Sibo Cheng

Che Liu, Sibo Cheng, Miaojing Shi et al.

In the field of medical Vision-Language Pre-training (VLP), significant efforts have been devoted to deriving text and image features from both clinical reports and associated medical images. However, most existing methods may have overlooked the opportunity in leveraging the inherent hierarchical structure of clinical reports, which are generally split into `findings' for descriptive content and `impressions' for conclusive observation. Instead of utilizing this rich, structured format, current medical VLP approaches often simplify the report into either a unified entity or fragmented tokens. In this work, we propose a novel clinical prior guided VLP framework named IMITATE to learn the structure information from medical reports with hierarchical vision-language alignment. The framework derives multi-level visual features from the chest X-ray (CXR) images and separately aligns these features with the descriptive and the conclusive text encoded in the hierarchical medical report. Furthermore, a new clinical-informed contrastive loss is introduced for cross-modal learning, which accounts for clinical prior knowledge in formulating sample correlations in contrastive learning. The proposed model, IMITATE, outperforms baseline VLP methods across six different datasets, spanning five medical imaging downstream tasks. Comprehensive experimental results highlight the advantages of integrating the hierarchical structure of medical reports for vision-language alignment. The code related to this paper is available at https://github.com/cheliu-computation/IMITATE-TMI2024.

Jun Li, Che Liu, Sibo Cheng et al.

The electrocardiogram (ECG) is one of the most commonly used non-invasive, convenient medical monitoring tools that assist in the clinical diagnosis of heart diseases. Recently, deep learning (DL) techniques, particularly self-supervised learning (SSL), have demonstrated great potential in the classification of ECG. SSL pre-training has achieved competitive performance with only a small amount of annotated data after fine-tuning. However, current SSL methods rely on the availability of annotated data and are unable to predict labels not existing in fine-tuning datasets. To address this challenge, we propose Multimodal ECG-Text Self-supervised pre-training (METS), the first work to utilize the auto-generated clinical reports to guide ECG SSL pre-training. We use a trainable ECG encoder and a frozen language model to embed paired ECG and automatically machine-generated clinical reports separately. The SSL aims to maximize the similarity between paired ECG and auto-generated report while minimize the similarity between ECG and other reports. In downstream classification tasks, METS achieves around 10% improvement in performance without using any annotated data via zero-shot classification, compared to other supervised and SSL baselines that rely on annotated data. Furthermore, METS achieves the highest recall and F1 scores on the MIT-BIH dataset, despite MIT-BIH containing different classes of ECG compared to the pre-trained dataset. The extensive experiments have demonstrated the advantages of using ECG-Text multimodal self-supervised learning in terms of generalizability, effectiveness, and efficiency.

Che Liu, Sibo Cheng, Weiping Ding et al.

Electrocardiography (ECG) signals can be considered as multi-variable time-series. The state-of-the-art ECG data classification approaches, based on either feature engineering or deep learning techniques, treat separately spectral and time domains in machine learning systems. No spectral-time domain communication mechanism inside the classifier model can be found in current approaches, leading to difficulties in identifying complex ECG forms. In this paper, we proposed a novel deep learning model named Spectral Cross-domain neural network (SCDNN) with a new block called Soft-adaptive threshold spectral enhancement (SATSE), to simultaneously reveal the key information embedded in spectral and time domains inside the neural network. More precisely, the domain-cross information is captured by a general Convolutional neural network (CNN) backbone, and different information sources are merged by a self-adaptive mechanism to mine the connection between time and spectral domains. In SATSE, the knowledge from time and spectral domains is extracted via the Fast Fourier Transformation (FFT) with soft trainable thresholds in modified Sigmoid functions. The proposed SCDNN is tested with several classification tasks implemented on the public ECG databases \textit{PTB-XL} and \textit{MIT-BIH}. SCDNN outperforms the state-of-the-art approaches with a low computational cost regarding a variety of metrics in all classification tasks on both databases, by finding appropriate domains from the infinite spectral mapping. The convergence of the trainable thresholds in the spectral domain is also numerically investigated in this paper. The robust performance of SCDNN provides a new perspective to exploit knowledge across deep learning models from time and spectral domains. The repository can be found: https://github.com/DL-WG/SCDNN-TS

Sibo Cheng, Cesar Quilodran-Casas, Said Ouala et al.

Data Assimilation (DA) and Uncertainty quantification (UQ) are extensively used in analysing and reducing error propagation in high-dimensional spatial-temporal dynamics. Typical applications span from computational fluid dynamics (CFD) to geoscience and climate systems. Recently, much effort has been given in combining DA, UQ and machine learning (ML) techniques. These research efforts seek to address some critical challenges in high-dimensional dynamical systems, including but not limited to dynamical system identification, reduced order surrogate modelling, error covariance specification and model error correction. A large number of developed techniques and methodologies exhibit a broad applicability across numerous domains, resulting in the necessity for a comprehensive guide. This paper provides the first overview of the state-of-the-art researches in this interdisciplinary field, covering a wide range of applications. This review aims at ML scientists who attempt to apply DA and UQ techniques to improve the accuracy and the interpretability of their models, but also at DA and UQ experts who intend to integrate cutting-edge ML approaches to their systems. Therefore, this article has a special focus on how ML methods can overcome the existing limits of DA and UQ, and vice versa. Some exciting perspectives of this rapidly developing research field are also discussed.

