Daily Papers

Biodiversity assessments are critically affected by the spatial scale at which species richness is measured. How species richness accumulates with sampling area depends on natural and anthropogenic processes whose effects can change depending on the spatial scale considered. These accumulation dynamics, described by the species-area relationship (SAR), are challenging to assess because most biodiversity surveys are restricted to sampling areas much smaller than the scales at which these processes operate. Here, we combine sampling theory and deep learning to predict local species richness within arbitrarily large sampling areas, enabling for the first time to estimate spatial differences in SARs. We demonstrate our approach by predicting vascular plant species richness across Europe and evaluate predictions against an independent dataset of plant community inventories. The resulting model, named deep SAR, delivers multi-scale species richness maps, improving coarse grain richness estimates by 32% compared to conventional methods, while delivering finer grain estimates. Additional to its predictive capabilities, we show how our deep SAR model can provide fundamental insights on the multi-scale effects of key biodiversity processes. The capacity of our approach to deliver comprehensive species richness estimates across the full spectrum of ecologically relevant scales is essential for robust biodiversity assessments and forecasts under global change.

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 multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), 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) that are 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.

The presence of species provides key insights into the ecological properties of a location such as land cover, climatic conditions or even soil properties. We propose a method to predict such ecological properties directly from remote sensing (RS) images by aligning them with species habitat descriptions. We introduce the EcoWikiRS dataset, consisting of high-resolution aerial images, the corresponding geolocated species observations, and, for each species, the textual descriptions of their habitat from Wikipedia. EcoWikiRS offers a scalable way of supervision for RS vision language models (RS-VLMs) for ecology. This is a setting with weak and noisy supervision, where, for instance, some text may describe properties that are specific only to part of the species' niche or is irrelevant to a specific image. We tackle this by proposing WINCEL, a weighted version of the InfoNCE loss. We evaluate our model on the task of ecosystem zero-shot classification by following the habitat definitions from the European Nature Information System (EUNIS). Our results show that our approach helps in understanding RS images in a more ecologically meaningful manner. The code and the dataset are available at https://github.com/eceo-epfl/EcoWikiRS.

We focus on the problem of species distribution modeling using global-scale presence-only data. Most previous studies have mapped the range of a given species using geographical and environmental features alone. To capture a stronger implicit relationship between species, we encode the taxonomic hierarchy of species using a large language model. This enables range mapping for any taxonomic rank and unseen species without additional supervision. Further, we propose a novel proximity-aware evaluation metric that enables evaluating species distribution models using any pixel-level representation of ground-truth species range map. The proposed metric penalizes the predictions of a model based on its proximity to the ground truth. We describe the effectiveness of our model by systematically evaluating on the task of species range prediction, zero-shot prediction and geo-feature regression against the state-of-the-art. Results show our model outperforms the strong baselines when trained with a variety of multi-label learning losses.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Despite the ecological significance of invertebrates, global trait databases remain heavily biased toward vertebrates and plants, limiting comprehensive ecological analyses of high-diversity groups like ground beetles. Ground beetles (Coleoptera: Carabidae) serve as critical bioindicators of ecosystem health, providing valuable insights into biodiversity shifts driven by environmental changes. While the National Ecological Observatory Network (NEON) maintains an extensive collection of carabid specimens from across the United States, these primarily exist as physical collections, restricting widespread research access and large-scale analysis. To address these gaps, we present a multimodal dataset digitizing over 13,200 NEON carabids from 30 sites spanning the continental US and Hawaii through high-resolution imaging, enabling broader access and computational analysis. The dataset includes digitally measured elytra length and width of each specimen, establishing a foundation for automated trait extraction using AI. Validated against manual measurements, our digital trait extraction achieves sub-millimeter precision, ensuring reliability for ecological and computational studies. By addressing invertebrate under-representation in trait databases, this work supports AI-driven tools for automated species identification and trait-based research, fostering advancements in biodiversity monitoring and conservation.

