Shengyu Chen

Shiyuan Luo, Juntong Ni, Shengyu Chen et al.

Modeling environmental ecosystems is critical for the sustainability of our planet, but is extremely challenging due to the complex underlying processes driven by interactions amongst a large number of physical variables. As many variables are difficult to measure at large scales, existing works often utilize a combination of observable features and locally available measurements or modeled values as input to build models for a specific study region and time period. This raises a fundamental question in advancing the modeling of environmental ecosystems: how to build a general framework for modeling the complex relationships among diverse environmental variables over space and time? In this paper, we introduce a framework, FREE, that enables the use of varying features and available information to train a universal model. The core idea is to map available environmental data into a text space and then convert the traditional predictive modeling task in environmental science to a semantic recognition problem. Our evaluation on two societally important real-world applications, stream water temperature prediction and crop yield prediction, demonstrates the superiority of FREE over multiple baselines, even in data-sparse scenarios.

Shengyu Chen, Tianshu Bao, Peyman Givi et al.

Simulating turbulence is critical for many societally important applications in aerospace engineering, environmental science, the energy industry, and biomedicine. Large eddy simulation (LES) has been widely used as an alternative to direct numerical simulation (DNS) for simulating turbulent flows due to its reduced computational cost. However, LES is unable to capture all of the scales of turbulent transport accurately. Reconstructing DNS from low-resolution LES is critical for many scientific and engineering disciplines, but it poses many challenges to existing super-resolution methods due to the spatio-temporal complexity of turbulent flows. In this work, we propose a new physics-guided neural network for reconstructing the sequential DNS from low-resolution LES data. The proposed method leverages the partial differential equation that underlies the flow dynamics in the design of spatio-temporal model architecture. A degradation-based refinement method is also developed to enforce physical constraints and further reduce the accumulated reconstruction errors over long periods. The results on two different types of turbulent flow data confirm the superiority of the proposed method in reconstructing the high-resolution DNS data and preserving the physical characteristics of flow transport.

Shengyu Chen, Shihang Feng, Yao Huang et al.

Hybrid Optimization Software Suite (HOSS), which is a combined finite-discrete element method (FDEM), is one of the advanced approaches to simulating high-fidelity fracture and fragmentation processes but the application of pure HOSS simulation is computationally expensive. At the same time, machine learning methods, shown tremendous success in several scientific problems, are increasingly being considered promising alternatives to physics-based models in the scientific domains. Thus, our goal in this work is to build a new data-driven methodology to reconstruct the crack fracture accurately in the spatial and temporal fields. We leverage physical constraints to regularize the fracture propagation in the long-term reconstruction. In addition, we introduce perceptual loss and several extra pure machine learning optimization approaches to improve the reconstruction performance of fracture data further. We demonstrate the effectiveness of our proposed method through both extrapolation and interpolation experiments. The results confirm that our proposed method can reconstruct high-fidelity fracture data over space and time in terms of pixel-wise reconstruction error and structural similarity. Visual comparisons also show promising results in long-term

Yilong Dai, Yiming Sun, Yiheng Chen et al.

Accurate autoregressive prediction of 3D turbulent flows remains challenging for neural PDE solvers, as small errors in fine-scale structures can accumulate rapidly over rollout. In this paper, we propose FlowRefiner, a flow matching-based iterative refinement framework for 3D turbulent flow simulation. The method replaces stochastic denoising refinement with deterministic ODE-based correction, uses a unified velocity-field regression objective across all refinement stages, and introduces a decoupled sigma schedule that fixes the noise range independently of refinement depth. These design choices yield stable and effective refinement in the small-noise regime. Experiments on large-scale 3D turbulence with rich multi-scale structures show that FlowRefiner achieves state-of-the-art autoregressive prediction accuracy and strong physical consistency. Although developed for turbulent flow simulation, the proposed framework is broadly applicable to iterative refinement problems in scientific modeling.

Xinshuai Dong, Haifeng Chen, Xuyuan Liu et al.

Large Language Models have achieved remarkable success and are increasingly deployed in critical applications involving tabular data, such as Table Question Answering. However, their robustness to the structure of this input remains a critical, unaddressed question. This paper demonstrates that modern LLMs exhibit a significant vulnerability to the layout of tabular data. Specifically, we show that semantically-invariant permutations of rows and columns - rearrangements that do not alter the table's underlying information - are sometimes sufficient to cause incorrect or inconsistent model outputs. To systematically probe this vulnerability, we introduce Adversarial Table Permutation, a novel, gradient-based attack that efficiently identifies worst-case permutations designed to maximally disrupt model performance. Our extensive experiments demonstrate that ATP significantly degrades the performance of a wide range of LLMs. This reveals a pervasive vulnerability across different model sizes and architectures, including the most recent and popular models. Our findings expose a fundamental weakness in how current LLMs process structured data, underscoring the urgent need to develop permutation-robust models for reliable, real-world applications.

