A Dataset and Model for Imputing Water Surface Elevation on a Large and Extremely Sparse Spatiotemporal Graph
Authors: Ruben Cartuyvels, Karim Douch, Gabriele Bertoli, Mounia El Baz, Artemis Vrettou, Sébastien Lefèvre, Diego Fernandez Prieto
Abstract
Continuous monitoring of water surface elevation across river networks is critical for flood forecasting, water resource management, and understanding the global water cycle. Yet, the scarcity of in situ gauges across much of the globe constrains the development of reliable modeling frameworks. Satellite altimetry has the potential to alleviate this problem but its use is currently hindered by sparse temporal coverage. To this end, we introduce AmazonSWE, a dataset for training and evaluating large-scale spatiotemporal graph imputation methods that integrates processed satellite altimetry measurements from a range of sources, including the recent wide-swath SWOT sensor. The dataset covers over 19K river sections and 10 years (2016-2026) in the Amazon river basin, with in situ gauges held out for evaluation. Besides contributing a novel real-world use case with the potential for societal impact, AmazonSWE introduces significant technical challenges: with fewer than 1% of sections observed per day, the dataset is far sparser than existing imputation benchmarks, and its directed acyclic river topology is both structurally different from and larger than graphs in existing datasets. We show that prior spatiotemporal graph imputation methods are not adapted to this topology, scale and sparsity, and propose a simple bidirectional selective state space model that outperforms them by sampling connected subgraphs and flattening space and time into a single token sequence with topology-aware positional encodings. Compared to the state-of-the-art published method for SWOT-based WSE densification, which integrates statistics with physical modeling, our model reduces RMSE against in situ gauges by 18-39%, while producing predictions for every river section rather than only those with sufficient nearby satellite coverage.
Missing data is a common challenge in spatiotemporal systems, arising in applications such as air quality monitoring and urban traffic management. Traditional machine learning approaches, like recurrent and graph neural networks, rely on iterative propagation, which tends to accumulate errors over time and space. Recent diffusion-based methods mitigate error propagation but require iterative sampling and often depend on problem-agnostic Gaussian priors, limiting both efficiency and effectiveness. To address these limitations, we propose GiFlow, a Graph-Informed Flow Matching framework for spatiotemporal imputation. GiFlow replaces the typical Gaussian prior with a graph-informed prior constructed via spatiotemporal filtering of observable signals, which better aligns the source distribution to the target and thereby simplifies the generation trajectory. The flow field is parameterized by a hybrid vector field model that integrates spatial attention, temporal attention, and spatiotemporal propagation, enabling joint modeling of spatial and temporal dependencies. Extensive experiments on both synthetic and real-world datasets demonstrate that the proposed GiFlow outperforms the state-of-the-art approaches in spatiotemporal imputation. The code is available at https://github.com/zepengzhang/GiFlow.
Remote sensing techniques have been increasingly utilised in aquatic applications in recent years. A common challenge in using optical satellite data is the presence of missing observations due to cloud cover. These data gaps can lead to missed detection of critical events, such as algal blooms, in lakes of high interest to water authorities. As a result, enhancing the completeness of optical satellite datasets is crucial for improving the monitoring and prediction of algal blooms. In this study, we compared a traditional data imputation method (i.e., linear interpolation) with deep learning models for reconstructing missing spectral bands across four lakes with historical records of algal blooms. The deep learning models adopted include CNN-based architectures (i.e., CNN, Inception Resnet, and Autoencoder) and CNN-LSTM-based architectures (i.e., CNN-LSTM, Resnet-LSTM, and Autoencoder-LSTM). Our results demonstrated that deep learning models substantially outperformed the baseline linear interpolation method in imputing spectral band values within artificially masked regions. Among these models, CNN delivered the best performance across most lakes. Furthermore, we evaluated the performance of algal bloom indices (i.e., Green/Red and NDCI) derived from the imputed imagery by comparing them with the observed data. Our results demonstrate that deep learning models are effective for imputing missing data in PlanetScope SuperDove imagery, enabling more reliable applications in water monitoring.
Reliable high-resolution flood extent mapping from satellite imagery remains constrained by limited data fidelity and sensor-specific artifacts. Multispectral optical imagery is degraded by clouds, shadows, and urban confounders, while synthetic aperture radar (SAR) imagery is affected by speckle noise and sensor co-registration uncertainty. This work presents an integrated flood mapping framework that jointly addresses these limitations through curated datasets and novel learning strategies. We introduce a new Sentinel-2 (S2) and Sentinel-1 (S1) dataset covering the contiguous United States, featuring pixel-accurate 10 m water masks with emphasis on challenging weather conditions and urban environments that are underrepresented in existing benchmarks. High-quality S2 annotations are manually produced using rigorous geospatial labeling protocols and transferred to SAR imagery through weakly labeled temporally coincident acquisitions. To address SAR-specific artifacts, a shift-invariant loss function is employed to tolerate residual geolocation uncertainty between SAR imagery and optical-derived labels, and a Conditional Variational Autoencoder (CVAE) is trained on multitemporal SAR composites to suppress speckle while preserving flood-relevant spatial structure. Experiments using UNet and UNet++ architectures demonstrate strong multispectral performance (AUPRC up to 0.956) and statistically significant improvements in SAR flood mapping when using shift-invariant loss and CVAE-based despeckling compared to classical filters. These results underscore the importance of dataset fidelity, misalignment-robust training, and demonstrate the viability of generative despeckling for operational flood mapping.