Sibo Cheng, Jianhua Chen, Charitos Anastasiou et al.

Reduced-order modelling and low-dimensional surrogate models generated using machine learning algorithms have been widely applied in high-dimensional dynamical systems to improve the algorithmic efficiency. In this paper, we develop a system which combines reduced-order surrogate models with a novel data assimilation (DA) technique used to incorporate real-time observations from different physical spaces. We make use of local smooth surrogate functions which link the space of encoded system variables and the one of current observations to perform variational DA with a low computational cost. The new system, named Generalised Latent Assimilation can benefit both the efficiency provided by the reduced-order modelling and the accuracy of data assimilation. A theoretical analysis of the difference between surrogate and original assimilation cost function is also provided in this paper where an upper bound, depending on the size of the local training set, is given. The new approach is tested on a high-dimensional CFD application of a two-phase liquid flow with non-linear observation operators that current Latent Assimilation methods can not handle. Numerical results demonstrate that the proposed assimilation approach can significantly improve the reconstruction and prediction accuracy of the deep learning surrogate model which is nearly 1000 times faster than the CFD simulation.

Che Liu, Sibo Cheng, Chen Chen et al.

Medical vision-language models enable co-learning and integrating features from medical imaging and clinical text. However, these models are not easy to train and the latent representation space can be complex. Here we propose a novel way for pre-training and regularising medical vision-language models. The proposed method, named Medical vision-language pre-training with Frozen language models and Latent spAce Geometry optimization (M-FLAG), leverages a frozen language model for training stability and efficiency and introduces a novel orthogonality loss to harmonize the latent space geometry. We demonstrate the potential of the pre-trained model on three downstream tasks: medical image classification, segmentation, and object detection. Extensive experiments across five public datasets demonstrate that M-FLAG significantly outperforms existing medical vision-language pre-training approaches and reduces the number of parameters by 78\%. Notably, M-FLAG achieves outstanding performance on the segmentation task while using only 1\% of the RSNA dataset, even outperforming ImageNet pre-trained models that have been fine-tuned using 100\% of the data.

Yinda Chen, Che Liu, Wei Huang et al.

Vision-Language Pretraining (VLP) has demonstrated remarkable capabilities in learning visual representations from textual descriptions of images without annotations. Yet, effective VLP demands large-scale image-text pairs, a resource that suffers scarcity in the medical domain. Moreover, conventional VLP is limited to 2D images while medical images encompass diverse modalities, often in 3D, making the learning process more challenging. To address these challenges, we present Generative Text-Guided 3D Vision-Language Pretraining for Unified Medical Image Segmentation (GTGM), a framework that extends of VLP to 3D medical images without relying on paired textual descriptions. Specifically, GTGM utilizes large language models (LLM) to generate medical-style text from 3D medical images. This synthetic text is then used to supervise 3D visual representation learning. Furthermore, a negative-free contrastive learning objective strategy is introduced to cultivate consistent visual representations between augmented 3D medical image patches, which effectively mitigates the biases associated with strict positive-negative sample pairings. We evaluate GTGM on three imaging modalities - Computed Tomography (CT), Magnetic Resonance Imaging (MRI), and electron microscopy (EM) over 13 datasets. GTGM's superior performance across various medical image segmentation tasks underscores its effectiveness and versatility, by enabling VLP extension into 3D medical imagery while bypassing the need for paired text.

Che Liu, Zhongwei Wan, Sibo Cheng et al.

In the domain of cardiovascular healthcare, the Electrocardiogram (ECG) serves as a critical, non-invasive diagnostic tool. Although recent strides in self-supervised learning (SSL) have been promising for ECG representation learning, these techniques often require annotated samples and struggle with classes not present in the fine-tuning stages. To address these limitations, we introduce ECG-Text Pre-training (ETP), an innovative framework designed to learn cross-modal representations that link ECG signals with textual reports. For the first time, this framework leverages the zero-shot classification task in the ECG domain. ETP employs an ECG encoder along with a pre-trained language model to align ECG signals with their corresponding textual reports. The proposed framework excels in both linear evaluation and zero-shot classification tasks, as demonstrated on the PTB-XL and CPSC2018 datasets, showcasing its ability for robust and generalizable cross-modal ECG feature learning.

Armand de Villeroché, Rem-Sophia Mouradi, Vincent Le Guen et al.