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, Shengyu Chen, Yiqun Xie et al.

Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional methods frequently struggle with the inherent complexity, interconnectedness, and limited data of such systems. Foundation models, with their large-scale pre-training and universal representations, offer transformative opportunities by integrating diverse data sources, capturing spatiotemporal dependencies, and adapting to a broad range of tasks. This survey presents a comprehensive overview of foundation model applications in environmental science, highlighting advancements in forward prediction, data generation, data assimilation, downscaling, model ensembling, and decision-making across domains. We also detail the development process of these models, covering data collection, architecture design, training, tuning, and evaluation. By showcasing these emerging methods, we aim to foster interdisciplinary collaboration and advance the integration of cutting-edge machine learning for sustainable solutions in environmental science.

Yilong Dai, Shengyu Chen, Xiaowei Jia et al.

Partial differential equations (PDEs) govern nearly every physical process in science and engineering, yet solving them at scale remains prohibitively expensive. Generative AI has transformed language, vision, and protein science, but learned PDE solvers have not undergone a comparable shift. Existing paradigms each capture part of the problem. Physics-informed neural networks embed residual structure, yet they are often difficult to optimize in stiff, multiscale, or large-domain regimes. Neural operators amortize across instances, yet they commonly inherit a snapshot-prediction view of solving and can degrade over long rollouts. Diffusion-based solvers model uncertainty, yet they are often built on a solver template that still centers on state regression. We argue that the core issue is the abstraction used to train learned solvers. Many models are asked to predict states, while many scientific settings require modeling how uncertainty moves through constrained dynamics. The relevant object is transport over physically admissible futures. This motivates \emph{flow learners}: models that parameterize transport vector fields and generate trajectories through integration, echoing the continuous dynamics that define PDE evolution. This physics-to-physics alignment supports continuous-time prediction, native uncertainty quantification, and new opportunities for physics-aware solver design. We explain why transport-based learning offers a stronger organizing principle for learned PDE solving and outline the research agenda that follows from this shift.

Yilong Dai, Shengyu Chen, Ziyi Wang et al.

Partial differential equations (PDEs) are central to scientific modeling. Modern workflows increasingly rely on learning-based components to support model reuse, inference, and integration across large computational processes. Despite the emergence of various physics-aware data-driven approaches, the field still lacks a unified perspective to uncover their relationships, limitations, and appropriate roles in scientific workflows. To this end, we propose a unifying perspective to place two dominant paradigms: Physics-Informed Neural Networks (PINNs) and Neural Operators (NOs), within a shared design space. We organize existing methods from three fundamental dimensions: what is learned, how physical structures are integrated into the learning process, and how the computational load is amortized across problem instances. In this way, many challenges can be best understood as consequences of these structural properties of learning PDEs. By analyzing advances through this unifying view, our survey aims to facilitate the development of reliable learning-based PDE solvers and catalyze a synthesis of physics and data.

Xuyuan Liu, Zhengzhang Chen, Xinshuai Dong et al.

Large language models (LLMs) often produce incorrect or outdated content. Updating their knowledge efficiently and accurately without costly retraining is a major challenge. This problem is particularly challenging for complex, unstructured knowledge in lifelong settings, where many edits must coexist without interference. We introduce RILKE (Representation Intervention for Lifelong KnowledgE Control), a robust and scalable method that treats knowledge control as interventions within the model's representation space. Leveraging representation-space expressiveness, we identify two key properties enabling RILKE to achieve fine-grained control over complex, unstructured knowledge while maintaining general utility with frozen base weights. During training, RILKE learns paraphrase-robust and edit-localized modules that limit each update to a low-dimensional subspace to minimize cross-edit interference. At inference, a query-adaptive router selects the appropriate module to guide the model's generation. Across LLaMA and Qwen models, RILKE scales effectively to large-scale benchmarks, demonstrating high edit success and strong paraphrase generalization while preserving general utility with modest memory overhead. These results show RILKE is an effective and scalable solution for lifelong knowledge control in LLMs.

Shengyu Chen, Shihang Feng, Yi Luo et al.

