Daily Papers

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.

Deep learning on climatic data holds potential for macroecological applications. However, its adoption remains limited among scientists outside the deep learning community due to storage, compute, and technical expertise barriers. To address this, we introduce Climplicit, a spatio-temporal geolocation encoder pretrained to generate implicit climatic representations anywhere on Earth. By bypassing the need to download raw climatic rasters and train feature extractors, our model uses x3500 less disk space and significantly reduces computational needs for downstream tasks. We evaluate our Climplicit embeddings on biomes classification, species distribution modeling, and plant trait regression. We find that single-layer probing our Climplicit embeddings consistently performs better or on par with training a model from scratch on downstream tasks and overall better than alternative geolocation encoding models.

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

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.

Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful static representations, but they do not explicitly model the distribution of cellular states for generative simulation. Here, we introduce Lingshu-Cell, a masked discrete diffusion model that learns transcriptomic state distributions and supports conditional simulation under perturbation. By operating directly in a discrete token space that is compatible with the sparse, non-sequential nature of single-cell transcriptomic data, Lingshu-Cell captures complex transcriptome-wide expression dependencies across approximately 18,000 genes without relying on prior gene selection, such as filtering by high variability or ranking by expression level. Across diverse tissues and species, Lingshu-Cell accurately reproduces transcriptomic distributions, marker-gene expression patterns and cell-subtype proportions, demonstrating its ability to capture complex cellular heterogeneity. Moreover, by jointly embedding cell type or donor identity with perturbation, Lingshu-Cell can predict whole-transcriptome expression changes for novel combinations of identity and perturbation. It achieves leading performance on the Virtual Cell Challenge H1 genetic perturbation benchmark and in predicting cytokine-induced responses in human PBMCs. Together, these results establish Lingshu-Cell as a flexible cellular world model for in silico simulation of cell states and perturbation responses, laying the foundation for a new paradigm in biological discovery and perturbation screening.

We consider estimating the conditional distribution of a multivariate outcome given covariates when its coordinates may be continuous, binary, categorical, ordinal or rankings, and are conditionally dependent on one another. Different statistical methods have been developed for each outcome type, and most of them target a summary of the conditional distribution, such as the mean of each coordinate, rather than the joint distribution of the outcome vector. We develop generalized engression models, a unified nonparametric distributional regression framework for outcomes of any type. The proposed method builds upon engression, a scoring-rule-based deep generative model, and introduces a data-type-specific link function and a stochastic perturbation that smooths the loss, enabling gradient-based training even with discontinuous links. We establish universal representation results for continuous, discrete and mixed outcomes. In simulations and in two applications, 242 species in a community ecology benchmark and a 17-dimensional mixed-type health outcome, the method matches type-specific models on marginal scores, improves on them on the joint distribution, and matches or exceeds purpose-built state-of-the-art joint species distribution models. Software is available in Python.

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.

Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently complex and interconnected processes and are further constrained by limited observational data in many environmental applications. Foundation models, which leverages large-scale pre-training and universal representations of complex and heterogeneous data, offer transformative opportunities for capturing spatiotemporal dynamics and dependencies in environmental processes, and facilitate adaptation to a broad range of applications. This survey presents a comprehensive overview of foundation model applications in environmental science, highlighting advancements in common environmental use cases including forward prediction, data generation, data assimilation, downscaling, inverse modeling, model ensembling, and decision-making across domains. We also detail the process of developing these models, covering data collection, architecture design, training, tuning, and evaluation. Through discussions on these emerging methods as well as their future opportunities, we aim to promote interdisciplinary collaboration that accelerates advancements in machine learning for driving scientific discovery in addressing critical environmental challenges.

We propose a metadata-aware self-supervised learning~(SSL)~framework useful for fine-grained classification and ecological mapping of bird species around the world. Our framework unifies two SSL strategies: Contrastive Learning~(CL) and Masked Image Modeling~(MIM), while also enriching the embedding space with metadata available with ground-level imagery of birds. We separately train uni-modal and cross-modal ViT on a novel cross-view global bird species dataset containing ground-level imagery, metadata (location, time), and corresponding satellite imagery. We demonstrate that our models learn fine-grained and geographically conditioned features of birds, by evaluating on two downstream tasks: fine-grained visual classification~(FGVC) and cross-modal retrieval. Pre-trained models learned using our framework achieve SotA performance on FGVC of iNAT-2021 birds and in transfer learning settings for CUB-200-2011 and NABirds datasets. Moreover, the impressive cross-modal retrieval performance of our model enables the creation of species distribution maps across any geographic region. The dataset and source code will be released at https://github.com/mvrl/BirdSAT}.

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.

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.

Camera traps are vital for large-scale biodiversity monitoring, yet accurate automated analysis remains challenging due to diverse deployment environments. While the computer vision community has mostly framed this challenge as cross-domain generalization, this perspective overlooks a primary challenge faced by ecological practitioners: maintaining reliable recognition at the fixed site over time, where the dynamic nature of ecosystems introduces profound temporal shifts in both background and animal distributions. To bridge this gap, we present the first unified study of camera-trap species recognition over time. We introduce a realistic benchmark comprising 546 camera traps with a streaming protocol that evaluates models over chronologically ordered intervals. Our end-user-centric study yields four key findings. (1) Biological foundation models (e.g., BioCLIP 2) underperform at numerous sites even in initial intervals, underscoring the necessity of site-specific adaptation. (2) Adaptation is challenging under realistic evaluation: when models are updated using past data and evaluated on future intervals (mirrors real deployment lifecycles), naive adaptation can even degrade below zero-shot performance. (3) We identify two drivers of this difficulty: severe class imbalance and pronounced temporal shift in both species distribution and backgrounds between consecutive intervals. (4) We find that effective integration of model-update and post-processing techniques can largely improve accuracy, though a gap from the upper bounds remains. Finally, we highlight critical open questions, such as predicting when zero-shot models will succeed at a new site and determining whether/when model updates are necessary. Our benchmark and analysis provide actionable deployment guidelines for ecological practitioners while establishing new directions for future research in vision and machine learning.

Species distributions encode valuable ecological and environmental information, yet their potential for guiding representation learning in remote sensing remains underexplored. We introduce WildSAT, which pairs satellite images with millions of geo-tagged wildlife observations readily-available on citizen science platforms. WildSAT employs a contrastive learning approach that jointly leverages satellite images, species occurrence maps, and textual habitat descriptions to train or fine-tune models. This approach significantly improves performance on diverse satellite image recognition tasks, outperforming both ImageNet-pretrained models and satellite-specific baselines. Additionally, by aligning visual and textual information, WildSAT enables zero-shot retrieval, allowing users to search geographic locations based on textual descriptions. WildSAT surpasses recent cross-modal learning methods, including approaches that align satellite images with ground imagery or wildlife photos, demonstrating the advantages of our approach. Finally, we analyze the impact of key design choices and highlight the broad applicability of WildSAT to remote sensing and biodiversity monitoring.

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state-space where such a tipping point might exist. We illustrate how a Bayesian Non-Parametric (BNP) approach using a Gaussian Process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a Stochastic Dynamic Programming (SDP) framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favors models without tipping points -- leading to harvest policies that guarantee extinction. The GPDP performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective, and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, since it does not underestimate the uncertainty outside of the observed data.

Although general text-to-image models excel in open-domain generation, their performance degrades significantly in specialized downstream domains, particularly when generating images of rare biological species. Hindered by long-tailed distributions, general models struggle to capture subtle fine-grained details, while per-species fine-tuning methods over-isolate individual species and consequently ignore the shared visual features among closely related taxa. To address this, we propose TreeAdapter, a novel framework that explicitly leverages hierarchical taxonomic data. Rather than using a monolithic model or independent per-species modules, TreeAdapter attaches lightweight adapters to every node of the taxonomic tree. Specifically, leaf-node adapters capture species-specific visual traits, while internal-node adapters encapsulate shared semantics among descendant taxa. We introduce a two-stage training paradigm where ancestor adapters are optimized to model only the residual visual features unexplained by their descendants. This model architecture and training paradigm enable the model to fully leverage hierarchical information, ensuring the accurate generation of visual features for each species. Extensive experiments across three large-scale biodiversity benchmarks demonstrate that TreeAdapter achieves state-of-the-art fine-grained generation quality, outperforming both general-purpose and domain-specific baselines.

Bats are key indicators of ecosystem health and are protected throughout Europe, making reliable population monitoring a conservation priority. Their cryptic nocturnal lifestyle makes passive acoustic monitoring essential, yet automated identification remains difficult as echolocation calls vary with behaviour and environment and overlap among species. We present a deep learning framework that jointly predicts species and genus and combines genus predictions with geographic species distributions at inference. When only one species of a predicted genus occurs in a region, the framework can resolve species absent from the learned taxonomy. This reframes geographic information as a means of extending, rather than constraining, a classifier's effective taxonomy. Using recordings spanning 35 European bat species, we evaluate closed-set classification, examine the instability of performance estimates for sparsely represented species, and conduct a controlled held-out proof-of-principle experiment. The rare-species analysis shows how limited evaluation data can obscure species-level performance, while the held-out experiment shows that genus predictions and location can recover labels unavailable to the species head. Geographic resolution extends operational coverage from 35 to 41 of the 48 native European bat species, increasing coverage from 73% to 85%. To our knowledge, this is the broadest operational coverage reported for automated European bat classification. More broadly, the bat framework provides proof of principle for resolving unseen fine-grained classes by combining coarse predictions with transparent external constraints.

World Models have emerged as a powerful paradigm for learning compact, predictive representations of environment dynamics, enabling agents to reason, plan, and generalize beyond direct experience. Despite recent interest in World Models, most available implementations remain publication-specific, severely limiting their reusability, increasing the risk of bugs, and reducing evaluation standardization. To mitigate these issues, we introduce stable-worldmodel (SWM), a modular, tested, and documented world-model research ecosystem that provides efficient data-collection tools, standardized environments, planning algorithms, and baseline implementations. In addition, each environment in SWM enables controllable factors of variation, including visual and physical properties, to support robustness and continual learning research. Finally, we demonstrate the utility of SWM by using it to study zero-shot robustness in DINO-WM.

The choice of representation for geographic location significantly impacts the accuracy of models for a broad range of geospatial tasks, including fine-grained species classification, population density estimation, and biome classification. Recent works like SatCLIP and GeoCLIP learn such representations by contrastively aligning geolocation with co-located images. While these methods work exceptionally well, in this paper, we posit that the current training strategies fail to fully capture the important visual features. We provide an information-theoretic perspective on why the resulting embeddings from these methods discard crucial visual information that is important for many downstream tasks. To solve this problem, we propose a novel retrieval-augmented strategy called RANGE. We build our method on the intuition that the visual features of a location can be estimated by combining the visual features from multiple similar-looking locations. We evaluate our method across a wide variety of tasks. Our results show that RANGE outperforms the existing state-of-the-art models with significant margins in most tasks. We show gains of up to 13.1% on classification tasks and 0.145 R^2 on regression tasks. All our code and models will be made available at: https://github.com/mvrl/RANGE.

Earth System Models (ESM) are our main tool for projecting the impacts of climate change. However, running these models at sufficient resolution for local-scale risk-assessments is not computationally feasible. Deep learning-based super-resolution models offer a promising solution to downscale ESM outputs to higher resolutions by learning from data. Yet, due to regional variations in climatic processes, these models typically require retraining for each geographical area-demanding high-resolution observational data, which is unevenly available across the globe. This highlights the need to assess how well these models generalize across geographic regions. To address this, we introduce RainShift, a dataset and benchmark for evaluating downscaling under geographic distribution shifts. We evaluate state-of-the-art downscaling approaches including GANs and diffusion models in generalizing across data gaps between the Global North and Global South. Our findings reveal substantial performance drops in out-of-distribution regions, depending on model and geographic area. While expanding the training domain generally improves generalization, it is insufficient to overcome shifts between geographically distinct regions. We show that addressing these shifts through, for example, data alignment can improve spatial generalization. Our work advances the global applicability of downscaling methods and represents a step toward reducing inequities in access to high-resolution climate information.

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

Recent work has established the ecological importance of developing algorithms for identifying animals individually from images. Typically, a separate algorithm is trained for each species, a natural step but one that creates significant barriers to wide-spread use: (1) each effort is expensive, requiring data collection, data curation, and model training, deployment, and maintenance, (2) there is little training data for many species, and (3) commonalities in appearance across species are not exploited. We propose an alternative approach focused on training multi-species individual identification (re-id) models. We construct a dataset that includes 49 species, 37K individual animals, and 225K images, using this data to train a single embedding network for all species. Our model employs an EfficientNetV2 backbone and a sub-center ArcFace loss function with dynamic margins. We evaluate the performance of this multispecies model in several ways. Most notably, we demonstrate that it consistently outperforms models trained separately on each species, achieving an average gain of 12.5% in top-1 accuracy. Furthermore, the model demonstrates strong zero-shot performance and fine-tuning capabilities for new species with limited training data, enabling effective curation of new species through both incremental addition of data to the training set and fine-tuning without the original data. Additionally, our model surpasses the recent MegaDescriptor on unseen species, averaging an 19.2% top-1 improvement per species and showing gains across all 33 species tested. The fully-featured code repository is publicly available on GitHub, and the feature extractor model can be accessed on HuggingFace for seamless integration with wildlife re-identification pipelines. The model is already in production use for 60+ species in a large-scale wildlife monitoring system.

Manual labeling of animal images remains a significant bottleneck in ecological research, limiting the scale and efficiency of biodiversity monitoring efforts. This study investigates whether state-of-the-art Vision Transformer (ViT) foundation models can reduce thousands of unlabeled animal images directly to species-level clusters. We present a comprehensive benchmarking framework evaluating five ViT models combined with five dimensionality reduction techniques and four clustering algorithms, two supervised and two unsupervised, across 60 species (30 mammals and 30 birds), with each test using a random subset of 200 validated images per species. We investigate when clustering succeeds at species-level, where it fails, and whether clustering within the species-level reveals ecologically meaningful patterns such as sex, age, or phenotypic variation. Our results demonstrate near-perfect species-level clustering (V-measure: 0.958) using DINOv3 embeddings with t-SNE and supervised hierarchical clustering methods. Unsupervised approaches achieve competitive performance (0.943) while requiring no prior species knowledge, rejecting only 1.14% of images as outliers requiring expert review. We further demonstrate robustness to realistic long-tailed distributions of species and show that intentional over-clustering can reliably extract intra-specific variation including age classes, sexual dimorphism, and pelage differences. We introduce an open-source benchmarking toolkit and provide recommendations for ecologists to select appropriate methods for sorting their specific taxonomic groups and data.