Natural selection for terrestrial locomotion has yielded unifying patterns in the body shape of legged animals, often manifesting as scaling laws. One such pattern appears in the frontal aspect ratio. Smaller animals like insects typically adopt a landscape frontal aspect ratio, with a wider side-to-side base of support than center of mass height. Larger animals like elephants, however, are taller than wide with a portrait aspect ratio. Known explanations for postural scaling are restricted to animal groups with similar anatomical and behavioural motifs, but the trend in frontal aspect ratio transcends such commonalities. Here we show that vertebrates and invertebrates with diverse body plans, ranging in mass from 28 mg to 22000 kg, exhibit size-dependent scaling of the frontal aspect ratio driven by the need for lateral stability on uneven natural terrain. Because natural terrain exhibit scale-dependent unevenness, and the frontal aspect ratio is important for lateral stability during locomotion, smaller animals need a wider aspect ratio for stability. This prediction is based on the fractal property of natural terrain unevenness, requires no anatomical or behavioural parameters, and agrees with the measured scaling despite vast anatomical and behavioural differences. Furthermore, a statistical phylogenetic comparative analysis found that shared ancestry and random trait evolution cannot explain the measured scaling. Thus, our findings reveal that terrain roughness, acting through natural selection for stability, likely drove the macroevolution of frontal shape in terrestrial animals.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

Estimating the geographical range of a species from sparse observations is a challenging and important geospatial prediction problem. Given a set of locations where a species has been observed, the goal is to build a model to predict whether the species is present or absent at any location. This problem has a long history in ecology, but traditional methods struggle to take advantage of emerging large-scale crowdsourced datasets which can include tens of millions of records for hundreds of thousands of species. In this work, we use Spatial Implicit Neural Representations (SINRs) to jointly estimate the geographical range of 47k species simultaneously. We find that our approach scales gracefully, making increasingly better predictions as we increase the number of species and the amount of data per species when training. To make this problem accessible to machine learning researchers, we provide four new benchmarks that measure different aspects of species range estimation and spatial representation learning. Using these benchmarks, we demonstrate that noisy and biased crowdsourced data can be combined with implicit neural representations to approximate expert-developed range maps for many species.

Biologists all over the world use camera traps to monitor biodiversity and wildlife population density. The computer vision community has been making strides towards automating the species classification challenge in camera traps, but it has proven difficult to to apply models trained in one region to images collected in different geographic areas. In some cases, accuracy falls off catastrophically in new region, due to both changes in background and the presence of previously-unseen species. We propose a pipeline that takes advantage of a pre-trained general animal detector and a smaller set of labeled images to train a classification model that can efficiently achieve accurate results in a new region.

Insects comprise millions of species, many experiencing severe population declines under environmental and habitat changes. High-throughput approaches are crucial for accelerating our understanding of insect diversity, with DNA barcoding and high-resolution imaging showing strong potential for automatic taxonomic classification. However, most image-based approaches rely on individual specimen data, unlike the unsorted bulk samples collected in large-scale ecological surveys. We present the Mixed Arthropod Sample Segmentation and Identification (MassID45) dataset for training automatic classifiers of bulk insect samples. It uniquely combines molecular and imaging data at both the unsorted sample level and the full set of individual specimens. Human annotators, supported by an AI-assisted tool, performed two tasks on bulk images: creating segmentation masks around each individual arthropod and assigning taxonomic labels to over 17 000 specimens. Combining the taxonomic resolution of DNA barcodes with precise abundance estimates of bulk images holds great potential for rapid, large-scale characterization of insect communities. This dataset pushes the boundaries of tiny object detection and instance segmentation, fostering innovation in both ecological and machine learning research.

The evolution of biological morphology is critical for understanding the diversity of the natural world, yet traditional analyses often involve subjective biases in the selection and coding of morphological traits. This study employs deep learning techniques, utilising a ResNet34 model capable of recognising over 10,000 bird species, to explore avian morphological evolution. We extract weights from the model's final fully connected (fc) layer and investigate the semantic alignment between the high-dimensional embedding space learned by the model and biological phenotypes. The results demonstrate that the high-dimensional embedding space encodes phenotypic convergence. Subsequently, we assess the morphological disparity among various taxa and evaluate the association between morphological disparity and species richness, demonstrating that species richness is the primary driver of morphospace expansion. Moreover, the disparity-through-time analysis reveals a visual "early burst" after the K-Pg extinction. While mainly aimed at evolutionary analysis, this study also provides insights into the interpretability of Deep Neural Networks. We demonstrate that hierarchical semantic structures (biological taxonomy) emerged in the high-dimensional embedding space despite being trained on flat labels. Furthermore, through adversarial examples, we provide evidence that our model in this task can overcome texture bias and learn holistic shape representations (body plans), challenging the prevailing view that CNNs rely primarily on local textures.