pwc-archive/papers-with-abstracts huggingface dataset:
Mitigating loss of variance in ensemble data assimilation: machine learning-based and distance-free localizations for better covariance estimation
Authors: Vinicius L. S. Silva, Gabriel S. Seabra, Alexandre A. Emerick
Date: 2025-06-16 00:00:00
Tasks: Computational Efficiency, Uncertainty Quantification

We propose two new methods based/inspired by machine learning for tabular data and distance-free localization to enhance the covariance estimations in an ensemble data assimilation. The main goal is to enhance the data assimilation results by mitigating loss of variance due to sampling errors. We also analyze the suitability of several machine learning models and the balance between accuracy and computational cost of the covariance estimations. We introduce two distance-free localization techniques leveraging machine learning methods specifically tailored for tabular data. The methods are integrated into the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) framework. The results show that the proposed localizations improve covariance accuracy and enhance data assimilation and uncertainty quantification results. We observe reduced variance loss for the input variables using the proposed methods. Furthermore, we compare several machine learning models, assessing their suitability for the problem in terms of computational cost, and quality of the covariance estimation and data match. The influence of ensemble size is also investigated, providing insights into balancing accuracy and computational efficiency. Our findings demonstrate that certain machine learning models are more suitable for this problem. This study introduces two novel methods that mitigate variance loss for model parameters in ensemble-based data assimilation, offering practical solutions that are easy to implement and do not require any additional numerical simulation or hyperparameter tuning.
SIMSHIFT: A Benchmark for Adapting Neural Surrogates to Distribution Shifts
Authors: Paul Setinek, Gianluca Galletti, Thomas Gross, Dominik Schnürer, Johannes Brandstetter, Werner Zellinger
Date: 2025-06-13 00:00:00
Tasks: Domain Adaptation

Neural surrogates for Partial Differential Equations (PDEs) often suffer significant performance degradation when evaluated on unseen problem configurations, such as novel material types or structural dimensions. Meanwhile, Domain Adaptation (DA) techniques have been widely used in vision and language processing to generalize from limited information about unseen configurations. In this work, we address this gap through two focused contributions. First, we introduce SIMSHIFT, a novel benchmark dataset and evaluation suite composed of four industrial simulation tasks: hot rolling, sheet metal forming, electric motor design and heatsink design. Second, we extend established domain adaptation methods to state of the art neural surrogates and systematically evaluate them. These approaches use parametric descriptions and ground truth simulations from multiple source configurations, together with only parametric descriptions from target configurations. The goal is to accurately predict target simulations without access to ground truth simulation data. Extensive experiments on SIMSHIFT highlight the challenges of out of distribution neural surrogate modeling, demonstrate the potential of DA in simulation, and reveal open problems in achieving robust neural surrogates under distribution shifts in industrially relevant scenarios. Our codebase is available at https://github.com/psetinek/simshift
Improvement of Nuclide Detection through Graph Spectroscopic Analysis Framework and its Application to Nuclear Facility Upset Detection
Authors: Pedro Rodríguez Fernández, Christian Svinth, Alex Hagen
Date: 2025-06-19 00:00:00

We present a method to improve the detection limit for radionuclides using spectroscopic radiation detectors and the arrival time of each detected radiation quantum. We enable this method using a neural network with an attention mechanism. We illustrate the method on the detection of Cesium release from a nuclear facility during an upset, and our method shows $2\times$ improvement over the traditional spectroscopic method. We hypothesize that our method achieves this performance increase by modulating its detection probability by the overall rate of probable detections, specifically by adapting detection thresholds based on temporal event distributions and local spectral features, and show evidence to this effect. We believe this method is applicable broadly and may be more successful for radionuclides with more complicated decay chains than Cesium; we also note that our method can generalize beyond the addition of arrival time and could integrate other data about each detection event, such as pulse quality, location in detector, or even combining the energy and time from detections in different detectors.
An application of machine learning to the motion response prediction of floating assets
Authors: Michael T. M. B. Morris-Thomas, Marius Martens
Date: 2025-05-31 00:00:00
Tasks: Decision Making