Ultrasound brain imaging remains challenging due to the large difference in sound speed between the skull and brain tissues and the difficulty of coupling large probes to the skull. This work aims to achieve quantitative transcranial ultrasound by reconstructing an accurate speed-of-sound (SoS) map of the brain. Traditional physics-based full-waveform inversion (FWI) is limited by weak signals caused by skull-induced attenuation, mode conversion, and phase aberration, as well as incomplete spatial coverage since full-aperture arrays are clinically impractical. In contrast, purely data-driven methods that learn directly from raw ultrasound data often fail to model the complex nonlinear and nonlocal wave propagation through bone, leading to anatomically plausible but quantitatively biased SoS maps under low signal-to-noise and sparse-aperture conditions. To address these issues, we propose BrainPuzzle, a hybrid two-stage framework that combines physical modeling with machine learning. In the first stage, reverse time migration (time-reversal acoustics) is applied to multi-angle acquisitions to produce migration fragments that preserve structural details even under low SNR. In the second stage, a transformer-based super-resolution encoder-decoder with a graph-based attention unit (GAU) fuses these fragments into a coherent and quantitatively accurate SoS image. A partial-array acquisition strategy using a movable low-count transducer set improves feasibility and coupling, while the hybrid algorithm compensates for the missing aperture. Experiments on two synthetic datasets show that BrainPuzzle achieves superior SoS reconstruction accuracy and image completeness, demonstrating its potential for advancing quantitative ultrasound brain imaging.

Shiyuan Luo, Runlong Yu, Shengyu Chen et al.

Understanding environmental ecosystems is vital for the sustainable management of our planet. However,existing physics-based and data-driven models often fail to generalize to varying spatial regions and scales due to the inherent data heterogeneity presented in real environmental ecosystems. This generalization issue is further exacerbated by the limited observation samples available for model training. To address these issues, we propose Geo-STARS, a geo-aware spatio-temporal modeling framework for predicting stream water temperature across different watersheds and spatial scales. The major innovation of Geo-STARS is the introduction of geo-aware embedding, which leverages geographic information to explicitly capture shared principles and patterns across spatial regions and scales. We further integrate the geo-aware embedding into a gated spatio-temporal graph neural network. This design enables the model to learn complex spatial and temporal patterns guided by geographic and hydrological context, even with sparse or no observational data. We evaluate Geo-STARS's efficacy in predicting stream water temperature, which is a master factor for water quality. Using real-world datasets spanning 37 years across multiple watersheds along the eastern coast of the United States, Geo-STARS demonstrates its superior generalization performance across both regions and scales, outperforming state-of-the-art baselines. These results highlight the promise of Geo-STARS for scalable, data-efficient environmental monitoring and decision-making.

Haoyue Bai, Haoyu Wang, Shengyu Chen et al.

Large Language Models (LLMs) have shown remarkable performance on general Question Answering (QA), yet they often struggle in domain-specific scenarios where accurate and up-to-date information is required. Retrieval-Augmented Generation (RAG) addresses this limitation by enriching LLMs with external knowledge, but existing systems primarily rely on unstructured documents, while largely overlooking relational databases, which provide precise, timely, and efficiently queryable factual information, serving as indispensable infrastructure in domains such as finance, healthcare, and scientific research. Motivated by this gap, we conduct a systematic analysis that reveals three central observations: (i) databases and documents offer complementary strengths across queries, (ii) naively combining both sources introduces noise and cost without consistent accuracy gains, and (iii) selecting the most suitable source for each query is crucial to balance effectiveness and efficiency. We further observe that query types show consistent regularities in their alignment with retrieval paths, suggesting that routing decisions can be effectively guided by systematic rules that capture these patterns. Building on these insights, we propose a rule-driven routing framework. A routing agent scores candidate augmentation paths based on explicit rules and selects the most suitable one; a rule-making expert agent refines the rules over time using QA feedback to maintain adaptability; and a path-level meta-cache reuses past routing decisions for semantically similar queries to reduce latency and cost. Experiments on three QA benchmarks demonstrate that our framework consistently outperforms static strategies and learned routing baselines, achieving higher accuracy while maintaining moderate computational cost.

Yiming Sun, Shuo Chen, Shengyu Chen et al.

Methane (CH$_4$) is the second most powerful greenhouse gas after carbon dioxide and plays a crucial role in climate change due to its high global warming potential. Accurately modeling CH$_4$ fluxes across the globe and at fine temporal scales is essential for understanding its spatial and temporal variability and developing effective mitigation strategies. In this work, we introduce the first-of-its-kind cross-scale global wetland methane benchmark dataset (X-MethaneWet), which synthesizes physics-based model simulation data from TEM-MDM and the real-world observation data from FLUXNET-CH$_4$. This dataset can offer opportunities for improving global wetland CH$_4$ modeling and science discovery with new AI algorithms. To set up AI model baselines for methane flux prediction, we evaluate the performance of various sequential deep learning models on X-MethaneWet. Furthermore, we explore four different transfer learning techniques to leverage simulated data from TEM-MDM to improve the generalization of deep learning models on real-world FLUXNET-CH$_4$ observations. Our extensive experiments demonstrate the effectiveness of these approaches, highlighting their potential for advancing methane emission modeling and contributing to the development of more accurate and scalable AI-driven climate models.