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.

Using the weights of trained Neural Network (NN) models as data modality has recently gained traction as a research field - dubbed Weight Space Learning (WSL). Multiple recent works propose WSL methods to analyze models, evaluate methods, or synthesize weights. Weight space learning methods require populations of trained models as datasets for development and evaluation. However, existing collections of models - called `model zoos' - are unstructured or follow a rudimentary definition of diversity. In parallel, work rooted in statistical physics has identified phases and phase transitions in NN models. Models are homogeneous within the same phase but qualitatively differ from one phase to another. We combine the idea of `model zoos' with phase information to create a controlled notion of diversity in populations. We introduce 12 large-scale zoos that systematically cover known phases and vary over model architecture, size, and datasets. These datasets cover different modalities, such as computer vision, natural language processing, and scientific ML. For every model, we compute loss landscape metrics and validate full coverage of the phases. With this dataset, we provide the community with a resource with a wide range of potential applications for WSL and beyond. Evidence suggests the loss landscape phase plays a role in applications such as model training, analysis, or sparsification. We demonstrate this in an exploratory study of the downstream methods like transfer learning or model weights averaging.

Camera traps are valuable tools in animal ecology for biodiversity monitoring and conservation. However, challenges like poor generalization to deployment at new unseen locations limit their practical application. Images are naturally associated with heterogeneous forms of context possibly in different modalities. In this work, we leverage the structured context associated with the camera trap images to improve out-of-distribution generalization for the task of species identification in camera traps. For example, a photo of a wild animal may be associated with information about where and when it was taken, as well as structured biology knowledge about the animal species. While typically overlooked by existing work, bringing back such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively integrating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that reformulates species classification as link prediction in a multimodal knowledge graph (KG). This framework seamlessly integrates various forms of multimodal context for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework successfully incorporates biological taxonomy for improved generalization and enhances sample efficiency for recognizing under-represented species.

This study presents a comprehensive analysis of bird diversity across Sri Lanka by integrating spatial, temporal, and environmental data. Bird observation records were combined with environmental variables, including weather conditions, air pollution, the Normalized Difference Vegetation Index (NDVI), land cover, elevation, and Artificial Light At Night (ALAN), and rigorously preprocessed to ensure data quality. Spatial analyses were conducted on multiple grid scales (2 km, 5 km, 10 km) to evaluate patterns in species richness while minimizing sampling bias through spatial thinning. Temporal trends were assessed using effort-corrected metrics including rarefied richness and occupancy rates to account for variations in observation effort over time. Environmental drivers of bird diversity were examined using multivariate statistical models, including Poisson Generalized Linear Models (GLMs) and correlation analyses, to identify key associations between ecological factors and species richness. Additionally, community structure, dominance patterns, and beta diversity were analyzed to understand variations in species composition across regions and time. The study found that land-cover type is a stronger predictor of bird diversity than individual continuous variables such as NDVI or temperature alone. Urbanization, measured by ALAN, exhibits nuanced scale-dependent effects, supporting high abundances of a few generalist species while reducing overall richness. The findings provide actionable insights into the patterns and drivers of avian diversity in Sri Lanka, offering a scalable and reproducible framework for biodiversity research and conservation planning.

Model merging is a powerful technique for integrating the specialized knowledge of multiple machine learning models into a single model. However, existing methods require manually partitioning model parameters into fixed groups for merging, which restricts the exploration of potential combinations and limits performance. To overcome these limitations, we propose Model Merging of Natural Niches (M2N2), an evolutionary algorithm with three key features: (1) dynamic adjustment of merging boundaries to progressively explore a broader range of parameter combinations; (2) a diversity preservation mechanism inspired by the competition for resources in nature, to maintain a population of diverse, high-performing models that are particularly well-suited for merging; and (3) a heuristicbased attraction metric to identify the most promising pairs of models for fusion. Our experimental results demonstrate, for the first time, that model merging can be used to evolve models entirely from scratch. Specifically, we apply M2N2 to evolve MNIST classifiers from scratch and achieve performance comparable to CMA-ES, while being computationally more efficient. Furthermore, M2N2 scales to merge specialized language and image generation models, achieving state-of-the-art performance. Notably, it preserves crucial model capabilities beyond those explicitly optimized by the fitness function, highlighting its robustness and versatility. Our code is available at https://github.com/SakanaAI/natural_niches

In this paper, we present WildlifeDatasets (https://github.com/WildlifeDatasets/wildlife-datasets) - an open-source toolkit intended primarily for ecologists and computer-vision / machine-learning researchers. The WildlifeDatasets is written in Python, allows straightforward access to publicly available wildlife datasets, and provides a wide variety of methods for dataset pre-processing, performance analysis, and model fine-tuning. We showcase the toolkit in various scenarios and baseline experiments, including, to the best of our knowledge, the most comprehensive experimental comparison of datasets and methods for wildlife re-identification, including both local descriptors and deep learning approaches. Furthermore, we provide the first-ever foundation model for individual re-identification within a wide range of species - MegaDescriptor - that provides state-of-the-art performance on animal re-identification datasets and outperforms other pre-trained models such as CLIP and DINOv2 by a significant margin. To make the model available to the general public and to allow easy integration with any existing wildlife monitoring applications, we provide multiple MegaDescriptor flavors (i.e., Small, Medium, and Large) through the HuggingFace hub (https://huggingface.co/BVRA).

Camera traps often run in the field on edge hardware with limited or no connectivity, making small, locally-deployable vision-language models (VLMs) -- not frontier-scale ones -- the practically relevant class to evaluate for species identification. We test whether models in this deployment-relevant 2--8B range carry genuine taxonomic knowledge, evaluating four such VLMs (Qwen3-VL 2B/4B/8B, Gemma3 4B) against the domain-specific specialist BioCLIP (300M parameters) on a 96-species task, comparing clean iNaturalist photographs against camera-trap imagery from 6 LILA.science collections, on two independently-sampled evaluation sets. All models identify species far above chance, but every model -- general-purpose or specialist -- degrades sharply on field imagery (domain gaps of 9.6--26.6 percentage points, consistent across taxonomic levels and both evaluation sets), indicating the degradation reflects general image legibility rather than fine-grained discrimination failure. BioCLIP substantially outperforms every VLM tested (by 33.2--59.2 percentage points across an expanded 200-image sample for every model) despite its far smaller size, suggesting the gap reflects specialized training data rather than model scale; yet BioCLIP's own domain gap (18.0 points) is statistically indistinguishable from the best VLM's (22.3 points), suggesting the clean-to-field degradation itself is a property of the image-quality shift rather than a general-purpose-model weakness. Under open-set prompting, 5.9--9.6% of responses are syntactically valid but taxonomically nonexistent species names; the relative fabrication-rate ranking across models replicates exactly across both evaluation sets, a more robust finding than any single point estimate.

Climate change is negatively impacting the world's biodiversity. To build automated systems to monitor these negative biodiversity impacts, large-scale, volunteer-collected datasets like iNaturalist are built from community-identified, natural imagery. However, such volunteer-based data are opportunistic and lack a structured sampling strategy, resulting in geographic, temporal, observation quality, and socioeconomic, biases that stymie uptake of these models for downstream biodiversity monitoring tasks. Here we introduce DivShift North American West Coast (DivShift-NAWC), a curated dataset of almost 8 million iNaturalist plant images across the western coast of North America, for exploring the effects of these biases on deep learning model performance. We compare model performance across four known biases and observe that they indeed confound model performance. We suggest practical strategies for curating datasets to train deep learning models for monitoring climate change's impacts on the world's biodiversity.

Biodiversity research requires complete and detailed information to study ecosystem dynamics at different scales. Employing data-driven methods like Machine Learning is getting traction in ecology and more specific biodiversity, offering alternative modelling pathways. For these methods to deliver accurate results there is the need for large, curated and multimodal datasets that offer granular spatial and temporal resolutions. In this work, we introduce BioCube, a multimodal, fine-grained global dataset for ecology and biodiversity research. BioCube incorporates species observations through images, audio recordings and descriptions, environmental DNA, vegetation indices, agricultural, forest, land indicators, and high-resolution climate variables. All observations are geospatially aligned under the WGS84 geodetic system, spanning from 2000 to 2020. The dataset will become available at https://huggingface.co/datasets/BioDT/BioCube while the acquisition and processing code base at https://github.com/BioDT/bfm-data.

Developing accurate and reliable models for forest types mapping is critical to support efforts for halting deforestation and for biodiversity conservation (such as European Union Deforestation Regulation (EUDR)). This work introduces ForTy, a benchmark for global-scale FORest TYpes mapping using multi-temporal satellite data1. The benchmark comprises 200,000 time series of image patches, each consisting of Sentinel-2, Sentinel-1, climate, and elevation data. Each time series captures variations at monthly or seasonal cadence. Per-pixel annotations, including forest types and other land use classes, support image segmentation tasks. Unlike most existing land use products that often categorize all forest areas into a single class, our benchmark differentiates between three forest types classes: natural forest, planted forest, and tree crops. By leveraging multiple public data sources, we achieve global coverage with this benchmark. We evaluate the forest types dataset using several baseline models, including convolution neural networks and transformer-based models. Additionally, we propose a novel transformer-based model specifically designed to handle multi-modal, multi-temporal satellite data for forest types mapping. Our experimental results demonstrate that the proposed model surpasses the baseline models in performance.

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.

We present TaxaBind, a unified embedding space for characterizing any species of interest. TaxaBind is a multimodal embedding space across six modalities: ground-level images of species, geographic location, satellite image, text, audio, and environmental features, useful for solving ecological problems. To learn this joint embedding space, we leverage ground-level images of species as a binding modality. We propose multimodal patching, a technique for effectively distilling the knowledge from various modalities into the binding modality. We construct two large datasets for pretraining: iSatNat with species images and satellite images, and iSoundNat with species images and audio. Additionally, we introduce TaxaBench-8k, a diverse multimodal dataset with six paired modalities for evaluating deep learning models on ecological tasks. Experiments with TaxaBind demonstrate its strong zero-shot and emergent capabilities on a range of tasks including species classification, cross-model retrieval, and audio classification. The datasets and models are made available at https://github.com/mvrl/TaxaBind.

Generating diverse responses from large language models (LLMs) is crucial for applications such as planning/search and synthetic data generation, where diversity provides distinct answers across generations. Prior approaches rely on increasing temperature to increase diversity. However, contrary to popular belief, we show not only does this approach produce lower quality individual generations as temperature increases, but it depends on model's next-token probabilities being similar to the true distribution of answers. We propose , an alternative approach that uses the language model itself to partition the space into strata. At inference, a random stratum is selected and a sample drawn from within the strata. To measure diversity, we introduce CoverageQA, a dataset of underspecified questions with multiple equally plausible answers, and assess diversity by measuring KL Divergence between the output distribution and uniform distribution over valid ground truth answers. As computing probability per response/solution for proprietary models is infeasible, we measure recall on ground truth solutions. Our evaluation show using SimpleStrat achieves higher recall by 0.05 compared to GPT-4o and 0.36 average reduction in KL Divergence compared to Llama 3.

Invasive species in water bodies pose a major threat to the environment and biodiversity globally. Due to increased transportation and trade, non-native species have been introduced to new environments, causing damage to ecosystems and leading to economic losses in agriculture, forestry, and fisheries. Therefore, there is a pressing need for risk assessment and management techniques to mitigate the impact of these invasions. This study aims to develop a new physics-inspired model to forecast maritime shipping traffic and thus inform risk assessment of invasive species spread through global transportation networks. Inspired by the gravity model for international trades, our model considers various factors that influence the likelihood and impact of vessel activities, such as shipping flux density, distance between ports, trade flow, and centrality measures of transportation hubs. Additionally, by analyzing the risk network of invasive species, we provide a comprehensive framework for assessing the invasion threat level given a pair of origin and destination. Accordingly, this paper introduces transformers to gravity models to rebuild the short- and long-term dependencies that make the risk analysis feasible. Thus, we introduce a physics-inspired framework that achieves an 89% segmentation accuracy for existing and non-existing trajectories and an 84.8% accuracy for the number of vessels flowing between key port areas, representing more than 10% improvement over the traditional deep-gravity model. Along these lines, this research contributes to a better understanding of invasive species risk assessment. It allows policymakers, conservationists, and stakeholders to prioritize management actions by identifying high-risk invasion pathways. Besides, our model is versatile and can include new data sources, making it suitable for assessing species invasion risks in a changing global landscape.

Agricultural pest management increasingly relies on timely and accurate access to expert knowledge, yet high quality labeled data and continuous expert support remain limited, particularly for farmers operating in rural regions with unstable/no internet connectivity. At the same time, the rapid growth of AI and LLMs has created new opportunities to deliver practical decision support tools directly to end users in agriculture through compact and deployable systems. This work addresses (i) generating a structured insect information dataset, and (ii) adapting a lightweight LLM model (leq 7B) by fine tuning it for edge device uses in agricultural pest management. The textual data collection was done by reviewing and collecting information from available pest databases and published manuscripts on nine selected pest species. These structured reports were then reviewed and validated by a domain expert. From these reports, we constructed Q/A pairs to support model training and evaluation. A LoRA-based fine-tuning approach was applied to multiple lightweight LLMs and evaluated. Initial evaluation shows that Mistral 7B achieves an 88.9\% pass rate on the domain-specific Q/A task, substantially outperforming Qwen 2.5 7B (63.9\%), and LLaMA 3.1 8B (58.7\%). Notably, Mistral demonstrates higher semantic alignment (embedding similarity: 0.865) despite lower lexical overlap (BLEU: 0.097), indicating that semantic understanding and robust reasoning are more predictive of task success than surface-level conformity in specialized domains. By combining expert organized data, well-structured Q/A pairs, semantic quality control, and efficient model adaptation, this work contributes towards providing support for farmer facing agricultural decision support tools and demonstrates the feasibility of deploying compact, high-performing language models for practical field-level pest management guidance.