Air flow modeling at a local scale is essential for applications such as pollutant dispersion modeling or wind farm modeling. To circumvent costly Computational Fluid Dynamics (CFD) computations, deep learning surrogate models have recently emerged as promising alternatives. However, in the context of urban air flow, deep learning models struggle to adapt to the high variations of the urban geometry and to large mesh sizes. To tackle these challenges, we introduce Anchored Branched Steady-state WInd Flow Transformer (AB-SWIFT), a transformer-based model with an internal branched structure uniquely designed for atmospheric flow modeling. We train our model on a specially designed database of atmospheric simulations around randomised urban geometries and with a mixture of unstable, neutral, and stable atmospheric stratifications. Our model reaches the best accuracy on all predicted fields compared to state-of-the-art transformers and graph-based models. Our code and data is available at https://github.com/cerea-daml/abswift.

Sibo Cheng, Che Liu, Yike Guo et al.

Variational Data Assimilation (DA) has been broadly used in engineering problems for field reconstruction and prediction by performing a weighted combination of multiple sources of noisy data. In recent years, the integration of deep learning (DL) techniques in DA has shown promise in improving the efficiency and accuracy in high-dimensional dynamical systems. Nevertheless, existing deep DA approaches face difficulties in dealing with unstructured observation data, especially when the placement and number of sensors are dynamic over time. We introduce a novel variational DA scheme, named Voronoi-tessellation Inverse operator for VariatIonal Data assimilation (VIVID), that incorporates a DL inverse operator into the assimilation objective function. By leveraging the capabilities of the Voronoi-tessellation and convolutional neural networks, VIVID is adept at handling sparse, unstructured, and time-varying sensor data. Furthermore, the incorporation of the DL inverse operator establishes a direct link between observation and state space, leading to a reduction in the number of minimization steps required for DA. Additionally, VIVID can be seamlessly integrated with Proper Orthogonal Decomposition (POD) to develop an end-to-end reduced-order DA scheme, which can further expedite field reconstruction. Numerical experiments in a fluid dynamics system demonstrate that VIVID can significantly outperform existing DA and DL algorithms. The robustness of VIVID is also accessed through the application of various levels of prior error, the utilization of varying numbers of sensors, and the misspecification of error covariance in DA.

Sibo Cheng, Yike Guo, Rossella Arcucci

Recent increase in wildfires worldwide has led to the need for real-time fire nowcasting. Physics-driven models, such as cellular automata and computational fluid dynamics can provide high-fidelity fire spread simulations but they are computationally expensive and time-consuming. Much effort has been put into developing machine learning models for fire prediction. However, these models are often region-specific and require a substantial quantity of simulation data for training purpose. This results in a significant amount of computational effort for different ecoregions. In this work, a generative model is proposed using a three-dimensional Vector-Quantized Variational Autoencoders to generate spatial-temporal sequences of unseen wildfire burned areas in a given ecoregion. The model is tested in the ecoregion of a recent massive wildfire event in California, known as the Chimney fire. Numerical results show that the model succeed in generating coherent and structured fire scenarios, taking into account the impact from geophysical variables, such as vegetation and slope. Generated data are also used to train a surrogate model for predicting wildfire dissemination, which has been tested on both simulation data and the real Chimney fire event.

Sibo Cheng, Jinyang Min, Che Liu et al.

Data assimilation techniques are often confronted with challenges handling complex high dimensional physical systems, because high precision simulation in complex high dimensional physical systems is computationally expensive and the exact observation functions that can be applied in these systems are difficult to obtain. It prompts growing interest in integrating deep learning models within data assimilation workflows, but current software packages for data assimilation cannot handle deep learning models inside. This study presents a novel Python package seamlessly combining data assimilation with deep neural networks to serve as models for state transition and observation functions. The package, named TorchDA, implements Kalman Filter, Ensemble Kalman Filter (EnKF), 3D Variational (3DVar), and 4D Variational (4DVar) algorithms, allowing flexible algorithm selection based on application requirements. Comprehensive experiments conducted on the Lorenz 63 and a two-dimensional shallow water system demonstrate significantly enhanced performance over standalone model predictions without assimilation. The shallow water analysis validates data assimilation capabilities mapping between different physical quantity spaces in either full space or reduced order space. Overall, this innovative software package enables flexible integration of deep learning representations within data assimilation, conferring a versatile tool to tackle complex high dimensional dynamical systems across scientific domains.

Hanyang Wang, Hao Zhou, Sibo Cheng

Despite the success of various methods in addressing the issue of spatial reconstruction of dynamical systems with sparse observations, spatio-temporal prediction for sparse fields remains a challenge. Existing Kriging-based frameworks for spatio-temporal sparse field prediction fail to meet the accuracy and inference time required for nonlinear dynamic prediction problems. In this paper, we introduce the Dynamical System Prediction from Sparse Observations using Voronoi Tessellation (DSOVT) framework, an innovative methodology based on Voronoi tessellation which combines convolutional encoder-decoder (CED) and long short-term memory (LSTM) and utilizing Convolutional Long Short-Term Memory (ConvLSTM). By integrating Voronoi tessellations with spatio-temporal deep learning models, DSOVT is adept at predicting dynamical systems with unstructured, sparse, and time-varying observations. CED-LSTM maps Voronoi tessellations into a low-dimensional representation for time series prediction, while ConvLSTM directly uses these tessellations in an end-to-end predictive model. Furthermore, we incorporate physics constraints during the training process for dynamical systems with explicit formulas. Compared to purely data-driven models, our physics-based approach enables the model to learn physical laws within explicitly formulated dynamics, thereby enhancing the robustness and accuracy of rolling forecasts. Numerical experiments on real sea surface data and shallow water systems clearly demonstrate our framework's accuracy and computational efficiency with sparse and time-varying observations.