The real-time prediction of floating offshore asset behavior under stochastic metocean conditions remains a significant challenge in offshore engineering. While traditional empirical and frequency-domain methods work well in benign conditions, they struggle with both extreme sea states and nonlinear responses. This study presents a supervised machine learning approach using multivariate regression to predict the nonlinear motion response of a turret-moored vessel in 400 m water depth. We developed a machine learning workflow combining a gradient-boosted ensemble method with a custom passive weathervaning solver, trained on approximately $10^6$ samples spanning 100 features. The model achieved mean prediction errors of less than 5% for critical mooring parameters and vessel heading accuracy to within 2.5 degrees across diverse metocean conditions, significantly outperforming traditional frequency-domain methods. The framework has been successfully deployed on an operational facility, demonstrating its efficacy for real-time vessel monitoring and operational decision-making in offshore environments.
FIGNN: Feature-Specific Interpretability for Graph Neural Network Surrogate Models
Authors: Riddhiman Raut, Romit Maulik, Shivam Barwey
Date: 2025-06-13 00:00:00
Tasks: Graph Neural Network

This work presents a novel graph neural network (GNN) architecture, the Feature-specific Interpretable Graph Neural Network (FIGNN), designed to enhance the interpretability of deep learning surrogate models defined on unstructured grids in scientific applications. Traditional GNNs often obscure the distinct spatial influences of different features in multivariate prediction tasks. FIGNN addresses this limitation by introducing a feature-specific pooling strategy, which enables independent attribution of spatial importance for each predicted variable. Additionally, a mask-based regularization term is incorporated into the training objective to explicitly encourage alignment between interpretability and predictive error, promoting localized attribution of model performance. The method is evaluated for surrogate modeling of two physically distinct systems: the SPEEDY atmospheric circulation model and the backward-facing step (BFS) fluid dynamics benchmark. Results demonstrate that FIGNN achieves competitive predictive performance while revealing physically meaningful spatial patterns unique to each feature. Analysis of rollout stability, feature-wise error budgets, and spatial mask overlays confirm the utility of FIGNN as a general-purpose framework for interpretable surrogate modeling in complex physical domains.
Efficacy of Temporal Fusion Transformers for Runoff Simulation
Authors: Sinan Rasiya Koya, Tirthankar Roy
Date: 2025-06-25 00:00:00

Combining attention with recurrence has shown to be valuable in sequence modeling, including hydrological predictions. Here, we explore the strength of Temporal Fusion Transformers (TFTs) over Long Short-Term Memory (LSTM) networks in rainfall-runoff modeling. We train ten randomly initialized models, TFT and LSTM, for 531 CAMELS catchments in the US. We repeat the experiment with five subsets of the Caravan dataset, each representing catchments in the US, Australia, Brazil, Great Britain, and Chile. Then, the performance of the models, their variability regarding the catchment attributes, and the difference according to the datasets are assessed. Our findings show that TFT slightly outperforms LSTM, especially in simulating the midsection and peak of hydrographs. Furthermore, we show the ability of TFT to handle longer sequences and why it can be a better candidate for higher or larger catchments. Being an explainable AI technique, TFT identifies the key dynamic and static variables, providing valuable scientific insights. However, both TFT and LSTM exhibit a considerable drop in performance with the Caravan dataset, indicating possible data quality issues. Overall, the study highlights the potential of TFT in improving hydrological modeling and understanding.
Forecasting the spatiotemporal evolution of fluid-induced microearthquakes with deep learning
Authors: Jaehong Chung, Michael Manga, Timothy Kneafsey, Tapan Mukerji, Mengsu Hu
Date: 2025-06-17 00:00:00