Insects represent half of all global biodiversity, yet many of the world's insects are disappearing, with severe implications for ecosystems and agriculture. Despite this crisis, data on insect diversity and abundance remain woefully inadequate, due to the scarcity of human experts and the lack of scalable tools for monitoring. Ecologists have started to adopt camera traps to record and study insects, and have proposed computer vision algorithms as an answer for scalable data processing. However, insect monitoring in the wild poses unique challenges that have not yet been addressed within computer vision, including the combination of long-tailed data, extremely similar classes, and significant distribution shifts. We provide the first large-scale machine learning benchmarks for fine-grained insect recognition, designed to match real-world tasks faced by ecologists. Our contributions include a curated dataset of images from citizen science platforms and museums, and an expert-annotated dataset drawn from automated camera traps across multiple continents, designed to test out-of-distribution generalization under field conditions. We train and evaluate a variety of baseline algorithms and introduce a combination of data augmentation techniques that enhance generalization across geographies and hardware setups. Code and datasets are made publicly available.

Bioacoustic foundation models rely on large-scale citizen science platforms like Xeno-Canto for geographically and ecologically diverse data. Recent work has shown that supervision alone can produce SotA species detection models when trained on this large-scale data -- however, there remains unutilized potential in the form of recording metadata readily available within these community-driven data hubs. In this work, we explore the use of metadata -- such as location and time -- as auxiliary supervision signals, allowing the model to leverage species-metadata correlations in its learned representation. Auxiliary metadata losses provide additional information beyond vocalizations alone that can encourage a richer, more robust representation that generalizes better to species distribution and acoustic domain shifts -- important challenges for deployment in real-world passive acoustic monitoring (PAM) settings. We introduce MetaPerch, a new foundation model that achieves strong species identification performance across multiple challenging domains and present an extensive empirical study of the effects of 9 diverse metadata sources on 17 bioacoustic datasets.

Global climate models typically operate at a grid resolution of hundreds of kilometers and fail to resolve atmospheric mesoscale processes, e.g., clouds, precipitation, and gravity waves (GWs). Model representation of these processes and their sources is essential to the global circulation and planetary energy budget, but subgrid scale contributions from these processes are often only approximately represented in models using parameterizations. These parameterizations are subject to approximations and idealizations, which limit their capability and accuracy. The most drastic of these approximations is the "single-column approximation" which completely neglects the horizontal evolution of these processes, resulting in key biases in current climate models. With a focus on atmospheric GWs, we present the first-ever global simulation of atmospheric GW fluxes using machine learning (ML) models trained on the WINDSET dataset to emulate global GW emulation in the atmosphere, as an alternative to traditional single-column parameterizations. Using an Attention U-Net-based architecture trained on globally resolved GW momentum fluxes, we illustrate the importance and effectiveness of global nonlocality, when simulating GWs using data-driven schemes.

Learning 3D models of all animals on the Earth requires massively scaling up existing solutions. With this ultimate goal in mind, we develop 3D-Fauna, an approach that learns a pan-category deformable 3D animal model for more than 100 animal species jointly. One crucial bottleneck of modeling animals is the limited availability of training data, which we overcome by simply learning from 2D Internet images. We show that prior category-specific attempts fail to generalize to rare species with limited training images. We address this challenge by introducing the Semantic Bank of Skinned Models (SBSM), which automatically discovers a small set of base animal shapes by combining geometric inductive priors with semantic knowledge implicitly captured by an off-the-shelf self-supervised feature extractor. To train such a model, we also contribute a new large-scale dataset of diverse animal species. At inference time, given a single image of any quadruped animal, our model reconstructs an articulated 3D mesh in a feed-forward fashion within seconds.

Global climate models represent small-scale processes such as clouds and convection using quasi-empirical models known as parameterizations, and these parameterizations are a leading cause of uncertainty in climate projections. A promising alternative approach is to use machine learning to build new parameterizations directly from high-resolution model output. However, parameterizations learned from three-dimensional model output have not yet been successfully used for simulations of climate. Here we use a random forest to learn a parameterization of subgrid processes from output of a three-dimensional high-resolution atmospheric model. Integrating this parameterization into the atmospheric model leads to stable simulations at coarse resolution that replicate the climate of the high-resolution simulation. The parameterization obeys physical constraints and captures important statistics such as precipitation extremes. The ability to learn from a fully three-dimensional simulation presents an opportunity for learning parameterizations from the wide range of global high-resolution simulations that are now emerging.

Due to their high predictive performance and flexibility, machine learning models are an appropriate and efficient tool for ecologists. However, implementing a machine learning model is not yet a trivial task and may seem intimidating to ecologists with no previous experience in this area. Here we provide a series of tips to help ecologists in implementing machine learning models. We focus on classification problems as many ecological studies aim to assign data into predefined classes such as ecological states or biological entities. Each of the nine tips identifies a common error, trap or challenge in developing machine learning models and provides recommendations to facilitate their use in ecological studies.

Automated video analysis is critical for wildlife conservation. A foundational task in this domain is multi-animal tracking (MAT), which underpins applications such as individual re-identification and behavior recognition. However, existing datasets are limited in scale, constrained to a few species, or lack sufficient temporal and geographical diversity - leaving no suitable benchmark for training general-purpose MAT models applicable across wild animal populations. To address this, we introduce SA-FARI, the largest open-source MAT dataset for wild animals. It comprises 11,609 camera trap videos collected over approximately 10 years (2014-2024) from 741 locations across 4 continents, spanning 99 species categories. Each video is exhaustively annotated culminating in ~46 hours of densely annotated footage containing 16,224 masklet identities and 942,702 individual bounding boxes, segmentation masks, and species labels. Alongside the task-specific annotations, we publish anonymized camera trap locations for each video. Finally, we present comprehensive benchmarks on SA-FARI using state-of-the-art vision-language models for detection and tracking, including SAM 3, evaluated with both species-specific and generic animal prompts. We also compare against vision-only methods developed specifically for wildlife analysis. SA-FARI is the first large-scale dataset to combine high species diversity, multi-region coverage, and high-quality spatio-temporal annotations, offering a new foundation for advancing generalizable multianimal tracking in the wild. The dataset is available at https://www.conservationxlabs.com/sa-fari{conservationxlabs.com/SA-FARI}.

We present OSMGraphCLIP, a CLIP-style geospatial representation model that learns global location embeddings from freely available OpenStreetMap (OSM) data. OSMGraphCLIP represents geographic environments as heterogeneous graphs of typed OSM features, preserving the topological and semantic relationships among roads, buildings, land-use regions, and points of interest. A multi-scale graph encoder captures both fine-grained local structure and broader landscape composition, and supervises a spherical-harmonics location encoder through a contrastive alignment objective. We evaluate OSMGraphCLIP across a diverse suite of downstream geospatial regression and classification tasks spanning climate, ecology, socioeconomic indicators, public health, land cover, biodiversity, and wildfire forecasting, and show that structured OSM data alone supports strong global location representations across domains. OSMGraphCLIP matches or exceeds satellite-based baselines on the majority of benchmarks, with the most pronounced advantage on socioeconomic and public-health tasks, where OSM's explicit semantic annotation of the built environment encodes patterns of human activity that satellite pixels can only capture indirectly. On ecological and environmental tasks, the model remains closely competitive with imagery-based methods despite using no Earth observation data. Qualitative analysis confirms that the learned embeddings organize geographic space coherently, recovering biome boundaries, urban gradients, and tropical--temperate distinctions from map topology alone.

Automated individual animal re-identification is essential for large-scale biodiversity monitoring; however, field imagery complicates separating identity cues from nuisance variation in pose, illumination, background, resolution, and species-specific morphology. The DS@GT ARC submission to AnimalCLEF 2026 introduces a multi-species image-clustering system for re-identifying Eurasian lynx, fire salamanders, loggerhead sea turtles, and Texas horned lizards. Instead of relying on a single descriptor or nearest-neighbor retrieval, this approach formulates re-identification as species-aware graph construction over candidate image pairs. The pipeline integrates tailored preprocessing, global candidate retrieval, LightGlue-based local verification with multiple keypoint families, LightGBM pair scoring, conservative edge admission, and Leiden community detection. This design directly addresses a primary failure mode of clustering-based re-identification: high-scoring false pairs that act as bridge edges and merge distinct individuals through transitive closure. Across species, ablation studies demonstrate that local feature support, foreground-aware preprocessing, and species-specific backbone selection enhance pair evidence, while graph operating points determine the trade-off between fragmentation and over-merging. The selected submission achieved a public ARI of 0.733 and a private ARI of 0.674, ranking fifth among 230 teams. These results indicate that robust wildlife re-identification requires not only strong visual representations but also calibrated integration of global similarity, local identity markings, neighborhood context, and graph-level constraints. The code can be found at https://github.com/dsgt-arc/animalclef-2026.

This paper presents a hybrid framework for literature reviews that augments traditional bibliometric methods with large language models (LLMs). By fine-tuning open-source LLMs, our approach enables scalable extraction of qualitative insights from large volumes of research content, enhancing both the breadth and depth of knowledge synthesis. To improve annotation efficiency and consistency, we introduce an error-focused validation process in which LLMs generate initial labels and human reviewers correct misclassifications. Applying this framework to over 20000 scientific articles about human migration, we demonstrate that a domain-adapted LLM can serve as a "specialist" model - capable of accurately selecting relevant studies, detecting emerging trends, and identifying critical research gaps. Notably, the LLM-assisted review reveals a growing scholarly interest in climate-induced migration. However, existing literature disproportionately centers on a narrow set of environmental hazards (e.g., floods, droughts, sea-level rise, and land degradation), while overlooking others that more directly affect human health and well-being, such as air and water pollution or infectious diseases. This imbalance highlights the need for more comprehensive research that goes beyond physical environmental changes to examine their ecological and societal consequences, particularly in shaping migration as an adaptive response. Overall, our proposed framework demonstrates the potential of fine-tuned LLMs to conduct more efficient, consistent, and insightful literature reviews across disciplines, ultimately accelerating knowledge synthesis and scientific discovery.

Vegetation monitoring under climate stress requires answering not only how it will evolve given the expected weather, but how it would respond to alternative meteorological conditions. Forecasting models return the expected vegetation state for the observed weather and cannot answer these scenario-conditioned questions, because future weather is fixed to the recorded trajectory. We present VegSim, a geospatial world model for scenario-conditioned vegetation simulation. VegSim infers a latent vegetation state from sparse satellite-derived NDVI histories, past meteorological covariates, and static spatial context, propagates it forward under future weather forcing through recurrent latent dynamics, and decodes predictive NDVI quantiles at each lead time. Because future forcing enters as a controllable input, the same trained model supports probabilistic forecasting under observed weather and conditional simulation under user-defined meteorological forcing, without supervision on scenario responses. We evaluate VegSim on GreenEarthNet across in-distribution data and spatial, temporal, and joint spatial-temporal shift, where it achieves strong point and probabilistic accuracy against time series and Earth observation forecasting baselines while using a compact architecture. We then simulate vegetation responses across Europe under four meteorological scenarios, and in a France summer 2022 case study, obtaining spatially coherent patterns consistent with known sensitivity to temperature and precipitation. The code is available at https://github.com/arco-group/vegsim.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Building world models that accurately and comprehensively represent the real world is the utmost aspiration for conditional image generative models as it would enable their use as world simulators. For these models to be successful world models, they should not only excel at image quality and prompt-image consistency but also ensure high representation diversity. However, current research in generative models mostly focuses on creative applications that are predominantly concerned with human preferences of image quality and aesthetics. We note that generative models have inference time mechanisms - or knobs - that allow the control of generation consistency, quality, and diversity. In this paper, we use state-of-the-art text-to-image and image-and-text-to-image models and their knobs to draw consistency-diversity-realism Pareto fronts that provide a holistic view on consistency-diversity-realism multi-objective. Our experiments suggest that realism and consistency can both be improved simultaneously; however there exists a clear tradeoff between realism/consistency and diversity. By looking at Pareto optimal points, we note that earlier models are better at representation diversity and worse in consistency/realism, and more recent models excel in consistency/realism while decreasing significantly the representation diversity. By computing Pareto fronts on a geodiverse dataset, we find that the first version of latent diffusion models tends to perform better than more recent models in all axes of evaluation, and there exist pronounced consistency-diversity-realism disparities between geographical regions. Overall, our analysis clearly shows that there is no best model and the choice of model should be determined by the downstream application. With this analysis, we invite the research community to consider Pareto fronts as an analytical tool to measure progress towards world models.

Accurate individual identification is essential for monitoring rare amphibians, yet invasive marking is often unsuitable for critically endangered species. We evaluate state-of-the-art computer-vision methods for photographic re-identification of the Hula painted frog (Latonia nigriventer) using 1,233 ventral images from 191 individuals collected during 2013-2020 capture-recapture surveys. We compare deep local-feature matching in a zero-shot setting with deep global-feature embedding models. The local-feature pipeline achieves 98% top-1 closed-set identification accuracy, outperforming all global-feature models; fine-tuning improves the best global-feature model to 60% top-1 (91% top-10) but remains below local matching. To combine scalability with accuracy, we implement a two-stage workflow in which a fine-tuned global-feature model retrieves a short candidate list that is re-ranked by local-feature matching, reducing end-to-end runtime from 6.5-7.8 hours to ~38 minutes while maintaining ~96% top-1 closed-set accuracy on the labeled dataset. Separation of match scores between same- and different-individual pairs supports thresholding for open-set identification, enabling practical handling of novel individuals. We deploy this pipeline as a web application for routine field use, providing rapid, standardized, non-invasive identification to support conservation monitoring and capture-recapture analyses. Overall, in this species, zero-shot deep local-feature matching outperformed global-feature embedding and provides a strong default for photo-identification.