Sibo Cheng, Hector Chassagnon, Matthew Kasoar et al.

Global wildfire models play a crucial role in anticipating and responding to changing wildfire regimes. JULES-INFERNO is a global vegetation and fire model simulating wildfire emissions and area burnt on a global scale. However, because of the high data dimensionality and system complexity, JULES-INFERNO's computational costs make it challenging to apply to fire risk forecasting with unseen initial conditions. Typically, running JULES-INFERNO for 30 years of prediction will take several hours on High Performance Computing (HPC) clusters. To tackle this bottleneck, two data-driven models are built in this work based on Deep Learning techniques to surrogate the JULES-INFERNO model and speed up global wildfire forecasting. More precisely, these machine learning models take global temperature, vegetation density, soil moisture and previous forecasts as inputs to predict the subsequent global area burnt on an iterative basis. Average Error per Pixel (AEP) and Structural Similarity Index Measure (SSIM) are used as metrics to evaluate the performance of the proposed surrogate models. A fine tuning strategy is also proposed in this work to improve the algorithm performance for unseen scenarios. Numerical results show a strong performance of the proposed models, in terms of both computational efficiency (less than 20 seconds for 30 years of prediction on a laptop CPU) and prediction accuracy (with AEP under 0.3\% and SSIM over 98\% compared to the outputs of JULES-INFERNO).

Yihang Zhou, Chao Lin, Hideki Kikumoto et al.

Real-time rooftop wind-speed distribution is important for the safe operation of drones and urban air mobility systems, wind control systems, and rooftop utilization. However, rooftop flows show strong nonlinearity, separation, and cross-direction variability, which make flow field reconstruction from sparse sensors difficult. This study develops a learning-from-observation framework using wind-tunnel experimental data obtained by Particle Image Velocimetry (PIV) and compares Kriging interpolation with three deep learning models: UNet, Vision Transformer Autoencoder (ViTAE), and Conditional Wasserstein GAN (CWGAN). We evaluate two training strategies, single wind-direction training (SDT) and mixed wind-direction training (MDT), across sensor densities from 5 to 30, test robustness under sensor position perturbations of plus or minus 1 grid, and optimize sensor placement via Proper Orthogonal Decomposition with QR decomposition. Results show that deep learning methods can reconstruct rooftop wind fields from sparse sensor data effectively. Compared with Kriging interpolation, the deep learning models improved SSIM by up to 32.7%, FAC2 by 24.2%, and NMSE by 27.8%. Mixed wind-direction training further improved performance, with gains of up to 173.7% in SSIM, 16.7% in FAC2, and 98.3% in MG compared with single-direction training. The results also show that sensor configuration, optimization, and training strategy should be considered jointly for reliable deployment. QR-based optimization improved robustness by up to 27.8% under sensor perturbations, although with metric-dependent trade-offs. Training on experimental rather than simulated data also provides practical guidance for method selection and sensor placement in different scenarios.

Yilin Zhuang, Sibo Cheng, Karthik Duraisamy

Diffusion models have gained attention for their ability to represent complex distributions and incorporate uncertainty, making them ideal for robust predictions in the presence of noisy or incomplete data. In this study, we develop and enhance score-based diffusion models in field reconstruction tasks, where the goal is to estimate complete spatial fields from partial observations. We introduce a condition encoding approach to construct a tractable mapping mapping between observed and unobserved regions using a learnable integration of sparse observations and interpolated fields as an inductive bias. With refined sensing representations and an unraveled temporal dimension, our method can handle arbitrary moving sensors and effectively reconstruct fields. Furthermore, we conduct a comprehensive benchmark of our approach against a deterministic interpolation-based method across various static and time-dependent PDEs. Our study attempts to addresses the gap in strong baselines for evaluating performance across varying sampling hyperparameters, noise levels, and conditioning methods. Our results show that diffusion models with cross-attention and the proposed conditional encoding generally outperform other methods under noisy conditions, although the deterministic method excels with noiseless data. Additionally, both the diffusion models and the deterministic method surpass the numerical approach in accuracy and computational cost for the steady problem. We also demonstrate the ability of the model to capture possible reconstructions and improve the accuracy of fused results in covariance-based correction tasks using ensemble sampling.

Kewei Zhu, Yanze Xin, Jinwei Hu et al.

