GreenHyperSpectra: A multi-source hyperspectral dataset for global vegetation trait prediction

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 Butterfly Effect: Neural Network Training Trajectories Are Highly Sensitive to Initial Conditions

Neural network training is inherently sensitive to initialization and the randomness induced by stochastic gradient descent. However, it is unclear to what extent such effects lead to meaningfully different networks, either in terms of the models' weights or the underlying functions that were learned. In this work, we show that during the initial "chaotic" phase of training, even extremely small perturbations reliably causes otherwise identical training trajectories to diverge-an effect that diminishes rapidly over training time. We quantify this divergence through (i) $L^2$ distance between parameters, (ii) the loss barrier when interpolating between networks, (iii) $L^2$ and barrier between parameters after permutation alignment, and (iv) representational similarity between intermediate activations; revealing how perturbations across different hyperparameter or fine-tuning settings drive training trajectories toward distinct loss minima. Our findings provide insights into neural network training stability, with practical implications for fine-tuning, model merging, and diversity of model ensembles.

Causal Climate Emulation with Bayesian Filtering

Traditional models of climate change use complex systems of coupled equations to simulate physical processes across the Earth system. These simulations are highly computationally expensive, limiting our predictions of climate change and analyses of its causes and effects. Machine learning has the potential to quickly emulate data from climate models, but current approaches are not able to incorporate physics-informed causal relationships. Here, we develop an interpretable climate model emulator based on causal representation learning. We derive a physics-informed approach including a Bayesian filter for stable long-term autoregressive emulation. We demonstrate that our emulator learns accurate climate dynamics, and we show the importance of each one of its components on a realistic synthetic dataset and data from two widely deployed climate models.

Bringing SAM to new heights: Leveraging elevation data for tree crown segmentation from drone imagery

Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring methods involve ground measurements, requiring extensive cost, time and labor. Advances in drone remote sensing and computer vision offer great potential for mapping individual trees from aerial imagery at broad-scale. Large pre-trained vision models, such as the Segment Anything Model (SAM), represent a particularly compelling choice given limited labeled data. In this work, we compare methods leveraging SAM for the task of automatic tree crown instance segmentation in high resolution drone imagery in three use cases: 1) boreal plantations, 2) temperate forests and 3) tropical forests. We also study the integration of elevation data into models, in the form of Digital Surface Model (DSM) information, which can readily be obtained at no additional cost from RGB drone imagery. We present BalSAM, a model leveraging SAM and DSM information, which shows potential over other methods, particularly in the context of plantations. We find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts. However, efficiently tuning SAM end-to-end and integrating DSM information are both promising avenues for tree crown instance segmentation models.

Assessing SAM for Tree Crown Instance Segmentation from Drone Imagery

The potential of tree planting as a natural climate solution is often undermined by inadequate monitoring of tree planting projects. Current monitoring methods involve measuring trees by hand for each species, requiring extensive cost, time, and labour. Advances in drone remote sensing and computer vision offer great potential for mapping and characterizing trees from aerial imagery, and large pre-trained vision models, such as the Segment Anything Model (SAM), may be a particularly compelling choice given limited labeled data. In this work, we compare SAM methods for the task of automatic tree crown instance segmentation in high resolution drone imagery of young tree plantations. We explore the potential of SAM for this task, and find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts, but that there is potential for methods which tune SAM further. We also show that predictions can be improved by adding Digital Surface Model (DSM) information as an input.

Open-Set Recognition of Novel Species in Biodiversity Monitoring

Machine learning is increasingly being applied to facilitate long-term, large-scale biodiversity monitoring. With most species on Earth still undiscovered or poorly documented, species-recognition models are expected to encounter new species during deployment. We introduce Open-Insects, a fine-grained image recognition benchmark dataset for open-set recognition and out-of-distribution detection in biodiversity monitoring. Open-Insects makes it possible to evaluate algorithms for new species detection on several geographical open-set splits with varying difficulty. Furthermore, we present a test set recently collected in the wild with 59 species that are likely new to science. We evaluate a variety of open-set recognition algorithms, including post-hoc methods, training-time regularization, and training with auxiliary data, finding that the simple post-hoc approach of utilizing softmax scores remains a strong baseline. We also demonstrate how to leverage auxiliary data to improve the detection performance when the training dataset is limited. Our results provide timely insights to guide the development of computer vision methods for biodiversity monitoring and species discovery.

Galileo: Learning Global and Local Features in Pretrained Remote Sensing Models

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.

Alberta Wells Dataset: Pinpointing Oil and Gas Wells from Satellite Imagery

Millions of abandoned oil and gas wells are scattered across the world, leaching methane into the atmosphere and toxic compounds into the groundwater. Many of these locations are unknown, preventing the wells from being plugged and their polluting effects averted. Remote sensing is a relatively unexplored tool for pinpointing abandoned wells at scale. We introduce the first large-scale benchmark dataset for this problem, leveraging medium-resolution multi-spectral satellite imagery from Planet Labs. Our curated dataset comprises over 213,000 wells (abandoned, suspended, and active) from Alberta, a region with especially high well density, sourced from the Alberta Energy Regulator and verified by domain experts. We evaluate baseline algorithms for well detection and segmentation, showing the promise of computer vision approaches but also significant room for improvement.

Causal Representation Learning in Temporal Data via Single-Parent Decoding

Scientific research often seeks to understand the causal structure underlying high-level variables in a system. For example, climate scientists study how phenomena, such as El Ni\~no, affect other climate processes at remote locations across the globe. However, scientists typically collect low-level measurements, such as geographically distributed temperature readings. From these, one needs to learn both a mapping to causally-relevant latent variables, such as a high-level representation of the El Ni\~no phenomenon and other processes, as well as the causal model over them. The challenge is that this task, called causal representation learning, is highly underdetermined from observational data alone, requiring other constraints during learning to resolve the indeterminacies. In this work, we consider a temporal model with a sparsity assumption, namely single-parent decoding: each observed low-level variable is only affected by a single latent variable. Such an assumption is reasonable in many scientific applications that require finding groups of low-level variables, such as extracting regions from geographically gridded measurement data in climate research or capturing brain regions from neural activity data. We demonstrate the identifiability of the resulting model and propose a differentiable method, Causal Discovery with Single-parent Decoding (CDSD), that simultaneously learns the underlying latents and a causal graph over them. We assess the validity of our theoretical results using simulated data and showcase the practical validity of our method in an application to real-world data from the climate science field.

Tree semantic segmentation from aerial image time series

Earth's forests play an important role in the fight against climate change, and are in turn negatively affected by it. Effective monitoring of different tree species is essential to understanding and improving the health and biodiversity of forests. In this work, we address the challenge of tree species identification by performing semantic segmentation of trees using an aerial image dataset spanning over a year. We compare models trained on single images versus those trained on time series to assess the impact of tree phenology on segmentation performances. We also introduce a simple convolutional block for extracting spatio-temporal features from image time series, enabling the use of popular pretrained backbones and methods. We leverage the hierarchical structure of tree species taxonomy by incorporating a custom loss function that refines predictions at three levels: species, genus, and higher-level taxa. Our findings demonstrate the superiority of our methodology in exploiting the time series modality and confirm that enriching labels using taxonomic information improves the semantic segmentation performance.