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arXiv 2025年

作者： Cheng, Sibo Bocquet, Marc Ding, Weiping Finn, Tobias Sebastian Fu, Rui Fu, Jinlong Guo, Yike Johnson, Eleda Li, Siyi Liu, Che Moro, Eric Newton Pan, Jie Piggott, Matthew Quilodran, Cesar Sharma, Prakhar Wang, Kun Xiao, Dunhui Xue, Xiao Zeng, Yong Zhang, Mingrui Zhou, Hao Zhu, Kewei Arcucci, Rossella CEREA ENPC EDF R&D Institut Polytechnique de Paris Île-de-France France School of Artificial Intelligence and Computer Science Nantong University Jiangsu Nantong226019 China School of Mathematical Sciences Key Laboratory of Intelligent Computing and Applications Tongji University Shanghai200092 China School of Engineering and Materials Science Faculty of Science and Engineering Queen Mary University of London LondonE1 4NS United Kingdom Zienkiewicz Centre for Modelling Data and AI Faculty of Science and Engineering Swansea University SwanseaSA1 8EN United Kingdom Department of Computer Science and Engineering Hong Kong university of science and technology Hong Kong Department of Earth Science & Engineering Imperial College London LondonSW7 2AZ United Kingdom Tianjin Key Laboratory of Imaging and Sensing Microelectronics Technology School of Microelectronics Tianjin University Tianjin300072 China Centre for Health Informatics Cumming School of Medicine University of Calgary CalgaryABT2N 1N4 Canada Department of Community Health Sciences Cumming School of Medicine University of Calgary CalgaryABT2N 1N4 Canada Undaunted Grantham Institute for Climate Change and the Environment Imperial College London LondonSW7 2AZ United Kingdom Culham Campus AbingdonOX14 3DB United Kingdom Centre for Computational Science Department of Chemistry University College London LondonWC1E 6BT United Kingdom Concordia Institute for Information Systems Engineering Concordia University MontrealQCH3G 1M8 Canada School of Mechanical Medical and Process Engineering Faculty of Engineering Queensland University of Technology BrisbaneQLD Australia Department of Chemical Engineering University College London LondonWC1E 6BT United Kingdom

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. © 2025, CC BY-NC-SA.

关键词： Mesh generation

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Neural mechanisms of top-down divided and selective spatial attention in visual and auditory perception

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Brain science Advances 2023年第2期9卷 95-113页

作者： Zhongtian Guan Meng Lin Qiong Wu Jinglong Wu Kewei Chen Hongbin Han Dehua Chui Xu Zhang Chunlin Li School of Biomedical Engineering Capital Medical UniversityBeijing 100069China Beijing Advanced Innovation Center for Big Data-based Precision Medicine Capital Medical UniversityBeijing 100069China Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application Capital Medical UniversityBeijing 100069China Peking University First Hospital Beijing 100034China Biomedical Engineering Laboratory Graduate School of Natural Science and TechnologyOkayama University3-1-1 Tsushima-nakaOkayamaJapan Key Laboratory of Biomimetic Robots and Systems Ministry of EducationBeijing Institute of TechnologyBeijing 100081China Computational Image Analysis Banner Alzheimer’s Institute and Banner Good Samaritan Medical CentrePET CentrePhoenixAZ 85006USA Radiology Peking University Third HospitalBeijing 100191China Neuroscience Research Institute/Peking University Third Hospital Beijing 100191China

Top-down attention mechanisms require the selection of specificobjects or locations;however,the brain mechanism involved when attention is allocated across different modalities is not well *** aim of this study was to use functional magnetic resonance imaging to define the neural mechanisms underlyingdivided and selective spatial attention.A concurrent audiovisual stimulus was used,and subjects were prompted to focus on a visual,auditory and audiovisual stimulus in a Posner *** results confirmed the better performance of selectiveattention compared to devided *** found differences in the activation level of the frontoparietal network,visual/auditorycortex,the putamen and the salience network under differentattention *** further used Granger causality(GC)toexplore effective connectivity differences between *** in GC connectivity between visual and auditory selective tasksreflected the visual dominance effect under spatial *** addition,our results supported the role of the putamen inredistributing attention and the functional separation of the *** summary,we explored the audiovisual top-down allocation of attention and observed the differences in neuralmechanisms under endogenous attention modes,which revealedthe differences in cross-modal expression in visual and auditory attention under attentional modulation.