Predicting high-dimensional dynamical systems with irregular time steps presents significant challenges for current data-driven algorithms. These irregularities arise from missing data, sparse observations, or adaptive computational techniques, reducing prediction accuracy. To address these limitations, we propose a novel method: a Physics-Spatiotemporal Masked Autoencoder. This method integrates convolutional autoencoders for spatial feature extraction with masked autoencoders optimised for irregular time series, leveraging attention mechanisms to reconstruct the entire physical sequence in a single prediction pass. The model avoids the need for data imputation while preserving physical integrity of the system. Here, 'physics' refers to high-dimensional fields generated by underlying dynamical systems, rather than the enforcement of explicit physical constraints or PDE residuals. We evaluate this approach on multiple simulated datasets and real-world ocean temperature data. The results demonstrate that our method achieves significant improvements in prediction accuracy, robustness to nonlinearities, and computational efficiency over traditional convolutional and recurrent network methods. The model shows potential for capturing complex spatiotemporal patterns without requiring domain-specific knowledge, with applications in climate modelling, fluid dynamics, ocean forecasting, environmental monitoring, and scientific computing.

Zhengsen Xu, Lanying Wang, Sibo Cheng et al.

In recent decades, the intensification of wildfire activity in western Canada has resulted in substantial socio-economic and environmental losses. Accurate wildfire risk prediction is hindered by the intrinsic stochasticity of ignition and spread and by nonlinear interactions among fuel conditions, meteorology, climate variability, topography, and human activities, challenging the reliability and interpretability of purely data-driven models. We propose a trustworthy data-driven wildfire risk prediction framework based on long-sequence, multi-scale temporal modeling, which integrates heterogeneous drivers while explicitly quantifying predictive uncertainty and enabling process-level interpretation. Evaluated over western Canada during the record-breaking 2023 and 2024 fire seasons, the proposed model outperforms existing time-series approaches, achieving an F1 score of 0.90 and a PR-AUC of 0.98 with low computational cost. Uncertainty-aware analysis reveals structured spatial and seasonal patterns in predictive confidence, highlighting increased uncertainty associated with ambiguous predictions and spatiotemporal decision boundaries. SHAP-based interpretation provides mechanistic understanding of wildfire controls, showing that temperature-related drivers dominate wildfire risk in both years, while moisture-related constraints play a stronger role in shaping spatial and land-cover-specific contrasts in 2024 compared to the widespread hot and dry conditions of 2023. Data and code are available at https://github.com/SynUW/mmFire.

Xiaoyuan Cheng, Wenxuan Yuan, Yiming Yang et al.

The Koopman operator provides a powerful framework for modeling dynamical systems and has attracted growing interest from the machine learning community. However, its infinite-dimensional nature makes identifying suitable finite-dimensional subspaces challenging, especially for deep architectures. We argue that these difficulties come from suboptimal representation learning, where latent variables fail to balance expressivity and simplicity. This tension is closely related to the information bottleneck (IB) dilemma: constructing compressed representations that are both compact and predictive. Rethinking Koopman learning through this lens, we demonstrate that latent mutual information promotes simplicity, yet an overemphasis on simplicity may cause latent space to collapse onto a few dominant modes. In contrast, expressiveness is sustained by the von Neumann entropy, which prevents such collapse and encourages mode diversity. This insight leads us to propose an information-theoretic Lagrangian formulation that explicitly balances this tradeoff. Furthermore, we propose a new algorithm based on the Lagrangian formulation that encourages both simplicity and expressiveness, leading to a stable and interpretable Koopman representation. Beyond quantitative evaluations, we further visualize the learned manifolds under our representations, observing empirical results consistent with our theoretical predictions. Finally, we validate our approach across a diverse range of dynamical systems, demonstrating improved performance over existing Koopman learning methods. The implementation is publicly available at https://github.com/Wenxuan52/InformationKoopman.

Hao Zhou, Sibo Cheng, Rossella Arcucci

Physics-constrained neural networks are commonly employed to enhance prediction robustness compared to purely data-driven models, achieved through the inclusion of physical constraint losses during the model training process. However, one of the major challenges of physics-constrained neural networks consists of the training complexity especially for high-dimensional systems. In fact, conventional physics-constrained models rely on singular-fidelity data necessitating the assessment of physical constraints within high-dimensional fields, which introduces computational difficulties. Furthermore, due to the fixed input size of the neural networks, employing multi-fidelity training data can also be cumbersome. In this paper, we propose the Multi-Scale Physics-Constrained Neural Network (MSPCNN), which offers a novel methodology for incorporating data with different levels of fidelity into a unified latent space through a customised multi-fidelity autoencoder. Additionally, multiple decoders are concurrently trained to map latent representations of inputs into various fidelity physical spaces. As a result, during the training of predictive models, physical constraints can be evaluated within low-fidelity spaces, yielding a trade-off between training efficiency and accuracy. In addition, unlike conventional methods, MSPCNN also manages to employ multi-fidelity data to train the predictive model. We assess the performance of MSPCNN in two fluid dynamics problems, namely a two-dimensional Burgers' system and a shallow water system. Numerical results clearly demonstrate the enhancement of prediction accuracy and noise robustness when introducing physical constraints in low-fidelity fields. On the other hand, as expected, the training complexity can be significantly reduced by computing physical constraint loss in the low-fidelity field rather than the high-fidelity one.

