its use (for web or mobile version) for production of validated plant observations used to train deep learning model developed within task 3.1.
Web version of Pl@ntNet identification tool
15
CIRAD-INRIA
Introduction to the tools for collecting botanical observations through Pl@ntNet
Pl@ntNet website
16
CIRAD-INRIA
Introduction to the tools for collecting botanical observations through Pl@ntNet
Pl@ntNet website
17
CIRAD-INRIA
GUARDEN system architecture description
GUARDEN website
18
CSIC
GUARDEN ICT tools description
GUARDEN website
19
HUA
Technical documentation on prediction of future trajectories of biodiversity and ecosystem services
GUARDEN website
20
INRIA
Technical documentation on prediction of maps of biodiversity indicators and habitats
GUARDEN website
21
MBG
Technical documentation on the improvement of species assemblages' prediction through species interactions
GUARDEN website
22
CIRAD-INRIA
Technical documentation on the community-level species identification services
GUARDEN website
23
CIRAD-INRIA
General introduction of the API for plant species identification
Web version of Pl@ntNet identification tool
24
CIRAD-INRIA
Technical documentation of the API structure for the plant species identification service
Web version of Pl@ntNet identification tool
25
CIRAD-INRIA
Technical documentation of the API structure for multi-species survey identification
Web version of Pl@ntNet identification tool
26
CIRAD-INRIA
Technical documentation on how to load the Dinov2 finetunes deep learning model provided to the participants to PlantCLEF2025 competition
Kaggle
27
CIRAD-INRIA
Technical documentation on how to perform inference on quadrat plant community images with a tiling-based approach
Kaggle
28
CIRAD-INRIA
Technical documentation on how to infer the available trained models on quadrat test images, for PlantCLEF 2025 participants
Kaggle
29
CIRAD-INRIA
Documentation of the Malpolon deep learning framework used to make plant species prediction based on environmental / satellite data
plantNet GitHub
30
CIRAD-INRIA
Detailed description of the "Spatial Plant Species Prediction Dataset, GeoPlant" published in "Advances in Neural Information Processing Systems". (Picek, L. et al., 2024, Geoplant: Spatial plant species prediction dataset. Advances in Neural Information Processing Systems, 37, 126653-126676.
arXiv
31
CIRAD-INRIA
Technical documentation of the GUARDEN pipeline, implemented to make plant species distribution and habitat predictions, published in proceedings of the CVPR workshop. (Leblanc, C. et al., 2025. Mapping biodiversity at very-high resolution in Europe. In Proceedings of the Computer Vision and Pattern Recognition Conference (pp. 2349-2358).
arXiv
32
CIRAD-INRIA
Technical documentation on how to download GeoPlant dataset from source
Kaggle
33
CIRAD-INRIA
Technical documentation on how to produce a baseline for the prediction of plant species distribution, based on GeoPlant dataset with Sentinel2 image patches
Kaggle
34
CIRAD-INRIA
Technical documentation on how to implement naive approaches for the prediction of plant species distributions, based on GeoPlant dataset
Kaggle
35
CIRAD-INRIA
Technical documentation on how to produce a baseline for the prediction of plant species distribution, based on GeoPlant dataset with Landsat Cubes
Kaggle
36
CIRAD-INRIA
Technical documentation on how to produce a baseline for the prediction of plant species distribution, based on GeoPlant dataset with Landsat, Bioclimatic Cubes and Sentinel2 images
Kaggle
37
CIRAD-INRIA
Technical documentation of the HDM framework, https://github.com/cesar-leblanc/hdm-framework/blob/main/README.md, published in Leblanc C., et al, 2025 (Leblanc, C., Bonnet, P., Servajean, M., Chytrý, M., Aćić, S., Argagnon, O., ... & Joly, A., 2024. A deep‐learning framework for enhancing habitat identification based on species composition. Applied vegetation science, 27(3), e12802.
GitHub
38
CIRAD-INRIA
Technical documentation of the Pl@ntBERT framework, https://github.com/cesar-leblanc/PlantBERT/blob/main/README.md, published in Leblanc C., et al, 2025 (Leblanc, C., Bonnet, P., Servajean, M., Thuiller, W., Chytrý, M., Aćić, S., ... & Joly, A. (2025). Learning the syntax of plant assemblages. Nature Plants 11, 2026–2040.
GitHub
Accessibility by WAH