arXiv subjects

Philipp Brun

Publications and source records attributed to Philipp Brun.

3 recordsLinked to original sources

arXiv2025

Multi-scale species richness estimation with deep learning

Biodiversity assessments depend critically on the spatial scale at which species richness is measured. How species richness accumulates with sampling area is influenced by natural and anthropogenic processes whose effects vary across spatial scales. These accumulation dynamics, described by the species-area relationship (SAR), are challenging to assess because most biodiversity surveys cover sampling areas far smaller than the scales at which these processes operate. Here, we combine sampling theory with deep learning to estimate species richness at arbitrary spatial scales across geographic space from existing ecological surveys. We apply our model, named MuScaRi, to ~350k vegetation surveys across Europe. Validated against independent regional plant inventories, MuScaRi reduces root mean squared error of vascular plant richness estimates by 61% relative to conventional estimators, yields substantially less biased predictions, and produces multi-scale richness maps alongside spatially explicit estimates of the species accumulation rate, a key indicator for biodiversity conservation. By encompassing the full spectrum of ecologically relevant spatial scales within a single unified framework, MuScaRi provides an essential tool for robust biodiversity assessments and forecasts under global change.

q-bio.PE↗

arXiv2025

SSL4Eco: A Global Seasonal Dataset for Geospatial Foundation Models in Ecology

With the exacerbation of the biodiversity and climate crises, macroecological pursuits such as global biodiversity mapping become more urgent. Remote sensing offers a wealth of Earth observation data for ecological studies, but the scarcity of labeled datasets remains a major challenge. Recently, self-supervised learning has enabled learning representations from unlabeled data, triggering the development of pretrained geospatial models with generalizable features. However, these models are often trained on datasets biased toward areas of high human activity, leaving entire ecological regions underrepresented. Additionally, while some datasets attempt to address seasonality through multi-date imagery, they typically follow calendar seasons rather than local phenological cycles. To better capture vegetation seasonality at a global scale, we propose a simple phenology-informed sampling strategy and introduce corresponding SSL4Eco, a multi-date Sentinel-2 dataset, on which we train an existing model with a season-contrastive objective. We compare representations learned from SSL4Eco against other datasets on diverse ecological downstream tasks and demonstrate that our straightforward sampling method consistently improves representation quality, highlighting the importance of dataset construction. The model pretrained on SSL4Eco reaches state of the art performance on 7 out of 8 downstream tasks spanning (multi-label) classification and regression. We release our code, data, and model weights to support macroecological and computer vision research at https://github.com/PlekhanovaElena/ssl4eco.

cs.CV↗

arXiv2021

Digital Taxonomist: Identifying Plant Species in Community Scientists' Photographs

Automatic identification of plant specimens from amateur photographs could improve species range maps, thus supporting ecosystems research as well as conservation efforts. However, classifying plant specimens based on image data alone is challenging: some species exhibit large variations in visual appearance, while at the same time different species are often visually similar; additionally, species observations follow a highly imbalanced, long-tailed distribution due to differences in abundance as well as observer biases. On the other hand, most species observations are accompanied by side information about the spatial, temporal and ecological context. Moreover, biological species are not an unordered list of classes but embedded in a hierarchical taxonomic structure. We propose a multimodal deep learning model that takes into account these additional cues in a unified framework. Our Digital Taxonomist is able to identify plant species in photographs better than a classifier trained on the image content alone, the performance gained is over 6 percent points in terms of accuracy.

cs.CV↗