Yiqun Xie

Runlong Yu, Chonghao Qiu, Robert Ladwig et al.

Physics-guided machine learning (PGML) has become a prevalent approach in studying scientific systems due to its ability to integrate scientific theories for enhancing machine learning (ML) models. However, most PGML approaches are tailored to isolated and relatively simple tasks, which limits their applicability to complex systems involving multiple interacting processes and numerous influencing features. In this paper, we propose a \textit{\textbf{P}hysics-\textbf{G}uided \textbf{F}oundation \textbf{M}odel (\textbf{PGFM})} that combines pre-trained ML models and physics-based models and leverages their complementary strengths to improve the modeling of multiple coupled processes. To effectively conduct pre-training, we construct a simulated environmental system that encompasses a wide range of influencing features and various simulated variables generated by physics-based models. The model is pre-trained in this system to adaptively select important feature interactions guided by multi-task objectives. We then fine-tune the model for each specific task using true observations, while maintaining consistency with established physical theories, such as the principles of mass and energy conservation. We demonstrate the effectiveness of this methodology in modeling water temperature and dissolved oxygen dynamics in real-world lakes. The proposed PGFM is also broadly applicable to a range of scientific fields where physics-based models are being used.

Runlong Yu, Shengyu Chen, Yiqun Xie et al.

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.

Runlong Yu, Robert Ladwig, Xiang Xu et al.

Accurate prediction of dissolved oxygen (DO) concentrations in lakes requires a comprehensive study of phenological patterns across ecosystems, highlighting the need for precise selection of interactions amongst external factors and internal physical-chemical-biological variables. This paper presents the Multi-population Cognitive Evolutionary Search (MCES), a novel evolutionary algorithm for complex feature interaction selection problems. MCES allows models within every population to evolve adaptively, selecting relevant feature interactions for different lake types and tasks. Evaluated on diverse lakes in the Midwestern USA, MCES not only consistently produces accurate predictions with few observed labels but also, through gene maps of models, reveals sophisticated phenological patterns of different lake types, embodying the innovative concept of "AI from nature, for nature".

Qi Cheng, Licheng Liu, Qing Zhu et al.

Evaluating ecological time series is critical for benchmarking model performance in many important applications, including predicting greenhouse gas fluxes, capturing carbon-nitrogen dynamics, and monitoring hydrological cycles. Traditional numerical metrics (e.g., R-squared, root mean square error) have been widely used to quantify the similarity between modeled and observed ecosystem variables, but they often fail to capture domain-specific temporal patterns critical to ecological processes. As a result, these methods are often accompanied by expert visual inspection, which requires substantial human labor and limits the applicability to large-scale evaluation. To address these challenges, we propose a novel framework that integrates metric learning with large language model (LLM)-based natural language policy extraction to develop interpretable evaluation criteria. The proposed method processes pairwise annotations and implements a policy optimization mechanism to generate and combine different assessment metrics. The results obtained on multiple datasets for evaluating the predictions of crop gross primary production and carbon dioxide flux have confirmed the effectiveness of the proposed method in capturing target assessment preferences, including both synthetically generated and expert-annotated model comparisons. The proposed framework bridges the gap between numerical metrics and expert knowledge while providing interpretable evaluation policies that accommodate the diverse needs of different ecosystem modeling studies.