Sibo Cheng, Marc Bocquet, Weiping Ding et al.

Unstructured grid data are essential for modelling complex geometries and dynamics in computational physics. Yet, their inherent irregularity presents significant challenges for conventional machine learning (ML) techniques. This paper provides a comprehensive review of advanced ML methodologies designed to handle unstructured grid data in high-dimensional dynamical systems. Key approaches discussed include graph neural networks, transformer models with spatial attention mechanisms, interpolation-integrated ML methods, and meshless techniques such as physics-informed neural networks. These methodologies have proven effective across diverse fields, including fluid dynamics and environmental simulations. This review is intended as a guidebook for computational scientists seeking to apply ML approaches to unstructured grid data in their domains, as well as for ML researchers looking to address challenges in computational physics. It places special focus on how ML methods can overcome the inherent limitations of traditional numerical techniques and, conversely, how insights from computational physics can inform ML development. To support benchmarking, this review also provides a summary of open-access datasets of unstructured grid data in computational physics. Finally, emerging directions such as generative models with unstructured data, reinforcement learning for mesh generation, and hybrid physics-data-driven paradigms are discussed to inspire future advancements in this evolving field.

Jiuming Qin, Che Liu, Sibo Cheng et al.

Modern healthcare often utilises radiographic images alongside textual reports for diagnostics, encouraging the use of Vision-Language Self-Supervised Learning (VL-SSL) with large pre-trained models to learn versatile medical vision representations. However, most existing VL-SSL frameworks are trained end-to-end, which is computation-heavy and can lose vital prior information embedded in pre-trained encoders. To address both issues, we introduce the backbone-agnostic Adaptor framework, which preserves medical knowledge in pre-trained image and text encoders by keeping them frozen, and employs a lightweight Adaptor module for cross-modal learning. Experiments on medical image classification and segmentation tasks across three datasets reveal that our framework delivers competitive performance while cutting trainable parameters by over 90% compared to current pre-training approaches. Notably, when fine-tuned with just 1% of data, Adaptor outperforms several Transformer-based methods trained on full datasets in medical image segmentation.

Dayou Chen, Sibo Cheng, Jinwei Hu et al.

Wildfire prediction has become increasingly crucial due to the escalating impacts of climate change. Traditional CNN-based wildfire prediction models struggle with handling missing oceanic data and addressing the long-range dependencies across distant regions in meteorological data. In this paper, we introduce an innovative Graph Neural Network (GNN)-based model for global wildfire prediction. We propose a hybrid model that combines the spatial prowess of Graph Convolutional Networks (GCNs) with the temporal depth of Long Short-Term Memory (LSTM) networks. Our approach uniquely transforms global climate and wildfire data into a graph representation, addressing challenges such as null oceanic data locations and long-range dependencies inherent in traditional models. Benchmarking against established architectures using an unseen ensemble of JULES-INFERNO simulations, our model demonstrates superior predictive accuracy. Furthermore, we emphasise the model's explainability, unveiling potential wildfire correlation clusters through community detection and elucidating feature importance via Integrated Gradient analysis. Our findings not only advance the methodological domain of wildfire prediction but also underscore the importance of model transparency, offering valuable insights for stakeholders in wildfire management.

Bo Pang, Sibo Cheng, Yuhan Huang et al.

Predicting the extent of massive wildfires once ignited is essential to reduce the subsequent socioeconomic losses and environmental damage, but challenging because of the complexity of fire behaviour. Existing physics-based models are limited in predicting large or long-duration wildfire events. Here, we develop a deep-learning-based predictive model, Fire-Image-DenseNet (FIDN), that uses spatial features derived from both near real-time and reanalysis data on the environmental and meteorological drivers of wildfire. We trained and tested this model using more than 300 individual wildfires that occurred between 2012 and 2019 in the western US. In contrast to existing models, the performance of FIDN does not degrade with fire size or duration. Furthermore, it predicts final burnt area accurately even in very heterogeneous landscapes in terms of fuel density and flammability. The FIDN model showed higher accuracy, with a mean squared error (MSE) about 82% and 67% lower than those of the predictive models based on cellular automata (CA) and the minimum travel time (MTT) approaches, respectively. Its structural similarity index measure (SSIM) averages 97%, outperforming the CA and FlamMap MTT models by 6% and 2%, respectively. Additionally, FIDN is approximately three orders of magnitude faster than both CA and MTT models. The enhanced computational efficiency and accuracy advancements offer vital insights for strategic planning and resource allocation for firefighting operations.

Wenbo Yu, Anirbit Ghosh, Tobias Sebastian Finn et al.

Thanks to recent advances in generative AI, computers can now simulate realistic and complex natural processes. We apply this capability to predict how wildfires spread, a task made difficult by the unpredictable nature of fire and the variety of environmental conditions it depends on. In this study, We present the first denoising diffusion model for predicting wildfire spread, a new kind of AI framework that learns to simulate fires not just as one fixed outcome, but as a range of possible scenarios. By doing so, it accounts for the inherent uncertainty of wildfire dynamics, a feature that traditional models typically fail to represent. Unlike deterministic approaches that generate a single prediction, our model produces ensembles of forecasts that reflect physically meaningful distributions of where fire might go next. This technology could help us develop smarter, faster, and more reliable tools for anticipating wildfire behavior, aiding decision-makers in fire risk assessment and response planning.