While many modern studies are dedicated to ML-based large-sample hydrologic modeling, these efforts have not necessarily translated into predictive improvements that are grounded in enhanced physical-conceptual understanding. Here, we report on a CONUS-wide large-sample study (spanning diverse hydro-geo-climatic conditions) using ML-augmented physically-interpretable catchment-scale models of varying complexity based in the Mass-Conserving Perceptron (MCP). Results were evaluated using attribute masks such as snow regime, forest cover, and climate zone. Our results indicate the importance of selecting model architectures of appropriate model complexity based on how process dominance varies with hydrological regime. Benchmark comparisons show that physically-interpretable mass-conserving MCP-based models can achieve performance comparable to data-based models based in the Long Short-Term Memory network (LSTM) architecture. Overall, this study highlights the potential of a theory-informed, physically grounded approach to large-sample hydrology, with emphasis on mechanistic understanding and the development of parsimonious and interpretable model architectures, thereby laying the foundation for future models of everywhere that architecturally encode information about spatially- and temporally-varying process dominance.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Global climate models parameterize a range of atmospheric-oceanic processes like gravity waves, clouds, moist convection, and turbulence that cannot be sufficiently resolved. These subgrid-scale closures for unresolved processes are a leading source of model uncertainty. Here, we present a new approach to developing machine learning parameterizations of small-scale climate processes by fine-tuning a pre-trained AI foundation model (FM). FMs are largely unexplored in climate research. A pre-trained encoder-decoder from a 2.3 billion parameter FM (NASA and IBM Research's Prithvi WxC) -- which contains a latent probabilistic representation of atmospheric evolution -- is fine-tuned (or reused) to create a deep learning parameterization for atmospheric gravity waves (GWs). The parameterization captures GW effects for a coarse-resolution climate model by learning the fluxes from an atmospheric reanalysis with 10 times finer resolution. A comparison of monthly averages and instantaneous evolution with a machine learning model baseline (an Attention U-Net) reveals superior predictive performance of the FM parameterization throughout the atmosphere, even in regions excluded from pre-training. This performance boost is quantified using the Hellinger distance, which is 0.11 for the baseline and 0.06 for the fine-tuned model. Our findings emphasize the versatility and reusability of FMs, which could be used to accomplish a range of atmosphere- and climate-related applications, leading the way for the creation of observations-driven and physically accurate parameterizations for more earth-system processes.

Knowledge of tree species distribution is fundamental to managing forests. New deep learning approaches promise significant accuracy gains for forest mapping, and are becoming a critical tool for mapping multiple tree species at scale. To advance the field, deep learning researchers need large benchmark datasets with high-quality annotations. To this end, we present the PureForest dataset: a large-scale, open, multimodal dataset designed for tree species classification from both Aerial Lidar Scanning (ALS) point clouds and Very High Resolution (VHR) aerial images. Most current public Lidar datasets for tree species classification have low diversity as they only span a small area of a few dozen annotated hectares at most. In contrast, PureForest has 18 tree species grouped into 13 semantic classes, and spans 339 km^2 across 449 distinct monospecific forests, and is to date the largest and most comprehensive Lidar dataset for the identification of tree species. By making PureForest publicly available, we hope to provide a challenging benchmark dataset to support the development of deep learning approaches for tree species identification from Lidar and/or aerial imagery. In this data paper, we describe the annotation workflow, the dataset, the recommended evaluation methodology, and establish a baseline performance from both 3D and 2D modalities.

Terrain modeling has traditionally relied on procedural techniques, which often require extensive domain expertise and handcrafted rules. In this paper, we present MESA - a novel data-centric alternative by training a diffusion model on global remote sensing data. This approach leverages large-scale geospatial information to generate high-quality terrain samples from text descriptions, showcasing a flexible and scalable solution for terrain generation. The model's capabilities are demonstrated through extensive experiments, highlighting its ability to generate realistic and diverse terrain landscapes. The dataset produced to support this work, the Major TOM Core-DEM extension dataset, is released openly as a comprehensive resource for global terrain data. The results suggest that data-driven models, trained on remote sensing data, can provide a powerful tool for realistic terrain modeling and generation.

Natural language processing (NLP) practitioners are leveraging large language models (LLM) to create structured datasets from semi-structured and unstructured data sources such as patents, papers, and theses, without having domain-specific knowledge. At the same time, ecological experts are searching for a variety of means to preserve biodiversity. To contribute to these efforts, we focused on endangered species and through in-context learning, we distilled knowledge from GPT-4. In effect, we created datasets for both named entity recognition (NER) and relation extraction (RE) via a two-stage process: 1) we generated synthetic data from GPT-4 of four classes of endangered species, 2) humans verified the factual accuracy of the synthetic data, resulting in gold data. Eventually, our novel dataset contains a total of 3.6K sentences, evenly divided between 1.8K NER and 1.8K RE sentences. The constructed dataset was then used to fine-tune both general BERT and domain-specific BERT variants, completing the knowledge distillation process from GPT-4 to BERT, because GPT-4 is resource intensive. Experiments show that our knowledge transfer approach is effective at creating a NER model suitable for detecting endangered species from texts.

New geospatial foundation models introduce a new model architecture and pretraining dataset, often sampled using different notions of data diversity. Performance differences are largely attributed to the model architecture or input modalities, while the role of the pretraining dataset is rarely studied. To address this research gap, we conducted a systematic study on how the geographic composition of pretraining data affects a model's downstream performance. We created global and per-continent pretraining datasets and evaluated them on global and per-continent downstream datasets. We found that the pretraining dataset from Europe outperformed global and continent-specific pretraining datasets on both global and local downstream evaluations. To investigate the factors influencing a pretraining dataset's downstream performance, we analysed 10 pretraining datasets using diversity across continents, biomes, landcover and spectral values. We found that only spectral diversity was strongly correlated with performance, while others were weakly correlated. This finding establishes a new dimension of diversity to be accounted for when creating a high-performing pretraining dataset. We open-sourced 7 new pretraining datasets, pretrained models, and our experimental framework at https://github.com/kerner-lab/pretrain-where.

A defining problem of the Anthropocene is to model the physical Earth and human societies as one coupled system, yet no learned representation spans their observational breadth. We argue the obstacle is geometric: the physical Earth is measured as continuous fields that ignore political borders, whereas societies are reported for administrative units. Earth-system foundation models serve the first geometry; coupling it to the second has required lossy averaging over borders. We introduce TerraNova, a foundation model trained on 1,024 physical and societal records in their native geometries: 512 gridded Earth-system fields and 512 national indicators. Dedicated encoders represent location, country, time and task, cross-modal transformers fuse them into a shared spatiotemporal state, and a hypernetwork generates a per-query decoder whose evidential head returns a predictive distribution. Two contrastive objectives couple the representation: a population-weighted alignment between each country and coordinates in its territory, and one to pretrained geospatial embeddings carrying image-derived semantics. Read out through that decoder, the representation is competitive with purpose-built geospatial encoders while spanning axes they do not represent (time, oceans and uncertainty) and supporting country-level capabilities. The frozen backbone reconstructs dense fields from sparse observations and adapts to unseen variables in minutes on consumer hardware.

Addressing the current lack of a standardized habitat classification system for cultivated land ecosystems, incomplete coverage of habitat types, and the inability of existing models to effectively integrate semantic and texture features-resulting in insufficient segmentation accuracy and blurred boundaries for multi-scale habitats (e.g., large-scale field plots and micro-habitats)-this study developed a comprehensively annotated ultra-high-resolution remote sensing image dataset encompassing 15 categories of cultivated land system habitats. Furthermore, we propose a Dynamic-Weighted Feature Fusion Network (DWFF-Net). The encoder of this model utilizes a frozen-parameter DINOv3 to extract foundational features. By analyzing the relationships between different category images and feature maps, we introduce a data-level adaptive dynamic weighting strategy for feature fusion. The decoder incorporates a dynamic weight computation network to achieve thorough integration of multi-layer features, and a hybrid loss function is adopted to optimize model training. Experimental results on the constructed dataset demonstrate that the proposed model achieves a mean Intersection over Union (mIoU) of 0.6979 and an F1-score of 0.8049, outperforming the baseline network by 0.021 and 0.0161, respectively. Ablation studies further confirm the complementary nature of multi-layer feature fusion, which effectively improves the IoU for micro-habitat categories such as field ridges. This study establishes a habitat identification framework for cultivated land systems based on adaptive multi-layer feature fusion, enabling sub-meter precision habitat mapping at a low cost and providing robust technical support for fine-grained habitat monitoring in cultivated landscapes.

With the success of machine learning (ML) applied to climate reaching further every day, emulators have begun to show promise not only for weather but for multi-year time scales in the atmosphere. Similar work for the ocean remains nascent, with state-of-the-art limited to models running for shorter time scales or only for regions of the globe. In this work, we demonstrate high-skill global emulation for surface ocean fields over 5-8 years of model rollout, accurately representing modes of variability for two different ML architectures (ConvNext and Transformers). In addition, we address the outstanding question of generalization, an essential consideration if the end-use of emulation is to model warming scenarios outside of the model training data. We show that 1) generalization is not an intrinsic feature of a data-driven emulator, 2) fine-tuning the emulator on only small amounts of additional data from a distribution similar to the test set can enable the emulator to perform well in a warmed climate, and 3) the forced emulators are robust to noise in the forcing.

The rise of accurate machine learning methods for weather forecasting is creating radical new possibilities for modeling the atmosphere. In the time of climate change, having access to high-resolution forecasts from models like these is also becoming increasingly vital. While most existing Neural Weather Prediction (NeurWP) methods focus on global forecasting, an important question is how these techniques can be applied to limited area modeling. In this work we adapt the graph-based NeurWP approach to the limited area setting and propose a multi-scale hierarchical model extension. Our approach is validated by experiments with a local model for the Nordic region.

Global plant maps of plant traits, such as leaf nitrogen or plant height, are essential for understanding ecosystem processes, including the carbon and energy cycles of the Earth system. However, existing trait maps remain limited by the high cost and sparse geographic coverage of field-based measurements. Citizen science initiatives offer a largely untapped resource to overcome these limitations, with over 50 million geotagged plant photographs worldwide capturing valuable visual information on plant morphology and physiology. In this study, we introduce PlantTraitNet, a multi-modal, multi-task uncertainty-aware deep learning framework that predictsfour key plant traits (plant height, leaf area, specific leaf area, and nitrogen content) from citizen science photos using weak supervision. By aggregating individual trait predictions across space, we generate global maps of trait distributions. We validate these maps against independent vegetation survey data (sPlotOpen) and benchmark them against leading global trait products. Our results show that PlantTraitNet consistently outperforms existing trait maps across all evaluated traits, demonstrating that citizen science imagery, when integrated with computer vision and geospatial AI, enables not only scalable but also more accurate global trait mapping. This approach offers a powerful new pathway for ecological research and Earth system modeling.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

The correlation between insect morphological traits and climate has been documented in physiological studies, but such studies remain limited by the time-consuming nature of the data analysis. In particular, the open source datasets often lack annotations of species' morphological traits, making dedicated annotations campaigns necessary; these efforts are typically local in scale and costly. In this paper, we propose a pipeline to identify and segment body parts of Odonates (dragonflies and damselflies) using deep neural networks, with the ultimate goal of extracting body parts' colouration. The pipeline is trained on a limited annotated dataset and refined with pseudo supervised data. We show that, by using open source images from citizen science platforms, our approach can segment each visible subject (Odonates) into head, thorax, abdomen, and wings and then extract a colour palette for each body part. This will enable large-scale statistical analysis of ecological correlations (e.g., between colouration and climate change, habitat loss, or geolocation) which are crucial for quantifying and assessing ecosystem biodiversity status.

In recent years, the development of robust multi-source models has emerged in the Earth Observation (EO) field. These are models that leverage data from diverse sources to improve predictive accuracy when there is missing data. Despite these advancements, the factors influencing the varying effectiveness of such models remain poorly understood. In this study, we evaluate the predictive performance of six state-of-the-art multi-source models in predicting scenarios where either a single data source is missing or only a single source is available. Our analysis reveals that the efficacy of these models is intricately tied to the nature of the task, the complementarity among data sources, and the model design. Surprisingly, we observe instances where the removal of certain data sources leads to improved predictive performance, challenging the assumption that incorporating all available data is always beneficial. These findings prompt critical reflections on model complexity and the necessity of all collected data sources, potentially shaping the way for more streamlined approaches in EO applications.

Visual Species Recognition (VSR) is pivotal to biodiversity assessment and conservation, evolution research, and ecology and ecosystem management. Training a machine-learned model for VSR typically requires vast amounts of annotated images. Yet, species-level annotation demands domain expertise, making it realistic for domain experts to annotate only a few examples. These limited labeled data motivate training an ''expert'' model via few-shot learning (FSL). Meanwhile, advanced Large Multimodal Models (LMMs) have demonstrated prominent performance on general recognition tasks. It is straightforward to ask whether LMMs excel in the highly specialized VSR task and whether they outshine FSL expert models. Somewhat surprisingly, we find that LMMs struggle in this task, despite using various established prompting techniques. LMMs even significantly underperform FSL expert models, which are as simple as finetuning a pretrained visual encoder on the few-shot images. However, our in-depth analysis reveals that LMMs can effectively post-hoc correct the expert models' incorrect predictions. Briefly, given a test image, when prompted with the top predictions from an FSL expert model, LMMs can recover the ground-truth label. Building on this insight, we derive a simple method called Post-hoc Correction (POC), which prompts an LMM to re-rank the expert model's top predictions using enriched prompts that include softmax confidence scores and few-shot visual examples. Across five challenging VSR benchmarks, POC outperforms prior art of FSL by +6.4% in accuracy without extra training, validation, or manual intervention. Importantly, POC generalizes to different pretrained backbones and LMMs, serving as a plug-and-play module to significantly enhance existing FSL methods.

Machine learning systems deployed in the wild are often trained on a source distribution but deployed on a different target distribution. Unlabeled data can be a powerful point of leverage for mitigating these distribution shifts, as it is frequently much more available than labeled data and can often be obtained from distributions beyond the source distribution as well. However, existing distribution shift benchmarks with unlabeled data do not reflect the breadth of scenarios that arise in real-world applications. In this work, we present the WILDS 2.0 update, which extends 8 of the 10 datasets in the WILDS benchmark of distribution shifts to include curated unlabeled data that would be realistically obtainable in deployment. These datasets span a wide range of applications (from histology to wildlife conservation), tasks (classification, regression, and detection), and modalities (photos, satellite images, microscope slides, text, molecular graphs). The update maintains consistency with the original WILDS benchmark by using identical labeled training, validation, and test sets, as well as the evaluation metrics. On these datasets, we systematically benchmark state-of-the-art methods that leverage unlabeled data, including domain-invariant, self-training, and self-supervised methods, and show that their success on WILDS is limited. To facilitate method development and evaluation, we provide an open-source package that automates data loading and contains all of the model architectures and methods used in this paper. Code and leaderboards are available at https://wilds.stanford.edu.

