Théo Larcher

Theo Larcher, Lukas Picek, Benjamin Deneu et al.

This paper describes a deep-SDM framework, MALPOLON. Written in Python and built upon the PyTorch library, this framework aims to facilitate training and inferences of deep species distribution models (deep-SDM) and sharing for users with only general Python language skills (e.g., modeling ecologists) who are interested in testing deep learning approaches to build new SDMs. More advanced users can also benefit from the framework's modularity to run more specific experiments by overriding existing classes while taking advantage of press-button examples to train neural networks on multiple classification tasks using custom or provided raw and pre-processed datasets. The framework is open-sourced on GitHub and PyPi along with extensive documentation and examples of use in various scenarios. MALPOLON offers straightforward installation, YAML-based configuration, parallel computing, multi-GPU utilization, baseline and foundational models for benchmarking, and extensive tutorials/documentation, aiming to enhance accessibility and performance scalability for ecologists and researchers.

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.

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.

Thomas Constum, Lucas Preel, Théo Larcher et al.

The EXO-POPP project aims to establish a comprehensive database comprising 300,000 marriage records from Paris and its suburbs, spanning the years 1880 to 1940, which are preserved in over 130,000 scans of double pages. Each marriage record may encompass up to 118 distinct types of information that require extraction from plain text. In this paper, we introduce the M-POPP dataset, a subset of the M-POPP database with annotations for full-page text recognition and information extraction in both handwritten and printed documents, and which is now publicly available. We present a fully end-to-end architecture adapted from the DAN, designed to perform both handwritten text recognition and information extraction directly from page images without the need for explicit segmentation. We showcase the information extraction capabilities of this architecture by achieving a new state of the art for full-page Information Extraction on Esposalles and we use this architecture as a baseline for the M-POPP dataset. We also assess and compare how different encoding strategies for named entities in the text affect the performance of jointly recognizing handwritten text and extracting information, from full pages.