Microearthquakes (MEQs) generated by subsurface fluid injection record the evolving stress state and permeability of reservoirs. Forecasting their full spatiotemporal evolution is therefore critical for applications such as enhanced geothermal systems (EGS), CO$_2$ sequestration and other geo-engineering applications. We present a transformer-based deep learning model that ingests hydraulic stimulation history and prior MEQ observations to forecast four key quantities: cumulative MEQ count, cumulative logarithmic seismic moment, and the 50th- and 95th-percentile extents ($P_{50}, P_{95}$) of the MEQ cloud. Applied to the EGS Collab Experiment 1 dataset, the model achieves $R^2 >0.98$ for the 1-second forecast horizon and $R^2 >0.88$ for the 15-second forecast horizon across all targets, and supplies uncertainty estimates through a learned standard deviation term. These accurate, uncertainty-quantified forecasts enable real-time inference of fracture propagation and permeability evolution, demonstrating the strong potential of deep-learning approaches to improve seismic-risk assessment and guide mitigation strategies in future fluid-injection operations.
Decadal sink-source shifts of forest aboveground carbon since 1988
Authors: Zhen Qian, Sebastian Bathiany, Teng Liu, Lana L. Blaschke, Hoong Chen Teo, Niklas Boers
Date: 2025-06-13 00:00:00
Tasks: Probabilistic Deep Learning

As enduring carbon sinks, forest ecosystems are vital to the terrestrial carbon cycle and help moderate global warming. However, the long-term dynamics of aboveground carbon (AGC) in forests and their sink-source transitions remain highly uncertain, owing to changing disturbance regimes and inconsistencies in observations, data processing, and analysis methods. Here, we derive reliable, harmonized AGC stocks and fluxes in global forests from 1988 to 2021 at high spatial resolution by integrating multi-source satellite observations with probabilistic deep learning models. Our approach simultaneously estimates AGC and associated uncertainties, showing high reliability across space and time. We find that, although global forests remained an AGC sink of 6.2 PgC over 30 years, moist tropical forests shifted to a substantial AGC source between 2001 and 2010 and, together with boreal forests, transitioned toward a source in the 2011-2021 period. Temperate, dry tropical and subtropical forests generally exhibited increasing AGC stocks, although Europe and Australia became sources after 2011. Regionally, pronounced sink-to-source transitions occurred in tropical forests over the past three decades. The interannual relationship between global atmospheric CO2 growth rates and tropical AGC flux variability became increasingly negative, reaching Pearson's r = -0.63 (p < 0.05) in the most recent decade. In the Brazilian Amazon, the contribution of deforested regions to AGC losses declined from 60% in 1989-2000 to 13% in 2011-2021, while the share from untouched areas increased from 33% to 76%. Our findings suggest a growing role of tropical forest AGC in modulating variability in the terrestrial carbon cycle, with anthropogenic climate change potentially contributing increasingly to AGC changes, particularly in previously untouched areas.
IMC-PINN-FE: A Physics-Informed Neural Network for Patient-Specific Left Ventricular Finite Element Modeling with Image Motion Consistency and Biomechanical Parameter Estimation
Authors: Siyu Mu, Wei Xuan Chan, Choon Hwai Yap
Date: 2025-06-25 00:00:00
Tasks: parameter estimation, Specificity

Elucidating the biomechanical behavior of the myocardium is crucial for understanding cardiac physiology, but cannot be directly inferred from clinical imaging and typically requires finite element (FE) simulations. However, conventional FE methods are computationally expensive and often fail to reproduce observed cardiac motions. We propose IMC-PINN-FE, a physics-informed neural network (PINN) framework that integrates imaged motion consistency (IMC) with FE modeling for patient-specific left ventricular (LV) biomechanics. Cardiac motion is first estimated from MRI or echocardiography using either a pre-trained attention-based network or an unsupervised cyclic-regularized network, followed by extraction of motion modes. IMC-PINN-FE then rapidly estimates myocardial stiffness and active tension by fitting clinical pressure measurements, accelerating computation from hours to seconds compared to traditional inverse FE. Based on these parameters, it performs FE modeling across the cardiac cycle at 75x speedup. Through motion constraints, it matches imaged displacements more accurately, improving average Dice from 0.849 to 0.927, while preserving realistic pressure-volume behavior. IMC-PINN-FE advances previous PINN-FE models by introducing back-computation of material properties and better motion fidelity. Using motion from a single subject to reconstruct shape modes also avoids the need for large datasets and improves patient specificity. IMC-PINN-FE offers a robust and efficient approach for rapid, personalized, and image-consistent cardiac biomechanical modeling.
Filling of incomplete sinograms from sparse PET detector configurations using a residual U-Net
Authors: Klara Leffler, Luigi Tommaso Luppino, Samuel Kuttner, Karin Söderkvist, Jan Axelsson
Date: 2025-06-24 00:00:00

