Christophe Botella

Lukas Picek, Christophe Botella, Maximilien Servajean et al.

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multimodal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10--50m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time series of climatic variables, and satellite time series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

Sébastien Gigot--Léandri, Gaétan Morand, Alexis Joly et al.

Species distribution models (SDMs) commonly produce probabilistic occurrence predictions that must be converted into binary presence-absence maps for ecological inference and conservation planning. However, this binarization step is typically heuristic and can substantially distort estimates of species prevalence and community composition. We present MaxExp, a decision-driven binarization framework that selects the most probable species assemblage by directly maximizing a chosen evaluation metric. MaxExp requires no calibration data and is flexible across several scores. We also introduce the Set Size Expectation (SSE) method, a computationally efficient alternative that predicts assemblages based on expected species richness. Using three case studies spanning diverse taxa, species counts, and performance metrics, we show that MaxExp consistently matches or surpasses widely used thresholding and calibration methods, especially under strong class imbalance and high rarity. SSE offers a simpler yet competitive option. Together, these methods provide robust, reproducible tools for multispecies SDM binarization.

Christophe Botella, Benjamin Deneu, Diego Marcos et al.

Understanding the spatio-temporal distribution of species is a cornerstone of ecology and conservation. By pairing species observations with geographic and environmental predictors, researchers can model the relationship between an environment and the species which may be found there. To advance the state-of-the-art in this area with deep learning models and remote sensing data, we organized an open machine learning challenge called GeoLifeCLEF 2023. The training dataset comprised 5 million plant species observations (single positive label per sample) distributed across Europe and covering most of its flora, high-resolution rasters: remote sensing imagery, land cover, elevation, in addition to coarse-resolution data: climate, soil and human footprint variables. In this multi-label classification task, we evaluated models ability to predict the species composition in 22 thousand small plots based on standardized surveys. This paper presents an overview of the competition, synthesizes the approaches used by the participating teams, and analyzes the main results. In particular, we highlight the biases faced by the methods fitted to single positive labels when it comes to the multi-label evaluation, and the new and effective learning strategy combining single and multi-label data in training.

Maxime Ryckewaert, Diego Marcos, Christophe Botella et al.

The rapid expansion of citizen science initiatives has led to a significant growth of biodiversity databases, and particularly presence-only (PO) observations. PO data are invaluable for understanding species distributions and their dynamics, but their use in a Species Distribution Model (SDM) is curtailed by sampling biases and the lack of information on absences. Poisson point processes are widely used for SDMs, with Maxent being one of the most popular methods. Maxent maximises the entropy of a probability distribution across sites as a function of predefined transformations of variables, called features. In contrast, neural networks and deep learning have emerged as a promising technique for automatic feature extraction from complex input variables. Arbitrarily complex transformations of input variables can be learned from the data efficiently through backpropagation and stochastic gradient descent (SGD). In this paper, we propose DeepMaxent, which harnesses neural networks to automatically learn shared features among species, using the maximum entropy principle. To do so, it employs a normalised Poisson loss where for each species, presence probabilities across sites are modelled by a neural network. We evaluate DeepMaxent on a benchmark dataset known for its spatial sampling biases, using PO data for calibration and presence-absence (PA) data for validation across six regions with different biological groups and covariates. Our results indicate that DeepMaxent performs better than Maxent and other leading SDMs across all regions and taxonomic groups. The method performs particularly well in regions of uneven sampling, demonstrating substantial potential to increase SDM performances. In particular, our approach yields more accurate predictions than traditional single-species models, which opens up new possibilities for methodological enhancement.

Elijah Cole, Benjamin Deneu, Titouan Lorieul et al.

Understanding the geographic distribution of species is a key concern in conservation. By pairing species occurrences with environmental features, researchers can model the relationship between an environment and the species which may be found there. To facilitate research in this area, we present the GeoLifeCLEF 2020 dataset, which consists of 1.9 million species observations paired with high-resolution remote sensing imagery, land cover data, and altitude, in addition to traditional low-resolution climate and soil variables. We also discuss the GeoLifeCLEF 2020 competition, which aims to use this dataset to advance the state-of-the-art in location-based species recommendation.

Benjamin Deneu, Maximilien Servajean, Christophe Botella et al.

This paper presents an evaluation of several approaches of plants species distribution modeling based on spatial, environmental and co-occurrences data using machine learning methods. In particular, we re-evaluate the environmental convolutional neural network model that obtained the best performance of the GeoLifeCLEF 2018 challenge but on a revised dataset that fixes some of the issues of the previous one. We also go deeper in the analysis of co-occurrences information by evaluating a new model that jointly takes environmental variables and co-occurrences as inputs of an end-to-end network. Results show that the environmental models are the best performing methods and that there is a significant amount of complementary information between co-occurrences and environment. Indeed, the model learned on both inputs allows a significant performance gain compared to the environmental model alone.