arXiv subjects

Wilfried Thuiller

Publications and source records attributed to Wilfried Thuiller.

9 recordsLinked to original sources

arXiv2026

BotaCLIP: Contrastive Learning for Botany-Aware Representation of Earth Observation Data

Foundation models have demonstrated a remarkable ability to learn rich, transferable representations across diverse modalities such as images, text, and audio. In modern machine learning pipelines, these representations often replace raw data as the primary input for downstream tasks. In this paper, we address the challenge of adapting a pre-trained foundation model to inject domain-specific knowledge, without retraining from scratch or incurring significant computational costs. To this end, we introduce BotaCLIP, a lightweight multimodal contrastive framework that adapts a pre-trained Earth Observation foundation model (DOFA) by aligning high-resolution aerial imagery with botanical relevés. Unlike generic embeddings, BotaCLIP internalizes ecological structure through contrastive learning with a regularization strategy that mitigates catastrophic forgetting. Once trained, the resulting embeddings serve as transferable representations for downstream predictors. Motivated by real-world applications in biodiversity modeling, we evaluated BotaCLIP representations in three ecological tasks: plant presence prediction, butterfly occurrence modeling, and soil trophic group abundance estimation. The results showed consistent improvements over those derived from DOFA and supervised baselines. More broadly, this work illustrates how domain-aware adaptation of foundation models can inject expert knowledge into data-scarce settings, enabling frugal representation learning.

cs.CV↗

arXiv2025

Continental-scale habitat distribution modelling with multimodal earth observation foundation models

Habitats integrate the abiotic conditions, vegetation composition and structure that support biodiversity and sustain nature's contributions to people. Most habitats face mounting pressures from human activities, which requires accurate, high-resolution habitat mapping for effective conservation and restoration. Yet, current habitat maps often fall short in thematic or spatial resolution because they must (1) model several mutually exclusive habitat types that co-occur across landscapes and (2) cope with severe class imbalance that complicates exhaustive multi-class training. Here, we evaluated how high-resolution remote sensing (RS) data and Artificial Intelligence (AI) tools can improve habitat mapping across large geographical extents at fine spatial and thematic resolution. Using vegetation plots from the European Vegetation Archive, we modelled the distribution of Level 3 EUNIS habitat types across Europe and assessed multiple modelling strategies against independent validation datasets. Strategies that exploited the hierarchical nature of habitat classifications resolved classification ambiguities, especially in fragmented habitats. Integrating satellite-borne multispectral and radar imagery, particularly through Earth Observation (EO) Foundation models (EO-FMs), enhanced within-formation discrimination and overall performance. Finally, ensemble machine learning that corrects class imbalance boosted predictive accuracy even further. Our methodological framework is transferable beyond Europe and adaptable to other classification systems. Future research should advance temporal modelling of habitat dynamics, extend to habitat segmentation and quality assessment, and exploit next-generation EO data paired with higher-quality in situ observations.

cs.LG↗

arXiv2025

Uncovering symmetric and asymmetric species associations from community and environmental data

There is no much doubt that biotic interactions shape community assembly and ultimately the spatial co-variations between species. There is a hope that the signal of these biotic interactions can be observed and retrieved by investigating the spatial associations between species while accounting for the direct effects of the environment. By definition, biotic interactions can be both symmetric and asymmetric. Yet, most models that attempt to retrieve species associations from co-occurrence or co-abundance data internally assume symmetric relationships between species. Here, we propose and validate a machine-learning framework able to retrieve bidirectional associations by analyzing species community and environmental data. Our framework (1) models pairwise species associations as directed influences from a source to a target species, parameterized with two species-specific latent embeddings: the effect of the source species on the community, and the response of the target species to the community; and (2) jointly fits these associations within a multi-species conditional generative model with different modes of interactions between environmental drivers and biotic associations. Using both simulated and empirical data, we demonstrate the ability of our framework to recover known asymmetric and symmetric associations and highlight the properties of the learned association networks. By comparing our approach to other existing models such as joint species distribution models and probabilistic graphical models, we show its superior capacity at retrieving symmetric and asymmetric interactions. The framework is intuitive, modular and broadly applicable across various taxonomic groups.

stat.ML↗

arXiv2025

EUNIS Habitat Maps: Enhancing Thematic and Spatial Resolution for Europe through Machine Learning

The EUNIS habitat classification is crucial for categorising European habitats, supporting European policy on nature conservation and implementing the Nature Restoration Law. To meet the growing demand for detailed and accurate habitat information, we provide spatial predictions for 260 EUNIS habitat types at hierarchical level 3, together with independent validation and uncertainty analyses. Using ensemble machine learning models, together with high-resolution satellite imagery and ecologically meaningful climatic, topographic and edaphic variables, we produced a European habitat map indicating the most probable EUNIS habitat at 100-m resolution across Europe. Additionally, we provide information on prediction uncertainty and the most probable habitats at level 3 within each EUNIS level 1 formation. This product is particularly useful for both conservation and restoration purposes. Predictions were cross-validated at European scale using a spatial block cross-validation and evaluated against independent data from France (forests only), the Netherlands and Austria. The habitat maps obtained strong predictive performances on the validation datasets with distinct trade-offs in terms of recall and precision across habitat formations.

stat.AP↗

arXiv2025

Digging deeper: deep joint species distribution modeling reveals environmental drivers of Earthworm Communities