Long axial field-of-view PET scanners offer increased field-of-view and sensitivity compared to traditional PET scanners. However, a significant cost is associated with the densely packed photodetectors required for the extended-coverage systems, limiting clinical utilisation. To mitigate the cost limitations, alternative sparse system configurations have been proposed, allowing an extended field-of-view PET design with detector costs similar to a standard PET system, albeit at the expense of image quality. In this work, we propose a deep sinogram restoration network to fill in the missing sinogram data. Our method utilises a modified Residual U-Net, trained on clinical PET scans from a GE Signa PET/MR, simulating the removal of 50% of the detectors in a chessboard pattern (retaining only 25% of all lines of response). The model successfully recovers missing counts, with a mean absolute error below two events per pixel, outperforming 2D interpolation in both sinogram and reconstructed image domain. Notably, the predicted sinograms exhibit a smoothing effect, leading to reconstructed images lacking sharpness in finer details. Despite these limitations, the model demonstrates a substantial capacity for compensating for the undersampling caused by the sparse detector configuration. This proof-of-concept study suggests that sparse detector configurations, combined with deep learning techniques, offer a viable alternative to conventional PET scanner designs. This approach supports the development of cost-effective, total body PET scanners, allowing a significant step forward in medical imaging technology.
Exploring Strategies for Personalized Radiation Therapy Part I Unlocking Response-Related Tumor Subregions with Class Activation Mapping
Authors: Hao Peng, Steve Jiang, Robert Timmerman
Date: 2025-06-21 00:00:00
Tasks: Binary Classification

Personalized precision radiation therapy requires more than simple classification, it demands the identification of prognostic, spatially informative features and the ability to adapt treatment based on individual response. This study compares three approaches for predicting treatment response: standard radiomics, gradient based features, and convolutional neural networks enhanced with Class Activation Mapping. We analyzed 69 brain metastases from 39 patients treated with Gamma Knife radiosurgery. An integrated autoencoder classifier model was used to predict whether tumor volume would shrink by more than 20 percent at a three months follow up, framed as a binary classification task. The results highlight their strength in hierarchical feature extraction and the classifiers discriminative capacity. Among the models, pixel wise CAM provides the most detailed spatial insight, identifying lesion specific regions rather than relying on fixed patterns, demonstrating strong generalization. In non responding lesions, the activated regions may indicate areas of radio resistance. Pixel wise CAM outperformed both radiomics and gradient based methods in classification accuracy. Moreover, its fine grained spatial features allow for alignment with cellular level data, supporting biological validation and deeper understanding of heterogeneous treatment responses. Although further validation is necessary, these findings underscore the promise in guiding personalized and adaptive radiotherapy strategies for both photon and particle therapies.
Exploring Strategies for Personalized Radiation Therapy Part II Predicting Tumor Drift Patterns with Diffusion Models
Authors: Hao Peng, Steve Jiang, Robert Timmerman
Date: 2025-06-20 00:00:00
Tasks: Denoising

Radiation therapy outcomes are decided by two key parameters, dose and timing, whose best values vary substantially across patients. This variability is especially critical in the treatment of brain cancer, where fractionated or staged stereotactic radiosurgery improves safety compared to single fraction approaches, but complicates the ability to predict treatment response. To address this challenge, we employ Personalized Ultra-fractionated Stereotactic Adaptive Radiotherapy (PULSAR), a strategy that dynamically adjusts treatment based on how each tumor evolves over time. However, the success of PULSAR and other adaptive approaches depends on predictive tools that can guide early treatment decisions and avoid both overtreatment and undertreatment. However, current radiomics and dosiomics models offer limited insight into the evolving spatial and temporal patterns of tumor response. To overcome these limitations, we propose a novel framework using Denoising Diffusion Implicit Models (DDIM), which learns data-driven mappings from pre to post treatment imaging. In this study, we developed single step and iterative denoising strategies and compared their performance. The results show that diffusion models can effectively simulate patient specific tumor evolution and localize regions associated with treatment response. The proposed strategy provides a promising foundation for modeling heterogeneous treatment response and enabling early, adaptive interventions, paving the way toward more personalized and biologically informed radiotherapy.
Unsupervised deep learning model for fast energy layer pre-selection of delivery-efficient proton arc therapy plan optimization of nasopharyngeal carcinoma
Authors: Bohan Yang, Gang Liu, Rirao Dao, Yujia Qian, Ke Shi, Anke Tang, Yong Luo, Jingnan Liu
Date: 2025-06-18 00:00:00
Tasks: ARC