Machine learning (ML) has emerged as a cost-effective approach to complement dynamical downscaling for producing high-resolution regional climate projections. However, the absence of standardised training and evaluation protocols, applied consistently across multiple domains, continues to hinder meaningful model intercomparison. We introduce CORDEX-ML-Bench, a benchmark aligned with CORDEX, which constitutes the first phase of a community initiative to advance data-driven downscaling toward operational readiness, and complement future dynamical downscaling efforts under CMIP7. The framework targets downscaled daily maximum temperature and precipitation to ~10 km resolution (20x increase) across three pilot regions; European Alps, New Zealand, and Southern Africa. Using a perfect-model experimental design, we evaluate 40 ML configurations developed independently, spanning traditional ML, convolutional U-Nets, vision transformers, graph neural networks, and generative models based on diffusion, flow matching, and generative adversarial networks. Models are trained under two experimental periods, an empirical-statistical downscaling pseudo-reality (historical period only) and Emulator (historical and future periods) -and are evaluated against a core set of metrics developed specifically for assessing downscaling skill. Generative models consistently outperform deterministic approaches for precipitation, better capturing fine-scale variability and extremes. For temperature, the generative advantage narrows and deterministic architectures remain competitive. Models trained solely on the historical period systematically underestimate future climate-change signals while those additionally trained on a future period perform better. These findings raise concerns about historically trained models widely used in an operational setting, underscoring the need for rigorous extrapolation testing.

Machine-learning (ML) models, such as the AIFS at the ECMWF, have revolutionised weather forecasting in recent years. We present an extension of the AIFS that jointly models the atmosphere and surface ocean, including ocean waves and sea ice. The primary objective of this extension is to enhance machine-learning medium-range forecasting and enable new use cases by expanding the weather state to better capture coupled surface processes. Our approach departs from traditional numerical models by not having two separate models for the atmosphere and marine components. The joint model instead learns correlations across the entire atmosphere-ocean interface in a component-agnostic way, and can exploit the expressive capacity of ML architectures to learn cross-component relationships directly from the data. We leverage tailored and targeted datasets and solve model design challenges such as missing values over land, multi-scale temporal dynamics, and physical realism of forecast fields and demonstrate the utility of loss scaling in guiding the learning process. We evaluate how representing the surface ocean affects medium-range weather forecasts. We also assess the model's ability to predict surface-ocean fields, including wave swell and tropical-cyclone cold wakes. For nearly all evaluated marine variables, we observe an improvement of approximately one day in forecast skill at medium-range lead times compared to physics-based models. Furthermore, we demonstrate that the model is robust to idealised initial conditions outside the training distribution and responds to them in a physically consistent way. Overall, our findings suggest that the joint AIFS modelling approach offers significant potential for combined atmosphere-ocean forecasting. Our work provides a solid foundation for future development of data-driven coupled Earth system models with greater flexibility and physical fidelity.

Biodiversity plays a crucial role in maintaining the balance of the ecosystem. However, poaching and unintentional human activities contribute to the decline in the population of many species. Hence, active monitoring is required to preserve these endangered species. Current human-led monitoring techniques are prone to errors and are labor-intensive. Therefore, we study the application of deep learning methods like Convolutional Neural Networks (CNNs) and transfer learning, which can aid in automating the process of monitoring endangered species. For this, we create our custom dataset utilizing trustworthy online databases like iNaturalist and ZooChat. To choose the best model for our use case, we compare the performance of different architectures like DenseNet, ResNet, VGGNet, and YOLOv8 on the custom wildlife dataset. Transfer learning reduces training time by freezing the pre-trained weights and replacing only the output layer with custom, fully connected layers designed for our dataset. Our results indicate that YOLOv8 performs better, achieving a training accuracy of 97.39 % and an F1 score of 96.50 %, surpassing other models. Our findings suggest that integrating YOLOv8 into conservation efforts could revolutionize wildlife monitoring with its high accuracy and efficiency, potentially transforming how endangered species are monitored and protected worldwide.

Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, conventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing. Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods. Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. All code and data are available at: https://github.com/echerif18/HyspectraSSL.

The proliferation of pretrained models, as a result of advancements in pretraining techniques, has led to the emergence of a vast zoo of publicly available models. Effectively utilizing these resources to obtain models with robust out-of-distribution generalization capabilities for downstream tasks has become a crucial area of research. Previous research has primarily focused on identifying the most powerful models within the model zoo, neglecting to fully leverage the diverse inductive biases contained within. This paper argues that the knowledge contained in weaker models is valuable and presents a method for leveraging the diversity within the model zoo to improve out-of-distribution generalization capabilities. Specifically, we investigate the behaviors of various pretrained models across different domains of downstream tasks by characterizing the variations in their encoded representations in terms of two dimensions: diversity shift and correlation shift. This characterization enables us to propose a new algorithm for integrating diverse pretrained models, not limited to the strongest models, in order to achieve enhanced out-of-distribution generalization performance. Our proposed method demonstrates state-of-the-art empirical results on a variety of datasets, thus validating the benefits of utilizing diverse knowledge.

This paper introduces ClimateGPT, a model family of domain-specific large language models that synthesize interdisciplinary research on climate change. We trained two 7B models from scratch on a science-oriented dataset of 300B tokens. For the first model, the 4.2B domain-specific tokens were included during pre-training and the second was adapted to the climate domain after pre-training. Additionally, ClimateGPT-7B, 13B and 70B are continuously pre-trained from Llama~2 on a domain-specific dataset of 4.2B tokens. Each model is instruction fine-tuned on a high-quality and human-generated domain-specific dataset that has been created in close cooperation with climate scientists. To reduce the number of hallucinations, we optimize the model for retrieval augmentation and propose a hierarchical retrieval strategy. To increase the accessibility of our model to non-English speakers, we propose to make use of cascaded machine translation and show that this approach can perform comparably to natively multilingual models while being easier to scale to a large number of languages. Further, to address the intrinsic interdisciplinary aspect of climate change we consider different research perspectives. Therefore, the model can produce in-depth answers focusing on different perspectives in addition to an overall answer. We propose a suite of automatic climate-specific benchmarks to evaluate LLMs. On these benchmarks, ClimateGPT-7B performs on par with the ten times larger Llama-2-70B Chat model while not degrading results on general domain benchmarks. Our human evaluation confirms the trends we saw in our benchmarks. All models were trained and evaluated using renewable energy and are released publicly.

Forest inventories increasingly rely on artificial intelligence (AI) models to derive forest attributes from large-scale 3D point clouds. Current models are typically specialized to a single task, sensor, and forest type, making adaptation expensive in terms of annotations, computation, and expertise. We ask whether a single pretrained model can instead learn transferable representations across diverse forest inventory settings. Inspired by recent developments in language modelling and computer vision, we take a step toward a foundation model (FM) for 3D forestry. Using LitePT as backbone, we first establish a strong supervised baseline that sets a new state of the art on forest semantic and instance segmentation, tree species classification, and age regression benchmarks. We then curate a large-scale unlabelled corpus spanning airborne, UAV, and mobile laser scanning across diverse forest ecosystems, and pretrain the same backbone using self-supervised learning. We systematically evaluate representation learning strategies by comparing training from scratch, supervised pretraining, and self-supervised pretraining across four representative forestry tasks, under varying annotation budgets. Compared with training from scratch, self-supervised pretraining accelerates model convergence and consistently improves performance when annotations are scarce. Compared with task-specific supervised pretraining, self-supervised pretraining yields more transferable representations across downstream forestry tasks. These findings identify the practical regime in which pretrained representations are most valuable and suggest that instance discrimination, rather than forest semantics, is the main remaining obstacle to a general-purpose 3D forest foundation model. Code and models are available at: https://github.com/prs-eth/ForPT.

Large language models (LLMs) have achieved remarkable success and demonstrated superior performance across various tasks, including natural language processing (NLP), weather forecasting, biological protein folding, text generation, and solving mathematical problems. However, many real-world data exhibit highly non-Euclidean latent hierarchical anatomy, such as protein networks, transportation networks, financial networks, brain networks, and linguistic structures or syntactic trees in natural languages. Effectively learning intrinsic semantic entailment and hierarchical relationships from these raw, unstructured input data using LLMs remains an underexplored area. Due to its effectiveness in modeling tree-like hierarchical structures, hyperbolic geometry -- a non-Euclidean space -- has rapidly gained popularity as an expressive latent representation space for complex data modeling across domains such as graphs, images, languages, and multi-modal data. Here, we provide a comprehensive and contextual exposition of recent advancements in LLMs that leverage hyperbolic geometry as a representation space to enhance semantic representation learning and multi-scale reasoning. Specifically, the paper presents a taxonomy of the principal techniques of Hyperbolic LLMs (HypLLMs) in terms of four main categories: (1) hyperbolic LLMs through exp/log maps; (2) hyperbolic fine-tuned models; (3) fully hyperbolic LLMs, and (4) hyperbolic state-space models. We also explore crucial potential applications and outline future research directions. A repository of key papers, models, datasets, and code implementations is available at https://github.com/sarangp2402/Hyperbolic-LLM-Models/tree/main.

The objective of this study is to evaluate the potential for History Matching (HM) to tune a climate system with multi-scale dynamics. By considering a toy climate model, namely, the two-scale Lorenz96 model and producing experiments in perfect-model setting, we explore in detail how several built-in choices need to be carefully tested. We also demonstrate the importance of introducing physical expertise in the range of parameters, a priori to running HM. Finally we revisit a classical procedure in climate model tuning, that consists of tuning the slow and fast components separately. By doing so in the Lorenz96 model, we illustrate the non-uniqueness of plausible parameters and highlight the specificity of metrics emerging from the coupling. This paper contributes also to bridging the communities of uncertainty quantification, machine learning and climate modeling, by making connections between the terms used by each community for the same concept and presenting promising collaboration avenues that would benefit climate modeling research.

Machine-learning-based parameterizations (i.e. representation of sub-grid processes) of global climate models or turbulent simulations have recently been proposed as a powerful alternative to physical, but empirical, representations, offering a lower computational cost and higher accuracy. Yet, those approaches still suffer from a lack of generalization and extrapolation beyond the training data, which is however critical to projecting climate change or unobserved regimes of turbulence. Here we show that a multi-fidelity approach, which integrates datasets of different accuracy and abundance, can provide the best of both worlds: the capacity to extrapolate leveraging the physically-based parameterization and a higher accuracy using the machine-learning-based parameterizations. In an application to climate modeling, the multi-fidelity framework yields more accurate climate projections without requiring major increase in computational resources. Our multi-fidelity randomized prior networks (MF-RPNs) combine physical parameterization data as low-fidelity and storm-resolving historical run's data as high-fidelity. To extrapolate beyond the training data, the MF-RPNs are tested on high-fidelity warming scenarios, +4K, data. We show the MF-RPN's capacity to return much more skillful predictions compared to either low- or high-fidelity (historical data) simulations trained only on one regime while providing trustworthy uncertainty quantification across a wide range of scenarios. Our approach paves the way for the use of machine-learning based methods that can optimally leverage historical observations or high-fidelity simulations and extrapolate to unseen regimes such as climate change.

Generative models have the potential to transform the way we emulate Earth's changing climate. Previous generative approaches rely on weather-scale autoregression for climate emulation, but this is inherently slow for long climate horizons and has yet to demonstrate stable rollouts under nonstationary forcings. Here, we introduce Spatiotemporal Pyramid Flows (SPF), a new class of flow matching approaches that model data hierarchically across spatial and temporal scales. Inspired by cascaded video models, SPF partitions the generative trajectory into a spatiotemporal pyramid, progressively increasing spatial resolution to reduce computation and coupling each stage with an associated timescale to enable direct sampling at any temporal level in the pyramid. This design, together with conditioning each stage on prescribed physical forcings (e.g., greenhouse gases or aerosols), enables efficient, parallel climate emulation at multiple timescales. On ClimateBench, SPF outperforms strong flow matching baselines and pre-trained models at yearly and monthly timescales while offering fast sampling, especially at coarser temporal levels. To scale SPF, we curate ClimateSuite, the largest collection of Earth system simulations to date, comprising over 33,000 simulation-years across ten climate models and the first dataset to include simulations of climate interventions. We find that the scaled SPF model demonstrates good generalization to held-out scenarios across climate models. Together, SPF and ClimateSuite provide a foundation for accurate, efficient, probabilistic climate emulation across temporal scales and realistic future scenarios. Data and code is publicly available at https://github.com/stanfordmlgroup/spf .

Large-scale commercial platforms usually involve numerous business domains for diverse business strategies and expect their recommendation systems to provide click-through rate (CTR) predictions for multiple domains simultaneously. Existing promising and widely-used multi-domain models discover domain relationships by explicitly constructing domain-specific networks, but the computation and memory boost significantly with the increase of domains. To reduce computational complexity, manually grouping domains with particular business strategies is common in industrial applications. However, this pre-defined data partitioning way heavily relies on prior knowledge, and it may neglect the underlying data distribution of each domain, hence limiting the model's representation capability. Regarding the above issues, we propose an elegant and flexible multi-distribution modeling paradigm, named Adaptive Distribution Hierarchical Model (AdaptDHM), which is an end-to-end optimization hierarchical structure consisting of a clustering process and classification process. Specifically, we design a distribution adaptation module with a customized dynamic routing mechanism. Instead of introducing prior knowledge for pre-defined data allocation, this routing algorithm adaptively provides a distribution coefficient for each sample to determine which cluster it belongs to. Each cluster corresponds to a particular distribution so that the model can sufficiently capture the commonalities and distinctions between these distinct clusters. Extensive experiments on both public and large-scale Alibaba industrial datasets verify the effectiveness and efficiency of AdaptDHM: Our model achieves impressive prediction accuracy and its time cost during the training stage is more than 50% less than that of other models.