Earthworms are key drivers of soil function, influencing organic matter turnover, nutrient cycling, and soil structure. Understanding the environmental controls on their distribution is essential for predicting the impacts of land use and climate change on soil ecosystems. While local studies have identified abiotic drivers of earthworm communities, broad-scale spatial patterns remain underexplored. We developed a multi-species, multi-task deep learning model to jointly predict the distribution of 77 earthworm species across metropolitan France, using historical (1960-1970) and contemporary (1990-2020) records. The model integrates climate, soil, and land cover variables to estimate habitat suitability. We applied SHapley Additive exPlanations (SHAP) to identify key environmental drivers and used species clustering to reveal ecological response groups. The joint model achieved high predictive performance (TSS >= 0.7) and improved predictions for rare species compared to traditional species distribution models. Shared feature extraction across species allowed for more robust identification of common and contrasting environmental responses. Precipitation variability, temperature seasonality, and land cover emerged as dominant predictors of earthworm distribution. Species clustering revealed distinct ecological strategies tied to climatic and land use gradients. Our study advances both the methodological and ecological understanding of soil biodiversity. We demonstrate the utility of interpretable deep learning approaches for large-scale soil fauna modeling and provide new insights into earthworm habitat specialization. These findings support improved soil biodiversity monitoring and conservation planning in the face of global environmental change.

stat.AP↗

arXiv2024

Causal Discovery from Time Series with Hybrids of Constraint-Based and Noise-Based Algorithms

Constraint-based methods and noise-based methods are two distinct families of methods proposed for uncovering causal graphs from observational data. However, both operate under strong assumptions that may be challenging to validate or could be violated in real-world scenarios. In response to these challenges, there is a growing interest in hybrid methods that amalgamate principles from both methods, showing robustness to assumption violations. This paper introduces a novel comprehensive framework for hybridizing constraint-based and noise-based methods designed to uncover causal graphs from observational time series. The framework is structured into two classes. The first class employs a noise-based strategy to identify a super graph, containing the true graph, followed by a constraint-based strategy to eliminate unnecessary edges. In the second class, a constraint-based strategy is applied to identify a skeleton, which is then oriented using a noise-based strategy. The paper provides theoretical guarantees for each class under the condition that all assumptions are satisfied, and it outlines some properties when assumptions are violated. To validate the efficacy of the framework, two algorithms from each class are experimentally tested on simulated data, realistic ecological data, and real datasets sourced from diverse applications. Notably, two novel datasets related to Information Technology monitoring are introduced within the set of considered real datasets. The experimental results underscore the robustness and effectiveness of the hybrid approaches across a broad spectrum of datasets.

cs.AI↗

arXiv2024

Novel community data in ecology -- properties and prospects

New technologies for acquiring biological information such as eDNA, acoustic or optical sensors, make it possible to generate spatial community observations at unprecedented scales. The potential of these novel community data to standardize community observations at high spatial, temporal, and taxonomic resolution and at large spatial scale ('many rows and many columns') has been widely discussed, but so far, there has been little integration of these data with ecological models and theory. Here, we review these developments and highlight emerging solutions, focusing on statistical methods for analyzing novel community data, in particular joint species distribution models; the new ecological questions that can be answered with these data; and the potential implications of these developments for policy and conservation.

q-bio.PE↗

arXiv2023

Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Separating environmental effects from those of interspecific interactions on species distributions has always been a central objective of community ecology. Despite years of effort in analysing patterns of species co-occurrences and the developments of sophisticated tools, we are still unable to address this major objective. A key reason is that the wealth of ecological knowledge is not sufficiently harnessed in current statistical models, notably the knowledge on interspecific interactions. Here, we develop ELGRIN, a statistical model that simultaneously combines knowledge on interspecific interactions (i.e., the metanetwork), environmental data and species occurrences to tease apart their relative effects on species distributions. Instead of focusing on single effects of pairwise species interactions, which have little sense in complex communities, ELGRIN contrasts the overall effect of species interactions to that of the environment. Using various simulated and empirical data, we demonstrate the suitability of ELGRIN to address the objectives for various types of interspecific interactions like mutualism, competition and trophic interactions. We then apply the model on vertebrate trophic networks in the European Alps to map the effect of biotic interactions on species distributions.Data on ecological networks are everyday increasing and we believe the time is ripe to mobilize these data to better understand biodiversity patterns. ELGRIN provides this opportunity to unravel how interspecific interactions actually influence species distributions.

q-bio.PE↗

arXiv2022

Assessing mutualistic metacommunity capacity by integrating spatial and interaction networks

We develop a spatially realistic model of mutualistic metacommunities that exploits the joint structure of spatial and interaction networks. This model exhibits a sharp transition between a stable non-null equilibrium state and a global extinction state. This behaviour allows defining a threshold on colonisation/extinction parameters for the long-term metacommunity persistence. This threshold, the 'metacommunity capacity', extends the metapopulation capacity concept and can be calculated from the spatial and interaction networks without simulating the whole dynamics. In several applications we illustrate how the joint structure of the spatial and the interaction networks affects metacommunity capacity. It results that a weakly modular spatial network and a power-law degree distribution of the interaction network provide the most favourable configuration for the long-term persistence of a mutualistic metacommunity. Our model that encodes several explicit ecological assumptions should pave the way for a larger exploration of spatially realistic metacommunity models involving multiple interaction types.

q-bio.PE↗