Journal of Computational Science最新文献

{"title":"Real-time virtual intervention for simple and serial coronary artery disease using the HarVI framework","authors":"Cyrus Tanade,&nbsp;Amanda Randles","doi":"10.1016/j.jocs.2025.102570","DOIUrl":"10.1016/j.jocs.2025.102570","url":null,"abstract":"<div><div>Virtual planning tools that provide intuitive user interaction and immediate hemodynamic feedback are crucial for cardiologists to effectively treat coronary artery disease. Current FDA-approved tools for coronary intervention planning require days of preliminary processing and rely on conventional 2D displays for hemodynamic evaluation. Immersion offered by extended reality (XR) has been found to benefit intervention planning over traditional 2D displays. Building on our previous work (Tanade and Randles, 2024), we introduce HarVI, a coronary intervention planner that leverages machine learning for real-time hemodynamic analysis and extended reality for intuitive 3D user interaction. The framework uses a predefined set of 1D steady state computational fluid dynamics (CFD) simulations to perform one-shot training for our machine learning-based blood flow model. In a two-center cohort of 73 patients, 70 with focal lesions and 3 with serial lesions, we calculated fractional flow reserve — the gold standard biomarker of ischemia in coronary disease, flow rate, and wall shear stress using HarVI and 1D CFD models. HarVI was shown to almost perfectly recapitulate the results of 1D CFD simulations through continuous validation scores. In this study, we establish a machine learning-based process for virtual coronary treatment planning with an average turnaround time of just 62 min — around an order of magnitude improvement over literature standards, thus reducing the required time for one-shot training to less than one working day.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102570"},"PeriodicalIF":3.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of ship motion model based on IPPSA-MTCN-MHSA","authors":"Zhibo Yang,&nbsp;Haozhe Zhang,&nbsp;Xuguo Jiao,&nbsp;Chengxing Lv,&nbsp;Jiyi Sun","doi":"10.1016/j.jocs.2025.102572","DOIUrl":"10.1016/j.jocs.2025.102572","url":null,"abstract":"<div><div>An accurate ship motion model is crucial for predicting ship attitude, preventing accidents, and facilitating autonomous navigation systems. This paper treats ship motion modeling as a sequence modeling task and introduces a hybrid prediction model, termed MTCN-MHSA. The model integrates a Multi-Channel Temporal Convolutional Network (MTCN) and a Multi-Head Self-Attention Mechanism (MHSA). The MTCN, comprised of parallel TCN channels and a Bi-LSTM, extracts and fuses multi-dimensional features from the sequence. The MHSA mechanism is incorporated to minimize feature loss during information transmission, capture dependencies within the sequence, and enhance the model’s expressiveness and generalization capability. To optimize the hyperparameters of the MTCN-MHSA model, an Improved Positional PID-based Search Algorithm (IPPSA) is proposed, which builds upon the PID-based Search Algorithm (PSA). IPPSA exhibits superior global optimization capabilities and convergence speed, effectively identifying the optimal hyperparameters. Extensive comparative modeling experiments utilizing KVLCC2 and KCS ship maneuvering data validate the notable effectiveness and superiority of the proposed IPPSA-MTCN-MHSA model in ship motion prediction.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102572"},"PeriodicalIF":3.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143681938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of the properties of the elasticity modulus in the nasopharynx on the hydrodynamic characteristics of the flow in the upper respiratory tract","authors":"Alibek Issakhov ,&nbsp;Aidana Sabyrkulova ,&nbsp;Aizhan Abylkassymova","doi":"10.1016/j.jocs.2025.102576","DOIUrl":"10.1016/j.jocs.2025.102576","url":null,"abstract":"<div><div>In this study, the influence of the elasticity modulus (5–25 kPa) and inlet boundary conditions on the distribution of velocity, pressure, shear stress and strain in the upper airways was investigated using computational fluid dynamics (CFD) and fluid-structure interaction (FSI) models. Sinusoidal velocity profiles at the entrance to the nasal sinuses with oscillation amplitudes of 1.2 m/s, 2.4 m/s, 3.6 m/s were considered. The results show that the maximum value of deformation in the nasopharyngeal region occurred at a value of Young's modulus of 5 kPa, and values from 15 to 25 kPa gave deformation values lower by more than 20 % and had insignificant differences. In addition, the CFD model showed higher pressure and shear stress values than the FSI model, and the maximum velocity of the FSI models was higher than that of the CFD model. This study provides new data on the effect of modulus and inlet boundary conditions on velocity, pressure, shear stress, and strain distributions in the upper airways.