关键词： top-down mechanism divided spatial attention selective spatial attention fMRI Granger causality

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Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers

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Informatics in Medicine Unlocked 2023年 42卷

作者： Azim, Sayed Mehedi Sabab, Noor Hossain Nuri Noshadi, Iman Alinejad-Rokny, Hamid Sharma, Alok Shatabda, Swakkhar Dehzangi, Iman Center for Computational and Integrative Biology Rutgers University Camden 08102 NJ United States Department of Computer Science and Engineering United International University Plot 2 United City Madani Avenue BaddaDhaka 1212 Bangladesh Department of Bioengineering University of California Riverside 92507 CA United States BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering The University of New South Wales (UNSW Sydney) Sydney NSW 2052 Australia UNSW Data Science Hub UNSW Sydney Sydney NSW 2052 Australia Health Data Analytics Program AI-enabled Processes Research Centre Macquarie University Sydney 2109 Australia Institute for Integrated and Intelligent Systems Griffith University Brisbane Australia Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230-0045 Japan Department of Computer Science Rutgers University Camden 08102 NJ United States

The use of therapeutic peptides for the treatment of cancer has received tremendous attention in recent years. Anticancer peptides (ACPs) are considered new anticancer drugs which have several advantages over chemistry-based drugs including high specificity, strong tumor penetration capacity, and low toxicity level for normal cells. Due to the rise of experimentally verified bioactive peptides, several in silico approaches became imperative for the investigation of the characteristics of ACPs. In this paper, we proposed a new machine learning tool named iACP-RF that uses a combination of several sequence-based features and an ensemble of three heterogeneously trained Random Forest classifiers to accurately predict anticancer peptides. Experimental results show that our proposed model achieves an accuracy of 75.9% which outperforms other state-of-the-art methods by a significant margin. We also achieve 0.52, 75.6%, and 76.2% in terms of Matthews Correlation Coefficient (MCC), Sensitivity, and Specificity, respectively. iACP-RF as a standalone tool and its source code are publicly available at: https://***/MLBC-lab/iACP-RF. © 2023 The Authors

关键词： Anticancer peptides Ensemble learning Feature extraction Heterogeneous classifiers Machine learning Random Forest

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Differentiable Programming for Differential Equations: A Review

arXiv

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arXiv 2024年

作者： Sapienza, Facundo Bolibar, Jordi Schäfer, Frank Groenke, Brian Pal, Avik Boussange, Victor Heimbach, Patrick Hooker, Giles Pérez, Fernando Persson, Per-Olof Rackauckas, Christopher Department of Statistics University of California Berkeley United States Univ. Grenoble Alpes CNRS IRD G-INP Institut des Géosciences de l’Environnement Grenoble France TU Delft Department of Geosciences and Civil Engineering Delft Netherlands CSAIL Massachusetts Institute of Technology Cambridge United States TU Berlin Department of Electrical and Computer Engineering Berlin Germany Helmholtz Centre for Environmental Research Leipzig Germany Swiss Federal Research Institute WSL Birmensdorf Switzerland Oden Institute for Computational Engineering and Sciences University of Texas Austin United States Jackson School of Geosciences University of Texas Austin United States Department of Statistics and Data Science University of Pennsylvania United States Department of Mathematics University of California Berkeley United States Massachusetts Institute of Technology Cambridge United States JuliaHub Cambridge United States

The differentiable programming paradigm is a cornerstone of modern scientific computing. It refers to numerical methods for computing the gradient of a numerical model’s output. Many scientific models are based on differential equations, where differentiable programming plays a crucial role in calculating model sensitivities, inverting model parameters, and training hybrid models that combine differential equations with data-driven approaches. Furthermore, recognizing the strong synergies between inverse methods and machine learning offers the opportunity to establish a coherent framework applicable to both fields. Differentiating functions based on the numerical solution of differential equations is nontrivial. Numerous methods based on a wide variety of paradigms have been proposed in the literature, each with pros and cons specific to the type of problem investigated. Here, we provide a comprehensive review of existing techniques to compute derivatives of numerical solutions of differential equations. We first discuss the importance of gradients of solutions of differential equations in a variety of scientific domains. Second, we lay out the mathematical foundations of the various approaches and compare them with each other. Third, we cover the computational considerations and explore the solutions available in modern scientific software. Last but not least, we provide best-practices and recommendations for practitioners. We hope that this work accelerates the fusion of scientific models and data, and fosters a modern approach to scientific *** Codes 34-04, 49K40, 65D25, 65L09, 65M32, 86A22, 90C31 © 2024, CC BY.