Yiming Yang, Xiaoyuan Cheng, Daniel Giles et al.

Variational data assimilation estimates the dynamical system states by minimizing a cost function that fits the numerical models with the observational data. Although four-dimensional variational assimilation (4D-Var) is widely used, it faces high computational costs in complex nonlinear systems and depends on imperfect state-observation mappings. Deep learning (DL) offers more expressive approximators, while integrating DL models into 4D-Var is challenging due to their nonlinearities and lack of theoretical guarantees in assimilation results. In this paper, we propose Tensor-Var, a novel framework that integrates kernel conditional mean embedding (CME) with 4D-Var to linearize nonlinear dynamics, achieving convex optimization in a learned feature space. Moreover, our method provides a new perspective for solving 4D-Var in a linear way, offering theoretical guarantees of consistent assimilation results between the original and feature spaces. To handle large-scale problems, we propose a method to learn deep features using neural networks within the Tensor-Var framework. Experiments on chaotic systems and global weather prediction with real-time observations show that Tensor-Var outperforms conventional and DL hybrid 4D-Var baselines in accuracy while achieving a 10- to 20-fold speed improvement.

Zhengsen Xu, Jonathan Li, Sibo Cheng et al.

Wildfires pose a significant threat to ecosystems, wildlife, and human communities, leading to habitat destruction, pollutant emissions, and biodiversity loss. Accurate wildfire risk prediction is crucial for mitigating these impacts and safeguarding both environmental and human health. This paper provides a comprehensive review of wildfire risk prediction methodologies, with a particular focus on deep learning approaches combined with remote sensing. We begin by defining wildfire risk and summarizing the geographical distribution of related studies. In terms of data, we analyze key predictive features, including fuel characteristics, meteorological and climatic conditions, socioeconomic factors, topography, and hydrology, while also reviewing publicly available wildfire prediction datasets derived from remote sensing. Additionally, we emphasize the importance of feature collinearity assessment and model interpretability to improve the understanding of prediction outcomes. Regarding methodology, we classify deep learning models into three primary categories: time-series forecasting, image segmentation, and spatiotemporal prediction, and further discuss methods for converting model outputs into risk classifications or probability-adjusted predictions. Finally, we identify the key challenges and limitations of current wildfire-risk prediction models and outline several research opportunities. These include integrating diverse remote sensing data, developing multimodal models, designing more computationally efficient architectures, and incorporating cross-disciplinary methods--such as coupling with numerical weather-prediction models--to enhance the accuracy and robustness of wildfire-risk assessments.

Yihang Zhou, Ruige Kong, Zhengsen Xu et al.

Facing the escalating threat of global wildfires, numerous computer vision techniques using remote sensing data have been applied in this area. However, the selection of deep learning methods for wildfire prediction remains uncertain due to the lack of comparative analysis in a quantitative and explainable manner, crucial for improving prevention measures and refining models. This study aims to thoroughly compare the performance, efficiency, and explainability of four prevalent deep learning architectures: Autoencoder, ResNet, UNet, and Transformer-based Swin-UNet. Employing a real-world dataset that includes nearly a decade of remote sensing data from California, U.S., these models predict the spread of wildfires for the following day. Through detailed quantitative comparison analysis, we discovered that Transformer-based Swin-UNet and UNet generally outperform Autoencoder and ResNet, particularly due to the advanced attention mechanisms in Transformer-based Swin-UNet and the efficient use of skip connections in both UNet and Transformer-based Swin-UNet, which contribute to superior predictive accuracy and model interpretability. Then we applied XAI techniques on all four models, this not only enhances the clarity and trustworthiness of models but also promotes focused improvements in wildfire prediction capabilities. The XAI analysis reveals that UNet and Transformer-based Swin-UNet are able to focus on critical features such as 'Previous Fire Mask', 'Drought', and 'Vegetation' more effectively than the other two models, while also maintaining balanced attention to the remaining features, leading to their superior performance. The insights from our thorough comparative analysis offer substantial implications for future model design and also provide guidance for model selection in different scenarios.

Pouria Behnoudfar, Charlotte Moser, Marc Bocquet et al.

Computer models are indispensable tools for understanding the Earth system. While high-resolution operational models have achieved many successes, they exhibit persistent biases, particularly in simulating extreme events and statistical distributions. In contrast, coarse-grained idealized models isolate fundamental processes and can be precisely calibrated to excel in characterizing specific dynamical and statistical features. However, different models remain siloed by disciplinary boundaries. By leveraging the complementary strengths of models of varying complexity, we develop an explainable AI framework for Earth system emulators. It bridges the model hierarchy through a reconfigured latent data assimilation technique, uniquely suited to exploit the sparse output from the idealized models. The resulting bridging model inherits the high resolution and comprehensive variables of operational models while achieving global accuracy enhancements through targeted improvements from idealized models. Crucially, the mechanism of AI provides a clear rationale for these advancements, moving beyond black-box correction to physically insightful understanding in a computationally efficient framework that enables effective physics-assisted digital twins and uncertainty quantification. We demonstrate its power by significantly correcting biases in CMIP6 simulations of El Niño spatiotemporal patterns, leveraging statistically accurate idealized models. This work also highlights the importance of pushing idealized model development and advancing communication between modeling communities.