The persisting threats on migratory bird populations highlight the urgent need for effective monitoring techniques that could assist in their conservation. Among these, passive acoustic monitoring is an essential tool, particularly for nocturnal migratory species that are difficult to track otherwise. This work presents the Nocturnal Bird Migration (NBM) dataset, a collection of 13,359 annotated vocalizations from 117 species of the Western Palearctic. The dataset includes precise time and frequency annotations, gathered by dozens of bird enthusiasts across France, enabling novel downstream acoustic analysis. In particular, we prove the utility of this database by training an original two-stage deep object detection model tailored for the processing of audio data. While allowing the precise localization of bird calls in spectrograms, this model shows competitive accuracy on the 45 main species of the dataset with state-of-the-art systems trained on much larger audio collections. These results highlight the interest of fostering similar open-science initiatives to acquire costly but valuable fine-grained annotations of audio files. All data and code are made openly available.

Animal habitat surveys play a critical role in preserving the biodiversity of the land. One of the effective ways to gain insights into animal habitats involves identifying animal footprints, which offers valuable information about species distribution, abundance, and behavior. However, due to the scarcity of animal footprint images, there are no well-maintained public datasets, preventing recent advanced techniques in computer vision from being applied to animal tracking. In this paper, we introduce OpenAnimalTracks dataset, the first publicly available labeled dataset designed to facilitate the automated classification and detection of animal footprints. It contains various footprints from 18 wild animal species. Moreover, we build benchmarks for species classification and detection and show the potential of automated footprint identification with representative classifiers and detection models. We find SwinTransformer achieves a promising classification result, reaching 69.41% in terms of the averaged accuracy. Faster-RCNN achieves mAP of 0.295. We hope our dataset paves the way for automated animal tracking techniques, enhancing our ability to protect and manage biodiversity. Our dataset and code are available at https://github.com/dahlian00/OpenAnimalTracks.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Global vegetation structure mapping is critical for understanding the global carbon cycle and maximizing the efficacy of nature-based carbon sequestration initiatives. Moreover, vegetation structure mapping can help reduce the impacts of climate change by, for example, guiding actions to improve water security, increase biodiversity and reduce flood risk. Global satellite measurements provide an important set of observations for monitoring and managing deforestation and degradation of existing forests, natural forest regeneration, reforestation, biodiversity restoration, and the implementation of sustainable agricultural practices. In this paper, we explore the effectiveness of fine-tuning of a geospatial foundation model to estimate above-ground biomass (AGB) using space-borne data collected across different eco-regions in Brazil. The fine-tuned model architecture consisted of a Swin-B transformer as the encoder (i.e., backbone) and a single convolutional layer for the decoder head. All results were compared to a U-Net which was trained as the baseline model Experimental results of this sparse-label prediction task demonstrate that the fine-tuned geospatial foundation model with a frozen encoder has comparable performance to a U-Net trained from scratch. This is despite the fine-tuned model having 13 times less parameters requiring optimization, which saves both time and compute resources. Further, we explore the transfer-learning capabilities of the geospatial foundation models by fine-tuning on satellite imagery with sparse labels from different eco-regions in Brazil.

From crop mapping to flood detection, machine learning in remote sensing has a wide range of societally beneficial applications. The commonalities between remote sensing data in these applications present an opportunity for pretrained machine learning models tailored to remote sensing to reduce the labeled data and effort required to solve individual tasks. However, such models must be: (i) flexible enough to ingest input data of varying sensor modalities and shapes (i.e., of varying spatial and temporal dimensions), and (ii) able to model Earth surface phenomena of varying scales and types. To solve this gap, we present Galileo, a family of pretrained remote sensing models designed to flexibly process multimodal remote sensing data. We also introduce a novel and highly effective self-supervised learning approach to learn both large- and small-scale features, a challenge not addressed by previous models. Our Galileo models obtain state-of-the-art results across diverse remote sensing tasks.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

Open-access multispectral imagery from missions like Landsat 8-9 and Sentinel-2 has fueled the development of geospatial foundation models (GFMs) for humanitarian and environmental applications. Yet, their deployment remains limited by (i) the absence of automated geospatial data pipelines and (ii) the large size of fine-tuned models. Existing GFMs lack workflows for processing raw satellite imagery, and downstream adaptations often retain the full complexity of the original encoder. We present InstaGeo, an open-source, end-to-end framework that addresses these challenges by integrating: (1) automated data curation to transform raw imagery into model-ready datasets; (2) task-specific model distillation to derive compact, compute-efficient models; and (3) seamless deployment as interactive web-map applications. Using InstaGeo, we reproduced datasets from three published studies and trained models with marginal mIoU differences of -0.73 pp for flood mapping, -0.20 pp for crop segmentation, and +1.79 pp for desert locust prediction. The distilled models are up to 8x smaller than standard fine-tuned counterparts, reducing FLOPs and CO2 emissions with minimal accuracy loss. Leveraging InstaGeo's streamlined data pipeline, we also curated a larger crop segmentation dataset, achieving a state-of-the-art mIoU of 60.65%, a 12 pp improvement over prior baselines. Moreover, InstaGeo enables users to progress from raw data to model deployment within a single working day. By unifying data preparation, model compression, and deployment, InstaGeo transforms research-grade GFMs into practical, low-carbon tools for real-time, large-scale Earth observation. This approach shifts geospatial AI toward data quality and application-driven innovation. Source code, datasets, and model checkpoints are available at: https://github.com/instadeepai/InstaGeo-E2E-Geospatial-ML.git

1. The popularity of Machine learning (ML), Deep learning (DL), and Artificial intelligence (AI) has risen sharply in recent years. Despite this spike in popularity, the inner workings of ML and DL algorithms are often perceived as opaque, and their relationship to classical data analysis tools remains debated. 2. Although it is often assumed that ML and DL excel primarily at making predictions, ML and DL can also be used for analytical tasks traditionally addressed with statistical models. Moreover, most recent discussions and reviews on ML focus mainly on DL, missing out on synthesizing the wealth of ML algorithms with different advantages and general principles. 3. Here, we provide a comprehensive overview of the field of ML and DL, starting by summarizing its historical developments, existing algorithm families, differences to traditional statistical tools, and universal ML principles. We then discuss why and when ML and DL models excel at prediction tasks and where they could offer alternatives to traditional statistical methods for inference, highlighting current and emerging applications for ecological problems. Finally, we summarize emerging trends such as scientific and causal ML, explainable AI, and responsible AI that may significantly impact ecological data analysis in the future. 4. We conclude that ML and DL are powerful new tools for predictive modeling and data analysis. The superior performance of ML and DL algorithms compared to statistical models can be explained by their higher flexibility and automatic data-dependent complexity optimization. However, their use for causal inference is still disputed as the focus of ML and DL methods on predictions creates challenges for the interpretation of these models. Nevertheless, we expect ML and DL to become an indispensable tool in E&E, comparable to other traditional statistical tools.

Many of society's most pressing challenges, from pandemic response to supply chain disruptions to climate adaptation, emerge from the collective behavior of millions of autonomous agents making decisions over time. Large Population Models (LPMs) offer an approach to understand these complex systems by simulating entire populations with realistic behaviors and interactions at unprecedented scale. LPMs extend traditional modeling approaches through three key innovations: computational methods that efficiently simulate millions of agents simultaneously, mathematical frameworks that learn from diverse real-world data streams, and privacy-preserving communication protocols that bridge virtual and physical environments. This allows researchers to observe how agent behavior aggregates into system-level outcomes and test interventions before real-world implementation. While current AI advances primarily focus on creating "digital humans" with sophisticated individual capabilities, LPMs develop "digital societies" where the richness of interactions reveals emergent phenomena. By bridging individual agent behavior and population-scale dynamics, LPMs offer a complementary path in AI research illuminating collective intelligence and providing testing grounds for policies and social innovations before real-world deployment. We discuss the technical foundations and some open problems here. LPMs are implemented by the AgentTorch framework (github.com/AgentTorch/AgentTorch)

Geospatial Foundation Models (GeoFMs) are transforming Earth Observation (EO), but evaluation lacks standardized protocols. GEO-Bench-2 addresses this with a comprehensive framework spanning classification, segmentation, regression, object detection, and instance segmentation across 19 permissively-licensed datasets. We introduce ''capability'' groups to rank models on datasets that share common characteristics (e.g., resolution, bands, temporality). This enables users to identify which models excel in each capability and determine which areas need improvement in future work. To support both fair comparison and methodological innovation, we define a prescriptive yet flexible evaluation protocol. This not only ensures consistency in benchmarking but also facilitates research into model adaptation strategies, a key and open challenge in advancing GeoFMs for downstream tasks. Our experiments show that no single model dominates across all tasks, confirming the specificity of the choices made during architecture design and pretraining. While models pretrained on natural images (ConvNext ImageNet, DINO V3) excel on high-resolution tasks, EO-specific models (TerraMind, Prithvi, and Clay) outperform them on multispectral applications such as agriculture and disaster response. These findings demonstrate that optimal model choice depends on task requirements, data modalities, and constraints. This shows that the goal of a single GeoFM model that performs well across all tasks remains open for future research. GEO-Bench-2 enables informed, reproducible GeoFM evaluation tailored to specific use cases. Code, data, and leaderboard for GEO-Bench-2 are publicly released under a permissive license.

Earth system models suffer from various structural and parametric errors in their representation of nonlinear, multi-scale processes, leading to uncertainties in their long-term projections. The effects of many of these errors (particularly those due to fast physics) can be quantified in short-term simulations, e.g., as differences between the predicted and observed states (analysis increments). With the increase in the availability of high-quality observations and simulations, learning nudging from these increments to correct model errors has become an active research area. However, most studies focus on using neural networks, which while powerful, are hard to interpret, are data-hungry, and poorly generalize out-of-distribution. Here, we show the capabilities of Model Error Discovery with Interpretability and Data Assimilation (MEDIDA), a general, data-efficient framework that uses sparsity-promoting equation-discovery techniques to learn model errors from analysis increments. Using two-layer quasi-geostrophic turbulence as the test case, MEDIDA is shown to successfully discover various linear and nonlinear structural/parametric errors when full observations are available. Discovery from spatially sparse observations is found to require highly accurate interpolation schemes. While NNs have shown success as interpolators in recent studies, here, they are found inadequate due to their inability to accurately represent small scales, a phenomenon known as spectral bias. We show that a general remedy, adding a random Fourier feature layer to the NN, resolves this issue enabling MEDIDA to successfully discover model errors from sparse observations. These promising results suggest that with further development, MEDIDA could be scaled up to models of the Earth system and real observations.

Figuring out which Pre-Trained Model (PTM) from a model zoo fits the target task is essential to take advantage of plentiful model resources. With the availability of numerous heterogeneous PTMs from diverse fields, efficiently selecting the most suitable PTM is challenging due to the time-consuming costs of carrying out forward or backward passes over all PTMs. In this paper, we propose Model Spider, which tokenizes both PTMs and tasks by summarizing their characteristics into vectors to enable efficient PTM selection. By leveraging the approximated performance of PTMs on a separate set of training tasks, Model Spider learns to construct tokens and measure the fitness score between a model-task pair via their tokens. The ability to rank relevant PTMs higher than others generalizes to new tasks. With the top-ranked PTM candidates, we further learn to enrich task tokens with their PTM-specific semantics to re-rank the PTMs for better selection. Model Spider balances efficiency and selection ability, making PTM selection like a spider preying on a web. Model Spider demonstrates promising performance in various configurations of model zoos.

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a phylogenetic distance metrics based on the similarity of LLMs' output. The resulting metric is then used to construct dendrograms, which satisfactorily capture known relationships across a set of 111 open-source and 45 closed models. Furthermore, our phylogenetic distance predicts performance in standard benchmarks, thus demonstrating its functional validity and paving the way for a time and cost-effective estimation of LLM capabilities. To sum up, by translating population genetic concepts to machine learning, we propose and validate a tool to evaluate LLM development, relationships and capabilities, even in the absence of transparent training information.

The search for life beyond Earth will depend on detecting faint signatures in the atmospheres of potentially habitable exoplanets. Interpreting those signatures requires understanding the host planet's climate: the same molecule may signal life on one planet and abiotic chemistry on another. Global climate models (GCMs) provide this understanding, but individual runs can require up to millions of core-hours and substantial domain expert time. Machine-learning emulators could remove this bottleneck, but progress has been limited by the absence of a curated, multi-model exoclimate dataset. We introduce ThousandWorlds, an ML-ready benchmark for exoclimate emulation and for the broader regime of low-data, multi-simulator, parameter-to-field regression. The dataset contains approximately 1800 simulations from five GCMs, mapping eight planet parameters to 3D atmospheric fields including temperature, humidity, winds, clouds, and radiation. Three nested subsets define progressively harder challenges: single-simulator regression, multi-simulator regression with complete observations, and multi-simulator regression with structured missingness. We propose two evaluation protocols: one for ranking methods, and one that measures performance relative to the disagreement between GCMs themselves. We evaluate seven baselines spanning simple methods, deep learning, and Gaussian processes. GP-based methods perform best, suggesting that ThousandWorlds exposes a regime where off-the-shelf deep learning does not yet succeed. Data: https://doi.org/10.57967/hf/8695. Code: https://github.com/edstevenson/ThousandWorlds.

Camera traps enable the automatic collection of large quantities of image data. Biologists all over the world use camera traps to monitor animal populations. We have recently been making strides towards automatic species classification in camera trap images. However, as we try to expand the geographic scope of these models we are faced with an interesting question: how do we train models that perform well on new (unseen during training) camera trap locations? Can we leverage data from other modalities, such as citizen science data and remote sensing data? In order to tackle this problem, we have prepared a challenge where the training data and test data are from different cameras spread across the globe. For each camera, we provide a series of remote sensing imagery that is tied to the location of the camera. We also provide citizen science imagery from the set of species seen in our data. The challenge is to correctly classify species in the test camera traps.