关键词： Differential equations

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Tensor completion via gaussian process based initialization

arXiv

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arXiv 2019年

作者： Kapushev, Yermek Oseledets, Ivan Burnaev, Evgeny Center for Computational and Data-Intensive Science Engineering of Skolkovo Institute of Science and Technology Moscow Russia

In this paper, we consider the tensor completion problem representing the solution in the tensor train (TT) format. It is assumed that tensor is high-dimensional, and tensor values are generated by an unknown smooth function. The assumption allows us to develop an efficient initialization scheme based on Gaussian Process Regression and TT-cross approximation technique. The proposed approach can be used in conjunction with any optimization algorithm that is usually utilized in tensor completion problems. We empirically justify that in this case the reconstruction error improves compared to the tensor completion with random initialization. As an additional benefit, our technique automatically selects rank thanks to using the TT-cross approximation *** Codes 68W25, 65F99, 60G15 Copyright © 2019, The Authors. All rights reserved.

关键词： Tensors

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Gaussian polymer chains in a harmonic potential: The path integral approach

arXiv

引用

arXiv 2020年

作者： Paradezhenko, G.V. Gascoigne, C. Brilliantov, N.V. Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow121205 Russia Department of Mathematical Sciences University of Bath Claverton Down BathBA2 7AY United Kingdom

We study conformations of the Gaussian polymer chains in d-dimensional space in the presence of an external field with the harmonic potential. We apply a path integral approach to derive an explicit expression for the probability distribution function of the gyration radius. We calculate this function using Monte Carlo simulations and show that our numerical and theoretical results are in a good agreement for different values of the external *** Codes 82D60, 82M31 Copyright © 2020, The Authors. All rights reserved.

关键词： Monte Carlo methods

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Complex diffusion-based kinetics of photoluminescence in semiconductor nanoplatelets

arXiv

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arXiv 2021年

作者： Kurilovich, Aleksandr A. Mantsevich, Vladimir N. Stevenson, Keith J. Chechkin, Aleksei V. Palyulin, Vladimir V. Center for Energy Science and Technology Skolkovo Institute of Science and Technology Moscow121205 Russia Semiconductors and Cryoelectronics & Quantum Technology Center Physics department Lomonosov Moscow State University Moscow119991 Russia Institute for Physics & Astronomy University of Potsdam Potsdam-GolmD-14476 Germany Akhiezer Institute for Theoretical Physics National Science Center Kharkov Institute of Physics and Technology Kharkov61108 Ukraine Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow121205 Russia

We present a diffusion-based simulation and theoretical models for explanation of photoluminescence (PL) emission intensity in semiconductor nanoplatelets. It is shown that the shape of PL intensity curves can be reproduced by the interplay of recombination, diffusion and trapping of excitons. The emission intensity at short times is purely exponential and is defined by recombination. At long times it is governed by the release of excitons from surface traps and is characterized by a power-law tail. We show that the crossover from one limit to another is controlled by diffusion properties. This intermediate region exhibits a rich behaviour depending on the value of diffusivity. Proposed approach reproduces all the features of experimental curves measured for different nanoplatelet systems. Copyright © 2021, The Authors. All rights reserved.