Objective. Proton arc therapy (PAT) is an emerging and promising modality in radiotherapy, offering several advantages over conventional intensitymodulated proton therapy (IMPT). However, identifying the optimal energy layer (EL) sequence remains computationally intensive due to the large number of possible energy layer transitions. This study proposes an unsupervised deep learning framework for fast and effective EL pre-selection, aiming to minimize energy layer switch time while preserving high plan quality. Approach. We introduce a novel data representation method, spot-count representation, which encodes the number of proton spots intersecting the target and organs at risk (OARs) in a matrix structured by sorted gantry angles and energy layers. This representation is the input of a UNet-based architecture, SPArcdl, which is trained to optimize a tri-objective function: maximizing target coverage, minimizing OAR exposure, and reducing energy switching time. The model is evaluated on 54 nasopharyngeal cancer cases, and its performance is benchmarked against plans generated by SPArcparticle swarm. Main results. SPArcdl produces EL pre-selection that significantly improves both plan quality and delivery efficiency. Compared to SPArc particle swarm, it enhances the conformity index by 0.16 (p < 0.01), reduces the homogeneity index by 0.71 (p < 0.01), shortens the energy switching time by 38.4% (p < 0.01), and lowers the mean dose to brainstem by 0.21 (p < 0.01). The results unintentionally reveal employing unchanged ELS is more time-wise efficient than descended ELS. SPArcdl's inference time is within 1 second. Significance. SPArcdl is a fast and effective tool for generating high-quality PAT plans by strategically pre-selecting energy layers to reduce delivery time while maintaining excellent dosimetric performance.
Implicit neural representations for accurate estimation of the standard model of white matter
Authors: Tom Hendriks, Gerrit Arends, Edwin Versteeg, Anna Vilanova, Maxime Chamberland, Chantal M. W. Tax
Date: 2025-06-18 00:00:00
Tasks: Diffusion  MRI

Diffusion magnetic resonance imaging (dMRI) enables non-invasive investigation of tissue microstructure. The Standard Model (SM) of white matter aims to disentangle dMRI signal contributions from intra- and extra-axonal water compartments. However, due to the model its high-dimensional nature, extensive acquisition protocols with multiple b-values and diffusion tensor shapes are typically required to mitigate parameter degeneracies. Even then, accurate estimation remains challenging due to noise. This work introduces a novel estimation framework based on implicit neural representations (INRs), which incorporate spatial regularization through the sinusoidal encoding of the input coordinates. The INR method is evaluated on both synthetic and in vivo datasets and compared to parameter estimates using cubic polynomials, supervised neural networks, and nonlinear least squares. Results demonstrate superior accuracy of the INR method in estimating SM parameters, particularly in low signal-to-noise conditions. Additionally, spatial upsampling of the INR can represent the underlying dataset anatomically plausibly in a continuous way, which is unattainable with linear or cubic interpolation. The INR is fully unsupervised, eliminating the need for labeled training data. It achieves fast inference ($\sim$6 minutes), is robust to both Gaussian and Rician noise, supports joint estimation of SM kernel parameters and the fiber orientation distribution function with spherical harmonics orders up to at least 8 and non-negativity constraints, and accommodates spatially varying acquisition protocols caused by magnetic gradient non-uniformities. The combination of these properties along with the possibility to easily adapt the framework to other dMRI models, positions INRs as a potentially important tool for analyzing and interpreting diffusion MRI data.