World modeling has become a cornerstone in AI research, enabling agents to understand, represent, and predict the dynamic environments they inhabit. While prior work largely emphasizes generative methods for 2D image and video data, they overlook the rapidly growing body of work that leverages native 3D and 4D representations such as RGB-D imagery, occupancy grids, and LiDAR point clouds for large-scale scene modeling. At the same time, the absence of a standardized definition and taxonomy for ``world models'' has led to fragmented and sometimes inconsistent claims in the literature. This survey addresses these gaps by presenting the first comprehensive review explicitly dedicated to 3D and 4D world modeling and generation. We establish precise definitions, introduce a structured taxonomy spanning video-based (VideoGen), occupancy-based (OccGen), and LiDAR-based (LiDARGen) approaches, and systematically summarize datasets and evaluation metrics tailored to 3D/4D settings. We further discuss practical applications, identify open challenges, and highlight promising research directions, aiming to provide a coherent and foundational reference for advancing the field. A systematic summary of existing literature is available at https://github.com/worldbench/survey

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Benchmarks shape scientific conclusions about model capabilities and steer model development. This creates a feedback loop: stronger benchmarks drive better models, and better models demand more discriminative benchmarks. Ensuring benchmark reliability is therefore essential for trustworthy evaluation and meaningful progress. In this work, we study benchmark reliability from a distributional perspective and introduce benchmark harmony, which measures how uniformly a model's performance is distributed across the subdomains of a benchmark. We posit that high harmony is a desirable benchmark property, indicating that the aggregate metric reflects uniform competence across subdomains. Across 19 multiple-choice benchmarks and five model families, we map each benchmark onto a mean-variance plane of harmony computed across models, where high mean and low variance signal more reliable evaluation. Our analysis shows that less harmonious benchmarks can give misleading results, since overall accuracy may be disproportionately influenced by specific subdomains. For instance, ARC-Easy is overwhelmed by questions on Biological Concepts, overshadowing other critical subdomains such as Geography, Physics, Chemistry, and Environmental Science. By recommending that harmony should be reported alongside accuracy, we reframe evaluation from simple performance averages to a more robust, distributionally reliable measurement of performance.

Global climate models (GCMs) are the main tools for understanding and predicting climate change. However, due to limited numerical resolutions, these models suffer from major structural uncertainties; e.g., they cannot resolve critical processes such as small-scale eddies in atmospheric and oceanic turbulence. Thus, such small-scale processes have to be represented as a function of the resolved scales via closures (parametrization). The accuracy of these closures is particularly important for capturing climate extremes. Traditionally, such closures are based on heuristics and simplifying assumptions about the unresolved physics. Recently, supervised-learned closures, trained offline on high-fidelity data, have been shown to outperform the classical physics-based closures. However, this approach requires a significant amount of high-fidelity training data and can also lead to instabilities. Reinforcement learning is emerging as a potent alternative for developing such closures as it requires only low-order statistics and leads to stable closures. In Scientific Multi-Agent Reinforcement Learning (SMARL) computational elements serve a dual role of discretization points and learning agents. We leverage SMARL and fundamentals of turbulence physics to learn closures for prototypes of atmospheric and oceanic turbulence. The policy is trained using only the enstrophy spectrum, which is nearly invariant and can be estimated from a few high-fidelity samples (these few samples are far from enough for supervised/offline learning). We show that these closures lead to stable low-resolution simulations that, at a fraction of the cost, can reproduce the high-fidelity simulations' statistics, including the tails of the probability density functions. The results demonstrate the high potential of SMARL for closure modeling for GCMs, especially in the regime of scarce data and indirect observations.

Soil moisture-precipitation coupling (SMPC) plays a critical role in Earth's water and energy cycles but remains difficult to quantify due to synoptic-scale variability and the complex interplay of land-atmosphere processes. Here, we apply high-dimensional model representation (HDMR) to functionally decompose the structural, correlative, and cooperative contributions of key land-atmosphere variables to precipitation. Benchmark tests confirm that HDMR overcomes limitations of commonly used correlation and regression approaches in isolating direct versus indirect effects. For example, analysis of gross primary productivity using a light-use-efficiency model shows that linear regression underestimates the temperature effect, while HDMR captures it accurately. Applying HDMR to CONUS404 reanalysis data reveals that morning soil moisture explains up to 40 percent of the variance in summertime afternoon precipitation over the Great Plains, more than double prior estimates. On days with afternoon rainfall (12-hour totals of 4.7-8.2 mm), first-order SM effects can boost precipitation by up to 8 mm under wet conditions, with an additional 3 mm from second-order interactions involving temperature and moisture. By capturing real-world co-variability and higher-order effects, HDMR provides a physically grounded, data-driven framework for diagnosing land-atmosphere coupling. These results underscore the need for more nuanced, interaction-aware data analysis methods in climate modeling and prediction.

Accurate, spatially explicit characterization of tropical forest structure is essential for carbon accounting and ecosystem monitoring, yet most ML pipelines predict canopy-top height proxies (e.g., RH95/RH98) or AGBD as separate scalar targets, rather than learning the forest vertical structure as an ordered profile. The community lacks a ML-ready multimodal benchmark for predicting the entire GEDI RH profile jointly with AGBD, or for evaluating methods that enforce physically consistent ordering across RH percentiles. We address this with Biomazon, a 20 m multimodal benchmark dataset over the Amazon Basin that pairs GEDI RH and AGBD targets with multi-sensor predictors (Sentinel-1/2, ALOS-2 PALSAR-2, Copernicus DEM, Dynamic World LULC, and AlphaEarth embeddings) under standardized spatial splits and evaluation protocols. Using a shared encoder-decoder with task-specific heads as a baseline framework, we conduct a comprehensive ablation study of (i) backbone/model scale, (ii) modality contributions, and (iii) the use of auxiliary embeddings under standalone and fusion settings, and we report both single-target and joint-target results to quantify tradeoffs under a unified training protocol. Finally, we contextualize baseline performance through regionally aligned comparisons against existing gridded products, including GEDI L4D RH10-RH98 and AGBD, at matching temporal scale. Biomazon, together with the accompanying protocols and baseline results, establishes a reference benchmark for future work on structurally consistent RH-profile prediction and structure-biomass modeling in tropical forests.

This research advances individual tree crown (ITC) segmentation in lidar data, using a deep learning model applicable to various laser scanning types: airborne (ULS), terrestrial (TLS), and mobile (MLS). It addresses the challenge of transferability across different data characteristics in 3D forest scene analysis. The study evaluates the model's performance based on platform (ULS, MLS) and data density, testing five scenarios with varying input data, including sparse versions, to gauge adaptability and canopy layer efficacy. The model, based on PointGroup architecture, is a 3D CNN with separate heads for semantic and instance segmentation, validated on diverse point cloud datasets. Results show point cloud sparsification enhances performance, aiding sparse data handling and improving detection in dense forests. The model performs well with >50 points per sq. m densities but less so at 10 points per sq. m due to higher omission rates. It outperforms existing methods (e.g., Point2Tree, TLS2trees) in detection, omission, commission rates, and F1 score, setting new benchmarks on LAUTx, Wytham Woods, and TreeLearn datasets. In conclusion, this study shows the feasibility of a sensor-agnostic model for diverse lidar data, surpassing sensor-specific approaches and setting new standards in tree segmentation, particularly in complex forests. This contributes to future ecological modeling and forest management advancements.

Bioacoustics, the study of sounds produced by living organisms, plays a vital role in conservation, biodiversity monitoring, and behavioral studies. Many tasks in this field, such as species, individual, and behavior classification and detection, are well-suited to machine learning. However, they often suffer from limited annotated data, highlighting the need for a general-purpose bioacoustic encoder capable of extracting useful representations for diverse downstream tasks. Such encoders have been proposed before, but are often limited in scope due to a focus on a narrow range of species (typically birds), and a reliance on a single model architecture or training paradigm. Moreover, they are usually evaluated on a small set of tasks and datasets. In this work, we present a large-scale empirical study that covers aspects of bioacoustics that are relevant to research but have previously been scarcely considered: training data diversity and scale, model architectures and training recipes, and the breadth of evaluation tasks and datasets. We obtain encoders that are state-of-the-art on the existing and proposed benchmarks. We also identify what matters for training these encoders, such that this work can be extended when more data are available or better architectures are proposed. Specifically, across 26 datasets with tasks including species classification, detection, individual ID, and vocal repertoire discovery, we find self-supervised pre-training followed by supervised post-training on a mixed bioacoustics + general-audio corpus yields the strongest in- and out-of-distribution performance. We show the importance of data diversity in both stages. To support ongoing research and application, we will release the model checkpoints.

Wildfire burned-area mapping is essential for damage assessment, emissions modeling, and understanding fire-climate interactions across diverse ecological regions. Recent geospatial foundation models provide strong general-purpose representations for satellite imagery, yet there is still no clear understanding of how to efficiently adapt these models for downstream Earth observation tasks, particularly under geographic and temporal domain shift. This study evaluates three state-of-the-art Geospatial Foundation Models (GFMs) - Terramind, DINOv3, and Prithvi-v2 - for burned-area mapping across the United States and Canada using Sentinel-2 data. Leveraging 3,820 wildfire events from 2017-2023, we conduct spatial and temporal generalization tests across diverse biomes. We systematically compare full fine-tuning, decoder-only fine-tuning, and Low-Rank Adaptation (LoRA) for adapting each model. Across all experiments, LoRA provides the strongest cross-domain generalization while updating less than 1% of parameters, demonstrating a favorable trade-off between accuracy and efficiency. Prithvi-v2 with LoRA achieves the highest overall accuracy and the largest improvement compared to full fine-tuning. These findings indicate that geospatial foundation models, when adapted using lightweight parameter-efficient methods such as LoRA, offer a robust and scalable solution for large-scale burned-area mapping. Code is available at https://github.com/alishibli97/wildfire-lora-gfm.

Recent growth in reinforcement learning (RL) has surfaced a need for diverse, specialized training environments. Hand-curated environments with fixed task and reward difficulties become ineffective signals as model performance improves, and sparse rewards over long horizons induce mode collapse on specific workflows or tool structures. World models that simulate environment states have matched pure rollout performance, making them promising for scaling diversity on-demand. However, autoregressive (AR) world models suffer from a left-to-right bias preventing conditioning on globally interdependent state anchors such as tool schemas, prior turns, and expected outcomes. We (i) formalize text-based world modeling as a steerable transition-dynamics problem decomposed into initial state, task context, tool schemas, domain rules, and steering directives, and (ii) curate 239,403 grounded state-action trajectories spanning nine open-source environments and twelve frontier model families. We compare AR LMs and masked diffusion language models (MDLMs), showing MDLMs, via bidirectional anchor-aware denoising, achieve better coherence, groundedness, and empirically validated rollout diversity than LLMs over 4x their parameter size, at comparable inference latency. We introduce a plug-and-play GRPO training framework with deterministic state checks, and perform zero-shot transfer ablations on three OOD environments (ScienceWorld, ALFWorld, AppWorld) across three 1.2B-7B agent backbones (LFM2.5, Qwen3, Mistral), achieving up to 47% absolute gains over baselines without environment-specific fine-tuning. We further conduct behavioral analysis of failure modes under adversarial scenarios and human evaluation on realism, outcome correctness, and training utility. We open-source our work to encourage research in this direction.

Understanding animal species from multimodal data poses an emerging challenge at the intersection of computer vision and ecology. While recent biological models, such as BioCLIP, have demonstrated strong alignment between images and textual taxonomic information for species identification, the integration of the audio modality remains an open problem. We propose BioVITA, a novel visual-textual-acoustic alignment framework for biological applications. BioVITA involves (i) a training dataset, (ii) a representation model, and (iii) a retrieval benchmark. First, we construct a large-scale training dataset comprising 1.3 million audio clips and 2.3 million images, covering 14,133 species annotated with 34 ecological trait labels. Second, building upon BioCLIP2, we introduce a two-stage training framework to effectively align audio representations with visual and textual representations. Third, we develop a cross-modal retrieval benchmark that covers all possible directional retrieval across the three modalities (i.e., image-to-audio, audio-to-text, text-to-image, and their reverse directions), with three taxonomic levels: Family, Genus, and Species. Extensive experiments demonstrate that our model learns a unified representation space that captures species-level semantics beyond taxonomy, advancing multimodal biodiversity understanding. The project page is available at: https://dahlian00.github.io/BioVITA_Page/

Remote sensing foundation models (RSFMs) are commonly evaluated using aggregate metrics, which can hide systematic performance disparities across ecological regions. We introduce FairRSFM, a biome-aware benchmark for evaluating ecological group robustness in RSFMs. FairRSFM maps georeferenced samples from 14 terrestrial biome classes into six ecologically meaningful macro-groups and evaluates models under a unified frozen-backbone evaluation protocol. The benchmark covers four downstream datasets: m-EuroSAT, m-BigEarthNet, m-SA-Crop-Type, and MMEarth20K with Dynamic World label maps. Using Prithvi-EO-2.0, SatMAE, and DOFA across three random seeds, we show that aggregate performance consistently masks biome-dependent disparities across architectures and tasks. For example, Prithvi-EO-2.0 reaches 90.98% overall macro-F1 on m-EuroSAT but a mean worst-group score of only 83.72%, while m-SA-Crop-Type drops from 27.30% overall mIoU to 18.47% in the Xeric and Mineralogical group. We further evaluate Biome-Orthogonal Linear Probing (BOLP), Dynamic Biome Reweighting (DBR), and GroupDRO as complementary mitigation baselines. Their effectiveness is model- and task-dependent; for example, BOLP improves Prithvi-EO-2.0 worst-group F1@opt on m-BigEarthNet from 46.12% to 50.27% without updating the RSFM backbone. FairRSFM provides a reusable protocol for diagnosing and mitigating ecological robustness gaps in remote sensing foundation models. Code and datasets are available at: https://github.com/aminurhossain/FairRSFM.

Foundation models (FMs) for the Earth system learn statistical relationships between physical variables across massive datasets to enable versatile downstream applications through finetuning, separating them from task-specific weather models. Here, we introduce Earth System Foundation Model (ESFM), a fully open model building on the 3D Swin UNet backbone of the pioneering Aurora model. ESFM introduces extensions that increase functionality and foster adoption in climate sciences. First, the encoding scheme and training protocols have been extended to handle diverse datasets, including those containing missing values across all spatio-temporal dimensions such as satellite data, as well as station data, all under one backbone. Axial attention is introduced to capture inter-variable dependencies. As a result ESFM skillfully predicts variables in regions or on pressure levels where no data is present at the initial time, while preserving inter-variable relationships, for example between temperature, pressure, and humidity. Individual variable tokenization enables different sets of variables to be shuffled during training and simplifies the process of building extensions for new downstream tasks. Adaptive layer norm-based ensembles allow for a simple yet effective way to transform deterministic ESFM to a probabilistic FM. We present findings using dense gridded data (ERA5, CMIP6), regionally masked dense data, sparse gridded MODIS satellite data, and station data. Results demonstrate competitive or superior performance relative to state-of-the-art benchmarks. Case studies of Super Typhoon Doksuri (2023) and 2024 sudden stratospheric warming events show accurate positional and magnitude estimations of extreme weather. ESFM retains the strengths of previous foundation models, such as long-term stability, but facilitates application to a variety of downstream tasks.