关键词： Diffusion

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Automatic Diagnosis of Myocarditis Disease in Cardiac MRI Modality using Deep Transformers and Explainable Artificial Intelligence

arXiv

引用

arXiv 2022年

作者： Jafari, Mahboobeh Shoeibi, Afshin Ghassemi, Navid Heras, Jonathan Ling, Sai Ho Beheshti, Amin Zhang, Yu-Dong Wang, Shui-Hua Alizadehsani, Roohallah Gorriz, Juan M. Acharya, U. Rajendra Rokny, Hamid Alinejad Internship in BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia Data Science and Computational Intelligence Institute University of Granada Spain Department of Mathematics and Computer Science University of La Rioja La Rioja Spain Australia Data Analytics Lab Department of Computing Macquarie University SydneyNSW2109 Australia School of Computing and Mathematical Sciences University of Leicester Leicester United Kingdom Deakin University VIC3217 Australia Department of Psychiatry University of Cambridge United Kingdom School of Mathematics Physics and Computing University of Southern Queensland Springfield Australia BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia UNSW Data Science Hub The University of New South Wales SydneyNSW2052 Australia Research Centre Macquarie University Sydney2109 Australia

Myocarditis is a significant cardiovascular disease (CVD) that poses a threat to the health of many individuals by causing damage to the myocardium. The occurrence of microbes and viruses, including the likes of HIV, plays a crucial role in the development of myocarditis disease (MCD). The images produced during cardiac magnetic resonance imaging (CMRI) scans are low contrast, which can make it challenging to diagnose cardiovascular diseases. In other hand, checking numerous CMRI slices for each CVD patient can be a challenging task for medical doctors. To overcome the existing challenges, researchers have suggested the use of artificial intelligence (AI)-based computer-aided diagnosis systems (CADS). The presented paper outlines a CADS for the detection of MCD from CMR images, utilizing deep learning (DL) methods. The proposed CADS consists of several steps, including dataset, preprocessing, feature extraction, classification, and post-processing. First, the Z-Alizadeh dataset was selected for the experiments. Subsequently, the CMR images underwent various preprocessing steps, including denoising, resizing, as well as data augmentation (DA) via CutMix and MixUp techniques. In the following, the most current deep pre-trained and transformer models are used for feature extraction and classification on the CMR images. The findings of our study reveal that transformer models exhibit superior performance in detecting MCD as opposed to pre-trained architectures. In terms of DL architectures, the Turbulence Neural Transformer (TNT) model exhibited impressive accuracy, reaching 99.73% utilizing a 10-fold cross-validation approach. Additionally, to pinpoint areas of suspicion for MCD in CMRI images, the Explainable-based Grad Cam method was employed. © 2022, CC BY-NC-ND.

关键词： Diseases

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New lower bound on the rate of traceability set systems

New lower bound on the rate of traceability set systems

引用

International Symposium on Problems of Redundancy in Information and Control Systems (RED)

作者： Elena Egorova Ilya Vorobyev Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow Russia 127051

In this paper a new lower bound on the rate of IPP set systems with traceability property is proved. The new bound outperforms the previously known bounds.

ISBN: (数字)9781728119441

ISBN: (纸本)9781728119458

In this paper a new lower bound on the rate of IPP set systems with traceability property is proved. The new bound outperforms the previously known bounds.

关键词： Decoding Redundancy Encryption Control systems Hamming distance

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Towards Understanding of eSports Athletes' Potentialities: The Sensing System for data Collection and Analysis

Towards Understanding of eSports Athletes' Potentialities: T...

引用

Symposia and Workshops on Ubiquitous, Autonomic and Trusted Computing, UIC-ATC

作者： Alexander Korotin Nikita Khromov Anton Stepanov Andrey Lange Evgeny Burnaev Andrey Somov Center for Computational and Data-Intensive Science and Engineering (CDISE) Skolkovo Institute of Science and Technology Moscow Russia

ISBN: (数字)9781728140346

ISBN: (纸本)9781728140353

eSports is a developing multidisciplinary research area. At present, there is a lack of relevant data collected from real eSports athletes and lack of platforms which could be used for the data collection and further analysis. In this paper, we present a sensing system for enabling the data collection from professional athletes. Also, we report on the case study about collecting and analyzing the gaze data from Monolith professional eSports team specializing in Counter-Strike: Global Offensive (CS:GO) discipline. We perform a comparative study on assessing the gaze of amateur players and professional athletes. The results of our work are vital for ensuring eSports data collection and the following analysis in the scope of scouting or assessing the eSports players and athletes.

关键词： Games Sensors Measurement data collection Weapons Mice Affective computing

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