4.5 Editorial Material

Computational science for a better future

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Article Computer Science, Interdisciplinary Applications

Rational interpolation of the one-way Helmholtz propagator

Mikhail S. Lytaev

Summary: This study focuses on higher-order finite-difference numerical methods for solving the pseudo-differential parabolic equation in diffraction theory. It proposes using a rational approximation of exponential propagation on an interval instead of Pade approximation near a point. The advantages and disadvantages of three variants of rational approximation on the interval are analyzed, and the proposed method is shown to have advantages in the context of tropospheric radio-wave propagation and underwater acoustics. The study provides numerical examples and comparisons to demonstrate the benefits of the proposed approach.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Topology-based characterization of chemically-induced pore space changes using reduction of 3D digital images

Dmitry Prokhorov et al.

Summary: This study presents an algorithm for pore-scale simulation of reactive transport in a 3D case. The algorithm allows observation of pore space changes and estimation of macroscopic properties. Additionally, a algorithm to compute persistence diagrams for independent cycles in the pore space is developed to quantitatively characterize changes in pore space topology.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

PDE patch-based surface reconstruction from point clouds

Zaiping Zhu et al.

Summary: By extending the work published at ICCS 2021 by Zhu et al. (2021), this paper proposes a new method for reconstructing complex 3D shapes from point clouds using multiple explicit PDE surface patches. The method involves segmenting the point cloud into subsets, parameterizing the points, and fitting PDE patches to reconstruct the 3D shapes. Several surface reconstruction examples are provided to demonstrate the superiority of the proposed method compared to polygon-based surface reconstruction in terms of design variables and quality.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Big data for human security: The case of COVID-19

Pedro Cardenas et al.

Summary: The COVID-19 epidemic has brought about significant changes and challenges in health, economy, and public order. Governments' measures to contain the pandemic have resulted in social unrest and threats to human security. Big data analytics can support policymakers in addressing the virus and social unrest.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

MaMiCo: Non-local means and POD filtering with flexible data-flow for molecular-continuum HPC flow simulation

Piet Jarmatz et al.

Summary: In this paper, we propose a method for achieving stable coupling in fluid dynamics using noise filtering, and apply the Non-Local Means filtering technique in a novel space-time formulation to particle data. Our experiments on various flow scenarios and continuum solvers demonstrate that the Non-Local Means filtering not only improves the signal-to-noise ratio when extracting macroscopic flow information from particle ensembles, but also benefits transient two-way coupling.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Technical solution to counter potential crime: Text analysis to detect fake news and disinformation

Rafal Kozik et al.

Summary: This paper proposes a hybrid approach for detecting fake news, which bundles several smaller models using meta-learning techniques, aiming to solve the challenge of transferring NLP-based solutions to different domains.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Timing the race of vaccination, new variants, and relaxing restrictions during COVID-19 pandemic

Carolina Ribeiro Xavier et al.

Summary: This study used an extended SIRD model to evaluate the impact of the Delta variant in Germany, Israel, and Brazil, considering vaccination and mitigation policies. The results showed that the transmission rate of the Delta variant was highest in Israel, followed by Germany and Brazil. The study found that both vaccination and mitigation policies were crucial in reducing the spread and the number of deaths during the Delta wave.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Transfer learning-based UWB indoor localization using MHT-MDC and clusterization-based sparse fingerprinting

Barbara Morawska et al.

Summary: Indoor localization systems, especially Ultra-wideband (UWB), have gained popularity for their low cost and high accuracy. However, the accuracy of leading UWB systems often falls short of the claimed values. To address this issue, we propose a Multiple Hypothesis Tracker with Direction Motion Constraint (MHT-MDC) algorithm and a transfer learning approach. By training the neural network using fingerprinting in a controlled environment, and utilizing transfer learning, we can achieve high localization accuracy even with a small percentage of fingerprinting samples.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

On reaching the consensus by disagreeing

Tomasz Weron et al.

Summary: This study extends the research on the Sznajd model conducted by Weron and Sznajd-Weron (2021) by adding parameters and introducing agent movement to further generalize the model. Through Monte Carlo simulations, we demonstrate that the intriguing results, summarized as 'Better disagree with your neighbor', are also valid for the model with movement.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Demonstrating the viability of Lagrangian in situ reduction on supercomputers

Sudhanshu Sane et al.

Summary: This study evaluates the viability and effectiveness of Lagrangian analysis for reducing data in large-scale computational science applications. By exploring cosmology, seismology, and hydrodynamics applications, as well as conducting performance benchmarking in different environments, we demonstrate that Lagrangian analysis can significantly reduce data while maintaining accurate reconstruction, with minimal impact on total execution time.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Analysis of Vector Particle-In-Cell (VPIC) memory usage optimizations on cutting-edge computer architectures

Nigel Tan et al.

Summary: This paper discusses a suite of VPIC memory optimizations that significantly increase the number of particles in VPIC simulations, and evaluates their impact on performance for different computer architectures.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

A creative chain coding technique for bi-level image compression inspired by the NetLogo HIV agent-based modeling simulation

Khaldoon Dhou et al.

Summary: This paper presents a chain coding application based on an agent-based model for image compression. The method converts the image into a virtual environment and utilizes relative coding to achieve better compression ratios. The results show that this method outperforms other benchmarks and has statistically significant differences.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Surrogate-assisted performance prediction for data-driven knowledge discovery algorithms: Application to evolutionary modeling of clinical pathways

Anastasia A. Funkner et al.