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102576"},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143681882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A fast temporal second-order compact finite difference method for two-dimensional parabolic integro-differential equations with weakly singular kernel","authors":"Zi-Yun Zheng,&nbsp;Yuan-Ming Wang","doi":"10.1016/j.jocs.2025.102558","DOIUrl":"10.1016/j.jocs.2025.102558","url":null,"abstract":"<div><div>We propose a fast temporal second-order compact finite difference method for solving a class of two-dimensional parabolic integro-differential equations with weakly singular kernel. The sum-of-exponentials approximation of the kernel function is combined with the product averaged integration rule to approximate the weakly singular integral term, and the fourth-order compact finite difference method is employed to discretize the spatial derivative operator. We use the discrete energy technique to rigorously prove that the proposed fast method is almost unconditionally stable and convergent. Compared with the direct method, the fast method significantly reduces storage and computational costs while maintaining the temporal second-order convergence and spatial fourth-order convergence for weakly singular solutions. Some comparisons with the fast method using the exponential-sum-approximation technique, the fast Runge–Kutta convolution quadrature method and the explicit fast method based on the sum-of-exponentials approximation are discussed. The numerical results confirm the results of theoretical analysis and demonstrate the computational efficiency of the fast method.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102558"},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards universal MPI bindings for enhanced new language support","authors":"César Piñeiro ,&nbsp;Álvaro Vázquez ,&nbsp;Juan C. Pichel","doi":"10.1016/j.jocs.2025.102557","DOIUrl":"10.1016/j.jocs.2025.102557","url":null,"abstract":"<div><div>In the field of High Performance Computing (HPC), Message Passing Interface (MPI) is the most widely used and prevalent programming model. Only the low-level programming languages C, C++, and Fortran have bindings available in the standard. Although there are attempts to provide MPI bindings for other programming languages, these may be limited, which could lead to incompatibilities, performance overhead, and functional gaps. To address those problems, we present MPI4All, a brand-new tool designed to make the process of developing effective MPI bindings for any programming language more straightforward. Support for additional languages can be added with little difficulty, and MPI4All is independent of the MPI implementation. Programming language binding generators for Go and Java are included in the most recent version of MPI4All. We demonstrate their good performance results with respect to other state-of-the-art approaches. This work is an extended version of the ICCS-2024 conference paper (Piñeiro et al., 2024).</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102557"},"PeriodicalIF":3.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AJAS: A high performance direct solver for advancing high precision astrometry","authors":"Konstantin Ryabinin,&nbsp;Gerasimos Sarras,&nbsp;Wolfgang Löffler,&nbsp;Olga Erokhina,&nbsp;Michael Biermann","doi":"10.1016/j.jocs.2025.102554","DOIUrl":"10.1016/j.jocs.2025.102554","url":null,"abstract":"<div><div>In astrometry, the determination of three-dimensional positions and velocities of stars based on observations from a space telescope suffers from the uncertainty of random and systematic errors. The systematic errors are introduced by imperfections of the telescope’s optics and detectors as well as in the pointing accuracy of the satellite. The fine art of astrometry consists of heuristically finding the best possible calibration model that will account for and remove these systematic errors. Since this is a process based on trial and error, appropriate software is needed that is efficient enough to solve the system of astrometric equations and reveal the astrometric parameters of stars for the given calibration model within a reasonable time. This paper is an extended version of the conference paper published and discussed at the International Conference on Computational Science 2024. In this work, we propose a novel software architecture and corresponding prototype of a direct solver optimized for running on supercomputers. The main advantages expected from this direct method over an iterative one are the numerical robustness, accuracy of the method, and the explicit calculation of the variance–covariance matrix for the estimation of the accuracy and correlation of the unknown