Shengyu Chen, Peyman Givi, Can Zheng et al.

The precise simulation of turbulent flows holds immense significance across various scientific and engineering domains, including climate science, freshwater science, and energy-efficient manufacturing. Within the realm of simulating turbulent flows, large eddy simulation (LES) has emerged as a prevalent alternative to direct numerical simulation (DNS), offering computational efficiency. However, LES cannot accurately capture the full spectrum of turbulent transport scales and is present only at a lower spatial resolution. Reconstructing high-fidelity DNS data from the lower-resolution LES data is essential for numerous applications, but it poses significant challenges to existing super-resolution techniques, primarily due to the complex spatio-temporal nature of turbulent flows. This paper proposes a novel flow reconstruction approach that leverages physical knowledge to model flow dynamics. Different from traditional super-resolution techniques, the proposed approach uses LES data only in the testing phase through a degradation-based refinement approach to enforce physical constraints and mitigate cumulative reconstruction errors over time. Furthermore, a feature sampling strategy is developed to enable flow data reconstruction across different resolutions. The results on two distinct sets of turbulent flow data indicate the effectiveness of the proposed method in reconstructing high-resolution DNS data, preserving the inherent physical attributes of flow transport, and achieving DNS reconstruction at different resolutions.

Xiaowei Jia, Shengyu Chen, Yiqun Xie et al.

This paper proposes a new data-driven method for predicting water temperature in stream networks with reservoirs. The water flows released from reservoirs greatly affect the water temperature of downstream river segments. However, the information of released water flow is often not available for many reservoirs, which makes it difficult for data-driven models to capture the impact to downstream river segments. In this paper, we first build a state-aware graph model to represent the interactions amongst streams and reservoirs, and then propose a parallel learning structure to extract the reservoir release information and use it to improve the prediction. In particular, for reservoirs with no available release information, we mimic the water managers' release decision process through a pseudo-prospective learning method, which infers the release information from anticipated water temperature dynamics. For reservoirs with the release information, we leverage a physics-based model to simulate the water release temperature and transfer such information to guide the learning process for other reservoirs. The evaluation for the Delaware River Basin shows that the proposed method brings over 10\% accuracy improvement over existing data-driven models for stream temperature prediction when the release data is not available for any reservoirs. The performance is further improved after we incorporate the release data and physical simulations for a subset of reservoirs.

Shengyu Chen, Alison Appling, Samantha Oliver et al.

Accurate prediction of water temperature in streams is critical for monitoring and understanding biogeochemical and ecological processes in streams. Stream temperature is affected by weather patterns (such as solar radiation) and water flowing through the stream network. Additionally, stream temperature can be substantially affected by water releases from man-made reservoirs to downstream segments. In this paper, we propose a heterogeneous recurrent graph model to represent these interacting processes that underlie stream-reservoir networks and improve the prediction of water temperature in all river segments within a network. Because reservoir release data may be unavailable for certain reservoirs, we further develop a data assimilation mechanism to adjust the deep learning model states to correct for the prediction bias caused by reservoir releases. A well-trained temporal modeling component is needed in order to use adjusted states to improve future predictions. Hence, we also introduce a simulation-based pre-training strategy to enhance the model training. Our evaluation for the Delaware River Basin has demonstrated the superiority of our proposed method over multiple existing methods. We have extensively studied the effect of the data assimilation mechanism under different scenarios. Moreover, we show that the proposed method using the pre-training strategy can still produce good predictions even with limited training data.

Shengyu Chen, Shervin Sammak, Peyman Givi et al.

Direct numerical simulation (DNS) of turbulent flows is computationally expensive and cannot be applied to flows with large Reynolds numbers. Large eddy simulation (LES) is an alternative that is computationally less demanding, but is unable to capture all of the scales of turbulent transport accurately. Our goal in this work is to build a new data-driven methodology based on super-resolution techniques to reconstruct DNS data from LES predictions. We leverage the underlying physical relationships to regularize the relationships amongst different physical variables. We also introduce a hierarchical generative process and a reverse degradation process to fully explore the correspondence between DNS and LES data. We demonstrate the effectiveness of our method through a single-snapshot experiment and a cross-time experiment. The results confirm that our method can better reconstruct high-resolution DNS data over space and over time in terms of pixel-wise reconstruction error and structural similarity. Visual comparisons show that our method performs much better in capturing fine-level flow dynamics.