Summary: This paper proposes and investigates an approach for surrogate-assisted performance prediction of data-driven knowledge discovery algorithms. The approach is applied to the discovery of clinical pathways and uses surrogate models to predict the quality and performance of the target algorithm. An analytical software prototype is developed to provide a more interpretable prediction of the algorithm's performance and quality.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Multi-phase compositional modeling in porous media using iterative IMPEC scheme and constant volume-temperature flash

Tomas Smejkal et al.

Summary: In this paper, a numerical solution for the multi-phase compressible Darcy's flow of a multi-component mixture in a porous medium is presented. The mathematical model includes mass conservation equations for each component, extended Darcy's law for each phase, and appropriate initial and boundary conditions. The phase split is calculated using the phase equilibrium computation in the VTN-flash method. The transport equations are solved numerically using the mixed-hybrid finite element method and an iterative IMPEC scheme. The convergence of the numerical scheme is verified using the experimental orders of convergence (EOC). This is an extended version of a conference paper.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

From Missing Data Imputation to Data Generation

Diogo Telmo Neves et al.

Summary: This paper introduces three novel data imputation methods based on Generative Adversarial Networks (GAN), which play an important role in generating synthetic datasets. It also investigates how data imputation methods can help mitigate legal, ethical, and data privacy issues, as well as augment original data. Through experimental evaluation, it is found that these new methods perform well in incomplete data imputation.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Interdisciplinary curriculum for computational neuroscience at primarily undergraduate institutions

Sorinel A. Oprisan

Summary: Developing interdisciplinary undergraduate courses is challenging but beneficial for undergraduates. This study introduces a course called Biophysical Modeling of Excitable Cells (BMEC), which exposes students to computational biology, promotes scientific literacy, and encourages teamwork between different disciplines.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Estimation of wildfire wind conditions via perimeter and surface area optimization

Li Tan et al.

Summary: This paper proposes a method to improve wildfire progression prediction by estimating a single prevailing wind vector using grid search and optimization techniques. The method is validated using measured wildfire perimeters and demonstrated on two historical wildfire events.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Weighted Ensemble with one-class Classification and Over-sampling and Instance selection (WECOI): An approach for learning from imbalanced data streams

Ireneusz Czarnowski

Summary: This paper proposes a new approach for learning from data streams to tackle the problem of class-imbalanced data. By using weighted ensemble, over-sampling, and instance selection techniques, the class distribution is changed to achieve a more balanced dataset. The experimental results demonstrate that the proposed approach can enhance the performance of online learning algorithms.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Scalable large-scale multi-physics earthquake simulation on multiple GPUs with stabilization

Ryota Kusakabe et al.

Summary: In this study, a non-local approach was used to stabilize a high-resolution large-scale multi-physics earthquake simulation, achieving a resolution of 0.1 m and high weak scalability.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing

Julian Cascitti et al.

Summary: RNACache is a novel approach based on context-aware locality sensitive hashing for detecting local similarities between transcriptomes and RNA-seq reads. It consists of a three-step processing pipeline that accurately identifies truly expressed transcript isoforms and offers better performance and scalability compared to other lightweight mapping tools.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Computer Science, Interdisciplinary Applications

Automatic grouping of production data in Industry 4.0: The use case of internal logistics systems based on Automated Guided Vehicles

Tomasz Steclik et al.

Summary: This paper presents a method for automatically detecting the types of work performed by AGVs based on streaming information, and compares the results obtained using two clustering algorithms. The results show that the proposed method can automatically detect AGV work types and identify new types. This method can be used for production optimization, predictive maintenance, production technology verification, and more.

JOURNAL OF COMPUTATIONAL SCIENCE (2022)

Article Multidisciplinary Sciences

Uncertainty quantification of a three-dimensional in-stent restenosis model with surrogate modelling

Dongwei Ye et al.

Summary: This study presents an uncertainty quantification of a model for in-stent restenosis, focusing on four uncertain parameters: endothelium regeneration time, the threshold strain for smooth muscle bond breaking, blood flow velocity, and the percentage of fenestration in the internal elastic lamina. By developing a surrogate model based on Gaussian process regression with proper orthogonal decomposition, the researchers were able to evaluate the model response in the uncertainty quantification. The results showed that the level of fenestration primarily determines the uncertainty in neointimal growth at the initial stage, while blood flow velocity and endothelium regeneration time play a key role in determining the uncertainty at later clinically relevant stages of the restenosis process.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2022)

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20 years of computational science: Selected papers from 2020 International Conference on Computational Science

Sergey V. Kovalchuk et al.

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Praxis of Reproducible Computational Science

Lorena A. Barba

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Analysis of publication activity of computational science society in 2001-2017 using topic modelling and graph theory

Tesfamariam M. Abuhay et al.

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Big Data computing and clouds: Trends and future directions

Marcos D. Assuncao et al.

JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING (2015)

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Generalizing Surrogate-Assisted Evolutionary Computation

Dudy Lim et al.

IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION (2010)

Editorial Material Computer Science, Interdisciplinary Applications

Preface

Peter Sloot et al.

JOURNAL OF COMPUTATIONAL SCIENCE (2010)