Remote sensing world models aim to both explain observed changes and forecast plausible futures, two tasks that share spatiotemporal priors. Existing methods, however, typically address them separately, limiting cross-task transfer. We present RS-WorldModel, a unified world model for remote sensing that jointly handles spatiotemporal change understanding and text-guided future scene forecasting, and we build RSWBench-1.1M, a 1.1 million sample dataset with rich language annotations covering both tasks. RS-WorldModel is trained in three stages: (1) Geo-Aware Generative Pre-training (GAGP) conditions forecasting on geographic and acquisition metadata; (2) synergistic instruction tuning (SIT) jointly trains understanding and forecasting; (3) verifiable reinforcement optimization (VRO) refines outputs with verifiable, task-specific rewards. With only 2B parameters, RS-WorldModel surpasses open-source models up to 120 times larger on most spatiotemporal change question-answering metrics. It achieves an FID of 43.13 on text-guided future scene forecasting, outperforming all open-source baselines as well as the closed-source Gemini-2.5-Flash Image (Nano Banana).

Prediction of wildfire occurrence is a rare-event problem compounded by spatial heterogeneity and temporal distribution shift, as fire occurrences are vastly outnumbered by non-occurrences, and predictor--fire relationship varies across space and time. Models trained on historical fire data may perform poorly under new conditions and require adaptation to the target distribution before operational use. We propose PyroAdapt, a pretrain--retrieve--rank framework that adapts a pretrained model to target conditions by retrieving historical locations with similar conditions and fine-tuning on the retrievals through risk ranking. For spatial adaptation, we condition risk on terrain, ecoregion embeddings, and fire rates, accounting for spatial context in the retrieval, and learn risk ordering from same-day fire--nonfire cell pairs. We compare direct ranking, residual pairwise DPO (RDPO), and selective ranking through a unified score-gap formulation that characterizes their gradient allocation. Over California (discretized into 666 0.25x0.25 grid cells), these objectives raise daily average precision from 21.62% for continued focal fine-tuning to 24.35--24.57%, and Top5% recall from 18.70% to 22.11--22.79%. Under a fixed daily detection budget of 34 cells (5% area), selective ranking captures 344 additional positive cell--days. For fires in the top 5%/10%/20% of dry matter consumption, selective ranking raises recall by 39.70/28.18/20.50 percentage points, respectively. Furthermore, rolling evaluations over Yosemite show that the gains from ranking persist under temporal distribution shift. Together, these results show that PyroAdapt prioritizes the most fire-prone locations under a daily budget constraint and detects more extreme fire events.

Fine-grained recognition of aquatic species is challenging due to subtle morphological differences and long-tailed distributions, where ultra-rare species are underrepresented. A natural solution is to jointly model segmentation, morphological traits, and species classification within a multi-task learning (MTL) framework. However, existing MTL methods suffer from negative transfer caused by gradient conflicts between low-level dense tasks and high-level classification objectives, degrading fine-grained representations. To address this limitation, we identify gradient interference across hierarchical tasks as a fundamental bottleneck and propose FISHER, a gradient-decoupled hierarchical multi-task learning framework. FISHER aligns optimization with the biological hierarchy of aquatic species by enforcing a unidirectional information flow from segmentation to trait prediction and finally to species classification, while explicitly decoupling gradients across task boundaries. This design prevents high-level objectives from corrupting low-level morphological representations, effectively mitigating negative transfer while preserving the benefits of shared supervision. Furthermore, we introduce a prototype-based segmentation head with orthogonality regularization to encourage disentangled anatomical representations, and employ homoscedastic uncertainty weighting to dynamically balance task contributions during training. Our analysis shows that robust trait representations serve as a critical bridge for transferring knowledge to ultra-rare species. Extensive experiments on the Fish-Vista benchmark demonstrate that FISHER achieves 97.7% mAP for unseen trait identification and improves ultra-rare species classification accuracy by 13.4% over strong baselines, highlighting the effectiveness of gradient-decoupled hierarchical learning for long-tailed biodiversity recognition.

Modeling weather and climate is an essential endeavor to understand the near- and long-term impacts of climate change, as well as inform technology and policymaking for adaptation and mitigation efforts. In recent years, there has been a surging interest in applying data-driven methods based on machine learning for solving core problems such as weather forecasting and climate downscaling. Despite promising results, much of this progress has been impaired due to the lack of large-scale, open-source efforts for reproducibility, resulting in the use of inconsistent or underspecified datasets, training setups, and evaluations by both domain scientists and artificial intelligence researchers. We introduce ClimateLearn, an open-source PyTorch library that vastly simplifies the training and evaluation of machine learning models for data-driven climate science. ClimateLearn consists of holistic pipelines for dataset processing (e.g., ERA5, CMIP6, PRISM), implementation of state-of-the-art deep learning models (e.g., Transformers, ResNets), and quantitative and qualitative evaluation for standard weather and climate modeling tasks. We supplement these functionalities with extensive documentation, contribution guides, and quickstart tutorials to expand access and promote community growth. We have also performed comprehensive forecasting and downscaling experiments to showcase the capabilities and key features of our library. To our knowledge, ClimateLearn is the first large-scale, open-source effort for bridging research in weather and climate modeling with modern machine learning systems. Our library is available publicly at https://github.com/aditya-grover/climate-learn.

Score-based generative models (SGMs) are a powerful class of generative models that exhibit remarkable empirical performance. Score-based generative modelling (SGM) consists of a ``noising'' stage, whereby a diffusion is used to gradually add Gaussian noise to data, and a generative model, which entails a ``denoising'' process defined by approximating the time-reversal of the diffusion. Existing SGMs assume that data is supported on a Euclidean space, i.e. a manifold with flat geometry. In many domains such as robotics, geoscience or protein modelling, data is often naturally described by distributions living on Riemannian manifolds and current SGM techniques are not appropriate. We introduce here Riemannian Score-based Generative Models (RSGMs), a class of generative models extending SGMs to Riemannian manifolds. We demonstrate our approach on a variety of manifolds, and in particular with earth and climate science spherical data.

In the era of foundation models, achieving a unified understanding of different dynamic objects through a single network has the potential to empower stronger spatial intelligence. Moreover, accurate estimation of animal pose and shape across diverse species is essential for quantitative analysis in biological research. However, this topic remains underexplored due to the limited network capacity of previous methods and the scarcity of comprehensive multi-species datasets. To address these limitations, we introduce AniMer+, an extended version of our scalable AniMer framework. In this paper, we focus on a unified approach for reconstructing mammals (mammalia) and birds (aves). A key innovation of AniMer+ is its high-capacity, family-aware Vision Transformer (ViT) incorporating a Mixture-of-Experts (MoE) design. Its architecture partitions network layers into taxa-specific components (for mammalia and aves) and taxa-shared components, enabling efficient learning of both distinct and common anatomical features within a single model. To overcome the critical shortage of 3D training data, especially for birds, we introduce a diffusion-based conditional image generation pipeline. This pipeline produces two large-scale synthetic datasets: CtrlAni3D for quadrupeds and CtrlAVES3D for birds. To note, CtrlAVES3D is the first large-scale, 3D-annotated dataset for birds, which is crucial for resolving single-view depth ambiguities. Trained on an aggregated collection of 41.3k mammalian and 12.4k avian images (combining real and synthetic data), our method demonstrates superior performance over existing approaches across a wide range of benchmarks, including the challenging out-of-domain Animal Kingdom dataset. Ablation studies confirm the effectiveness of both our novel network architecture and the generated synthetic datasets in enhancing real-world application performance.

Ocean scientists have been collecting visual data to study marine organisms for decades. These images and videos are extremely valuable both for basic science and environmental monitoring tasks. There are tools for automatically processing these data, but none that are capable of handling the extreme variability in sample populations, image quality, and habitat characteristics that are common in visual sampling of the ocean. Such distribution shifts can occur over very short physical distances and in narrow time windows. Creating models that are able to recognize when an image or video sequence contains a new organism, an unusual collection of animals, or is otherwise out-of-sample is critical to fully leverage visual data in the ocean. The FathomNet2023 competition dataset presents a realistic scenario where the set of animals in the target data differs from the training data. The challenge is both to identify the organisms in a target image and assess whether it is out-of-sample.

A soundscape is composed of three types of sound: biophony (sounds made by animals), geophony (natural abiotic sounds) and anthropophony (sounds made by humans). A key research question in the field of soundscape ecology is how these components interact with each other, specifically how biophony responds to geophony and anthropophony. Nevertheless, as of today, there are not many analytical instruments that enable the distinct quantification of these elements. Recent machine learning (ML) approaches aim to support automated analysis but often rely on task-specific or clean data, limiting generalisation to noisy passive acoustic monitoring (PAM) recordings. This study presents a clear and reproducible structure to build ML models for coarse soundscape classification and introduces CoarseSoundNet, a deep learning model trained to distinguish biophony, geophony, and anthropophony under realistic PAM conditions. We systematically investigate model architectures, the influence of an additional training class, data composition, and evaluation strategies. Our findings suggest that model performance improves with additional PAM data, especially when similar to the target domain, and by introducing an explicit silence class during training. Class-specific decision thresholds and duration-based constraints further enhance performance, particularly for anthropophony and geophony. Error analyses exhibit challenges for anthropophony due to masking effects and confusions for silence and insect sounds for geophony and biophony. Finally, we conduct an ecological case study which shows that pre-filtering recordings with CoarseSoundNet yields acoustic index trends comparable to ground-truth filtering, supporting its use as an effective preprocessing tool for ecoacoustic analyses.

Monitoring deforestation-driven carbon emissions requires both spatially explicit and temporally continuous estimates of aboveground biomass density (AGBD) with calibrated uncertainty. NASA's Global Ecosystem Dynamics Investigation (GEDI) provides reliable LIDAR-derived AGBD, but its orbital sampling causes irregular spatiotemporal coverage, and occasional operational interruptions, including a 13-month hibernation from March 2023 to April 2024, leave extended gaps in the observational record. Prior work has used machine learning approaches to fill GEDI's spatial gaps using satellite-derived features, but temporal interpolation of biomass through unobserved periods, particularly across active disturbance events, remains largely unaddressed. Moreover, standard ensemble methods for biomass mapping have been shown to produce systematically miscalibrated prediction intervals. To address these gaps, we extend the Attentive Neural Process (ANP) framework, previously applied to spatial biomass interpolation, to jointly sparse spatiotemporal settings using geospatial foundation model embeddings. We treat space and time symmetrically, empirically validating a form of space-for-time substitution in which observations from nearby locations at other times inform predictions at held-out periods. Our results demonstrate that the ANP produces well-calibrated uncertainty estimates across disturbance regimes, supporting its use in Measurement, Reporting, and Verification (MRV) applications that require reliable uncertainty quantification for forest carbon accounting.

In precision agriculture, the detection and recognition of insects play an essential role in the ability of crops to grow healthy and produce a high-quality yield. The current machine vision model requires a large volume of data to achieve high performance. However, there are approximately 5.5 million different insect species in the world. None of the existing insect datasets can cover even a fraction of them due to varying geographic locations and acquisition costs. In this paper, we introduce a novel ``Insect-1M'' dataset, a game-changing resource poised to revolutionize insect-related foundation model training. Covering a vast spectrum of insect species, our dataset, including 1 million images with dense identification labels of taxonomy hierarchy and insect descriptions, offers a panoramic view of entomology, enabling foundation models to comprehend visual and semantic information about insects like never before. Then, to efficiently establish an Insect Foundation Model, we develop a micro-feature self-supervised learning method with a Patch-wise Relevant Attention mechanism capable of discerning the subtle differences among insect images. In addition, we introduce Description Consistency loss to improve micro-feature modeling via insect descriptions. Through our experiments, we illustrate the effectiveness of our proposed approach in insect modeling and achieve State-of-the-Art performance on standard benchmarks of insect-related tasks. Our Insect Foundation Model and Dataset promise to empower the next generation of insect-related vision models, bringing them closer to the ultimate goal of precision agriculture.

Training data for bioacoustics is scattered across taxa, regions, and institutions. Centralizing it all is often infeasible. We show that independently fine-tuned BEATs encoders can be composed into a unified 661-species classifier via task vector arithmetic without sharing data. We find that bioacoustic task vectors are near-orthogonal (cosine 0.01-0.09). Their separation aligns closely with spectral distribution distance, a gradient consistent with the acoustic niche hypothesis. This geometry makes simple averaging optimal while sign-conflict methods reduce accuracy by one to six percentage points. Composition also creates an asymmetric gap: species-rich groups lose accuracy relative to joint training while underrepresented taxa gain, a redistribution useful for equitable biodiversity monitoring. We verify linear mode connectivity across all taxonomic pairs, demonstrate zero-shot transfer to new regions, and identify domain negation as a boundary condition where composition fails. These results enable a collaborative paradigm for bioacoustics where institutions share only task vectors to assemble multi-taxa classifiers, preserving data privacy.

Large climate-model ensembles are computationally expensive; yet many downstream analyses would benefit from additional, statistically consistent realizations of spatiotemporal climate variables. We study a generative modeling approach for producing new realizations from a limited set of available runs by transferring structure learned across an ensemble. Using monthly near-surface temperature time series from ten independent reanalysis realizations (ERA5), we find that a vanilla conditional variational autoencoder (CVAE) trained jointly across realizations yields a fragmented latent space that fails to generalize to unseen ensemble members. To address this, we introduce a latent-constrained CVAE (LC-CVAE) that enforces cross-realization homogeneity of latent embeddings at a small set of shared geographic 'anchor' locations. We then use multi-output Gaussian process regression in the latent space to predict latent coordinates at unsampled locations in a new realization, followed by decoding to generate full time series fields. Experiments and ablations demonstrate (i) instability when training on a single realization, (ii) diminishing returns after incorporating roughly five realizations, and (iii) a trade-off between spatial coverage and reconstruction quality that is closely linked to the average neighbor distance in latent space.