Xiao Xue, Marco F. P. ten Eikelder, Mingyang Gao et al.

The lattice Boltzmann equation (LBE), rooted in kinetic theory, provides a powerful framework for capturing complex flow behaviour by describing the evolution of single-particle distribution functions (PDFs). Despite its success, solving the LBE numerically remains computationally intensive due to strict time-step restrictions imposed by collision kernels. Here, we introduce a physics-informed neural operator framework for the LBE that enables prediction over large time horizons without step-by-step integration, effectively bypassing the need to explicitly solve the collision kernel. We incorporate intrinsic moment-matching constraints of the LBE, along with global equivariance of the full distribution field, enabling the model to capture the complex dynamics of the underlying kinetic system. Our framework is discretization-invariant, enabling models trained on coarse lattices to generalise to finer ones (kinetic super-resolution). In addition, it is agnostic to the specific form of the underlying collision model, which makes it naturally applicable across different kinetic datasets regardless of the governing dynamics. Our results demonstrate robustness across complex flow scenarios, including von Karman vortex shedding, ligament breakup, and bubble adhesion. This establishes a new data-driven pathway for modelling kinetic systems.

Hao Zhou, Sibo Cheng

Data-driven methods are emerging as efficient alternatives to traditional numerical forecasting, offering fast inference and lower computational cost. Yet, for complex systems, long-term accuracy often deteriorates due to error accumulation, and autoregressive training (though effective) demands large GPU memory and may sacrifice short-term performance. We propose the Stochastic PushForward (SPF) framework, which retains one-step-ahead training while enabling multi-step learning. SPF builds a supplementary dataset from model predictions and combines it with ground truth via a stochastic acquisition strategy, balancing short- and long-term performance while reducing overfitting. Multi-step predictions are precomputed between epochs, keeping memory usage stable without storing full unrolled sequences. Experiments on the Burgers' equation and the Shallow Water benchmark show that SPF achieves higher long-term accuracy than autoregressive methods while lowering memory requirements, making it promising for resource-limited and complex simulations.

Zhongwei Wan, Che Liu, Mi Zhang et al.

The scarcity of data presents a critical obstacle to the efficacy of medical visionlanguage pre-training (VLP). A potential solution lies in the combination of datasets from various language communities. Nevertheless, the main challenge stems from the complexity of integrating diverse syntax and semantics, language-specific medical terminology, and culture-specific implicit knowledge. Therefore, one crucial aspect to consider is the presence of community bias caused by different languages. This paper presents a novel framework named Unifying Cross-Lingual Medical Vision-Language Pre-Training (Med-UniC), designed to integrate multimodal medical data from the two most prevalent languages, English and Spanish. Specifically, we propose Cross-lingual Text Alignment Regularization (CTR) to explicitly unify cross-lingual semantic representations of medical reports originating from diverse language communities. CTR is optimized through latent language disentanglement, rendering our optimization objective to not depend on negative samples, thereby significantly mitigating the bias from determining positive-negative sample pairs within analogous medical reports. Furthermore, it ensures that the cross-lingual representation is not biased toward any specific language community. Med-UniC reaches superior performance across 5 medical image tasks and 10 datasets encompassing over 30 diseases, offering a versatile framework for unifying multi-modal medical data within diverse linguistic communities. The experimental outcomes highlight the presence of community bias in cross-lingual VLP. Reducing this bias enhances the performance not only in vision-language tasks but also in uni-modal visual tasks.

Sibo Cheng, Mingming Qiu

Data assimilation techniques are widely used to predict complex dynamical systems with uncertainties, based on time-series observation data. Error covariance matrices modelling is an important element in data assimilation algorithms which can considerably impact the forecasting accuracy. The estimation of these covariances, which usually relies on empirical assumptions and physical constraints, is often imprecise and computationally expensive especially for systems of large dimension. In this work, we propose a data-driven approach based on long short term memory (LSTM) recurrent neural networks (RNN) to improve both the accuracy and the efficiency of observation covariance specification in data assimilation for dynamical systems. Learning the covariance matrix from observed/simulated time-series data, the proposed approach does not require any knowledge or assumption about prior error distribution, unlike classical posterior tuning methods. We have compared the novel approach with two state-of-the-art covariance tuning algorithms, namely DI01 and D05, first in a Lorenz dynamical system and then in a 2D shallow water twin experiments framework with different covariance parameterization using ensemble assimilation. This novel method shows significant advantages in observation covariance specification, assimilation accuracy and computational efficiency.