parameters. This solver can handle astrometric systems with billions of equations within several hours. To reach the desired performance, we use state-of-the-art libraries and methods for hybrid parallel and vectorized computing. The calibration model based on Legendre polynomials is tested by generating synthetic observations on grid-shaped constellation with specified distortions. For these small-sized test data, the solver can recover perfectly the correct physical solution under the condition that the correct amount of eigenvalues is zeroed out. During the space mission, the calibration model should be carefully fine-tuned according to the real operating conditions. The developed solver is furthermore tested using mock science data related to the Japan Astrometry Satellite Mission for Infrared Exploration. Up to 9.2 billion observations of 115 thousand stars can be processed in 8.5 h utilizing 5000 CPUs. A linear scaling with the number of CPUs and a quadratic scaling with the number of observations is demonstrated.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102554"},"PeriodicalIF":3.1,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143592646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of blood-related parameters for hyperthermia-based treatments for cancer","authors":"Gustavo Resende Fatigate ,&nbsp;Gustavo Coelho Martins ,&nbsp;Marcelo Lobosco ,&nbsp;Ruy Freitas Reis","doi":"10.1016/j.jocs.2025.102556","DOIUrl":"10.1016/j.jocs.2025.102556","url":null,"abstract":"<div><div>Hyperthermia is a cancer treatment method that uses controlled heat to induce tumor necrosis while preserving healthy tissue. This study uses computational simulations to investigate the effects of capillary network variability and blood flow dynamics on the thermal response during hyperthermia. A porous media bioheat model, coupled with uncertainty quantification (UQ) techniques using Monte Carlo simulations, was developed to analyze the influence of capillary angles, blood velocity, and capillary density on temperature distribution in biological tissues. The model demonstrates that under a range of physiological uncertainties, tumor tissues consistently reach the critical damage threshold temperature of <span><math><mrow><mn>4</mn><msup><mrow><mn>3</mn></mrow><mrow><mo>∘</mo></mrow></msup><mi>C</mi></mrow></math></span>, while healthy tissues remain below <span><math><mrow><mn>3</mn><msup><mrow><mn>8</mn></mrow><mrow><mo>∘</mo></mrow></msup><mi>C</mi></mrow></math></span>, minimizing collateral damage. To address the computational intensity of solving three-dimensional heat transfer equations with UQ analysis, high-performance computing methods were employed. A parallel implementation using CUDA achieved a speedup exceeding <span><math><mrow><mn>114</mn><mo>×</mo></mrow></math></span> compared to serial processing, while OpenMP achieved a <span><math><mrow><mn>16</mn><mo>×</mo></mrow></math></span> speedup.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102556"},"PeriodicalIF":3.1,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143576747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishing a massively parallel computational model of the adaptive immune response","authors":"Aristotle Martin,&nbsp;Max Nezdyur,&nbsp;Cyrus Tanade,&nbsp;Amanda Randles","doi":"10.1016/j.jocs.2025.102555","DOIUrl":"10.1016/j.jocs.2025.102555","url":null,"abstract":"<div><div>Parallel agent-based models of the adaptive immune response can efficiently recapitulate emerging spatiotemporal properties of T-cell motility during clonal selection across multiple length and time scales. Here, we present a distributed, three-dimensional (3D) computational model of T-cell priming, and associated parallel data structures and algorithms that enable fully deterministic cell simulations at scale. We demonstrate performant usage of modern clusters with over 350x speedup, and explore trade-offs between simulation accuracy, code complexity, and communication overhead. This study highlights the potential for parallel 3D models to explore immunological research questions and guides implementation and performance considerations for this class of biology-inspired agent-based models.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"87 ","pages":"Article 102555"},"PeriodicalIF":3.