Understanding and forecasting lake dynamics is critical for monitoring water quality and ecosystem health across lakes and reservoirs. While machine learning methods have been recently applied to ecological time-series data, existing works assume regular sampling in time and depth, and struggle to generalize across lakes with heterogeneous variables, depths, and observation patterns. To address these limitations, we introduce \textsc{LakeFM}, a foundation model for aquatic systems, pre-trained on large-scale ecological datasets comprising both simulated and observed lakes. Through extensive empirical evaluation, we show that \textsc{LakeFM} learns meaningful representations spanning broader lake-level characteristics, and achieves competitive or often superior-forecasting performance compared to existing time-series foundation and non-foundation models, while producing physically plausible predictions consistent with real-world lake dynamics.
Marine biogeochemical forecasting is increasingly important for managing marine ecosystems and the carbon cycle, yet global, seasonal forecast products lag far behind physical oceanography, held back by the complexity of the processes involved and by data scarcity. We introduce BG4Sea, which to our knowledge is the first global, data-driven system to produce multivariate seasonal forecasts of the marine biogeochemical state. BG4Sea is a modular architecture with a column autoencoder that compresses the vertical column into a low-dimensional latent space, a latent forecaster propagates this representation forward in time, a surface-forcing conditioner that injects physical boundary information via Feature-wise Linear Modulation (FiLM), and a horizontal-coupling module that incorporates neighboring-column context through cross-attention. The model is trained and evaluated on the global ocean reanalysis BIORYS4 (NEMO/PISCES), and produces six-month forecasts at 1/4 degree, monthly resolution for dissolved chemistry, biology, and carbon-pool variables, outperforming persistence and climatology across most variables and lead times. We position BG4Sea as an interpretable baseline for future, more expressive approaches, and discuss predictability attribution to each component, alongside the model's structural limitations.
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.
Large \emph{Time Series Foundation Models} (TSFMs) demonstrate strong zero-shot forecasting capabilities across diverse domains. However, their application to regional climate forecasting faces practical challenges: model weights are often proprietary, local training records are limited, and computational budgets are constrained, making traditional fine-tuning approaches infeasible. To address these constraints, we introduce a lightweight, black-box adaptation framework (requiring no access to backbone parameters and no backbone fine-tuning) that enhances frozen TSFMs at inference time through two plug-and-play wrappers: \textbf{SMR\textsuperscript{2}} (Stationarity aware multi-resolution Residual), which decomposes the input into multi-resolution temporal views, learns stride specific residual corrections that capture regional dynamics, then adaptively ensembles them into a single forecast, and \textbf{MBB} (Moving Block Bootstrap), which preserves temporal dependencies through block resampling and ensembles over temporally coherent residual perturbations to stabilize the point forecast. Both wrappers instantiate the same bagging style principle: they build diverse views of the input or its residuals, forecast each with the same frozen backbone, and aggregate, so all adaptation comes from inference time ensembling rather than any weight update. Evaluated on one month ahead Standardized Precipitation Evapotranspiration Index (SPEI) prediction across multiple sites in South Australia, our framework consistently improves forecasting performance across several backbone models, demonstrating up to 26% mean squared error (MSE) reduction over the corresponding frozen backbone while enabling practical deployment in resource constrained regional forecasting systems.