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unsupervised continual learning by cross-level, instance-group and pseudo-group discrimination with hard attention","authors":"Ankit Malviya,&nbsp;Sayak Dhole,&nbsp;Chandresh Kumar Maurya","doi":"10.1016/j.jocs.2025.102535","DOIUrl":"10.1016/j.jocs.2025.102535","url":null,"abstract":"<div><div>Extensive work has been done in supervised continual learning (SCL) , wherein models adapt to changing distributions with labeled data while mitigating catastrophic forgetting. However, this approach diverges from real-world scenarios where labeled data is scarce or non-existent. Unsupervised continual learning (UCL) emerges to bridge this disparity. Previous research has explored methods for unsupervised continuous feature learning by incorporating rehearsal to alleviate the problem of catastrophic forgetting. Although these techniques are effective, they may not be feasible for scenarios where storing training data is impractical. Moreover, rehearsal techniques may confront challenges pertaining to representation drifts and overfitting, particularly under limited buffer size conditions. To address these drawbacks, we employ parameter isolation as a strategy to mitigate forgetting. Specifically, we use task-specific hard attention to prevent updates to parameters important for previous tasks. In contrastive learning, loss is prone to be negatively affected by a reduction in the diversity of negative samples. Therefore, we incorporate instance-to-instance similarity into contrastive learning through both direct instance grouping and discrimination at the cross-level with local instance groups, as well as with local pseudo-instance groups. The masked model learns the features using cross-level discrimination, which naturally clusters similar data in the representation space. Extensive experimentation demonstrates that our proposed approach outperforms current state-of-the-art (SOTA) baselines by significant margins, all while exhibiting minimal or nearly zero forgetting, and without the need for any rehearsal buffer. Additionally, the model learns distinct task boundaries. It achieves an overall-average task and class incremental learning (TIL &amp; CIL) accuracy of 76.79% and 62.96% respectively with nearly zero forgetting, across standard datasets for varying task sequences ranging from 5 to 100. This surpasses SOTA baselines, which only reach 74.28% and 60.68% respectively in the UCL setting, where they experience substantial forgetting of almost over 4%. Moreover, our approach achieves performance nearly comparable to the SCL baseline and even surpasses it on some standard datasets, with a notable reduction in forgetting from almost 14.51% to nearly zero.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"86 ","pages":"Article 102535"},"PeriodicalIF":3.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143465131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A cluster-based opposition differential evolution algorithm boosted by a local search for ECG signal classification","authors":"Mehran Pourvahab ,&nbsp;Seyed Jalaleddin Mousavirad ,&nbsp;Virginie Felizardo ,&nbsp;Nuno Pombo ,&nbsp;Henriques Zacarias ,&nbsp;Hamzeh Mohammadigheymasi ,&nbsp;Sebastião Pais ,&nbsp;Seyed Nooreddin Jafari ,&nbsp;Nuno M. Garcia","doi":"10.1016/j.jocs.2025.102541","DOIUrl":"10.1016/j.jocs.2025.102541","url":null,"abstract":"<div><div>Electrocardiogram (ECG) signals, which capturethe heart's electrical activity, are used to diagnose and monitor cardiac problems. The accurate classification of ECG signals, particularly for distinguishing among various types of arrhythmias and myocardial infarctions, is crucial for the early detection and treatment of heart-related diseases. This paper proposes a novel approach based on an improved differential evolution (DE) algorithm for ECG signal classification for enhancing the performance. In the initial stages of our approach, the preprocessing step is followed by the extraction of several significant features from the ECG signals. These extracted features are then provided as inputs to an enhanced multi-layer perceptron (MLP). While MLPs are still widely used for ECG signal classification, using gradient-based training methods, the most widely used algorithm for the training process, has significant disadvantages, such as the possibility of being stuck in local optimums. This paper employs an enhanced differential evolution (DE) algorithm for the training process as one of the most effective population-based algorithms. To this end, we improved DE based on a clustering-based strategy, opposition-based learning, and a local search. Clustering-based strategies can act as crossover operators, while the goal of the opposition operator is to improve the exploration of the DE algorithm. The weights and biases found by the improved DE algorithm are then fed into six gradient-based local search algorithms. In other words, the weights found by the DE are employed as an initialization point. Therefore, we introduced six different algorithms for the training process (in terms of different local search algorithms). In an extensive set of experiments, we showed that our proposed training algorithm could provide better results than the conventional training algorithms.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"86 ","pages":"Article 102541"},"PeriodicalIF":3.1,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}