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Quantum Recurrent Neural Networks with Encoder-Decoder for Time-Dependent Partial Differential Equations

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arXiv 2025年

作者： Chen, Yuan Khaliq, Abdul Furati, Khaled M. Computational and Data Science Program Middle Tennessee State University MurfreesboroTN37132 United States Department of Mathematical Science Middle Tennessee State University MurfreesboroTN37132 United States Department of Mathematics King Fahd University of Petroleum & Minerals Dhahran31261 Saudi Arabia

Nonlinear time-dependent partial differential equations are essential in modeling complex phenomena across diverse fields, yet they pose significant challenges due to their computational complexity, especially in higher dimensions. This study explores Quantum Recurrent Neural Networks within an encoder-decoder framework, integrating Variational Quantum Circuits into Gated Recurrent Units and Long Short-Term Memory networks. Using this architecture, the model efficiently compresses high-dimensional spatiotemporal data into a compact latent space, facilitating more efficient temporal evolution. We evaluate the algorithms on the Hamilton-Jacobi-Bellman equation, Burgers’ equation, the Gray-Scott reaction-diffusion system, and the three dimensional Michaelis-Menten reaction-diffusion equation. The results demonstrate the superior performance of the quantum-based algorithms in capturing nonlinear dynamics, handling high-dimensional spaces, and providing stable solutions, highlighting their potential as an innovative tool in solving challenging and complex systems. Copyright © 2025, The Authors. All rights reserved.

关键词： Decoding

SRECG: ECG Signal Super-Resolution Framework for Portable/Wearable Devices in Cardiac Arrhythmias Classification

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IEEE Transactions on Consumer Electronics 2023年第3期69卷 250-260页

作者： Chen, Tsai-Min Tsai, Yuan-Hong Tseng, Huan-Hsin Liu, Kai-Chun Chen, Jhih-Yu Huang, Chih-Han Li, Guo-Yuan Shen, Chun-Yen Tsao, Yu National Taiwan University and Academia Sinica Graduate Program of Data Science Taipei106319 Taiwan Academia Sinica Research Center for Information Technology Innovation Taipei115 Taiwan Taiwan Artificial Intelligence Academy Foundation Program of Taiwan AI Academy New Taipei22065 Taiwan Artificial Intelligence Foundation Technology Development Center New Taipei24158 Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei10617 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei115 Taiwan National Taiwan University Department of Mathematics Taipei10617 Taiwan

A combination of cloud-based deep learning (DL) algorithms with portable/wearable (P/W) devices has been developed as a smart heath care system to support automatic cardiac arrhythmias (CAs) classification using electrocardiography (ECG). However, long-term and continuous ECG monitoring is challenging because of limitations of batteries and transmission bandwidth of P/W devices while incorporated with consumer electronics (CE). A feasible approach to address this challenge is to decrease sampling rates. However, low sampling rates lead to low-resolution signals that hinder the CAs classification performance. In this study, we propose a DL-based ECG signal super-resolution framework (called SRECG) to enhance low-resolution ECG signals by jointly considering the accuracies when applied to the DL-based high-resolution multiclass classifier (HMC) of CAs. In our experiments, we downsampled the ECG signals from the CPSC2018 dataset and evaluated their HMC accuracies with and without the SRECG. Experimental results show that SRECG can well improve the HMC accuracies as compared to traditional interpolation methods. Moreover, approximately half of the CAs classification accuracies of HMC were maintained within the enhanced ECG signals by SRECG. The promising results confirm that SRECG can be suitably used to enhance low-resolution ECG signals from P/W devices with CE to improve their cloud-based HMC performances. © 1975-2011 IEEE.

关键词： Electrocardiography

Position: Bayesian Deep Learning is Needed in the Age of Large-Scale AI 41

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Position: Bayesian Deep Learning is Needed in the Age of Lar...

41st International Conference on Machine Learning, ICML 2024

作者： Papamarkou, Theodore Skoularidou, Maria Palla, Konstantina Aitchison, Laurence Arbel, Julyan Dunson, David Filippone, Maurizio Fortuin, Vincent Hennig, Philipp Hernández-Lobato, José Miguel Hubin, Aliaksandr Immer, Alexander Karaletsos, Theofanis Khan, Mohammad Emtiyaz Kristiadi, Agustinus Li, Yingzhen Mandt, Stephan Nemeth, Christopher Osborne, Michael A. Rudner, Tim G.J. Rügamer, David Teh, Yee Whye Welling, Max Wilson, Andrew Gordon Zhang, Ruqi Department of Mathematics The University of Manchester Manchester United Kingdom Eric and Wendy Schmidt Center Broad Institute of MIT and Harvard Cambridge United States Spotify London United Kingdom Computational Neuroscience Unit University of Bristol Bristol United Kingdom Centre Inria de l'Université Grenoble Alpes Grenoble France Department of Statistical Science Duke University United States Statistics Program KAUST Saudi Arabia Helmholtz AI Munich Germany Department of Computer Science Technical University of Munich Munich Germany Munich Center for Machine Learning Munich Germany Tübingen AI Center University of Tübingen Tübingen Germany Department of Engineering University of Cambridge Cambridge United Kingdom Department of Mathematics University of Oslo Oslo Norway Bioinformatics and Applied Statistics Norwegian University of Life Sciences Ås Norway Department of Computer Science ETH Zurich Switzerland Chan Zuckerberg Initiative CA United States Center for Advanced Intelligence Project RIKEN Tokyo Japan Vector Institute Toronto Canada Department of Computing Imperial College London London United Kingdom Department of Computer Science UC Irvine Irvine United States Department of Mathematics and Statistics Lancaster University Lancaster United Kingdom Department of Engineering Science University of Oxford Oxford United Kingdom Center for Data Science New York University New York United States Department of Statistics LMU Munich Munich Germany DeepMind London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Informatics Institute University of Amsterdam Amsterdam Netherlands Courant Institute of Mathematical Sciences Center for Data Science Computer Science Department New York University New York United States Department of Computer Science Purdue University West Lafayette United States

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential. Copyright 2024 by the author(s)

关键词： Contrastive Learning

data Mining and Bioinformatics Approaches to Elucidate Bacterial Communities in the Extreme Environment

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Data Mining and Bioinformatics Approaches to Elucidate Bacte...

International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Joko Pebrianto Trinugroho Alam Ahmad Hidayat Rudi Nirwantono Faisal Asadi Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Mathematics Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia

Bacteria are microscopic organisms that can be found in many environments. They are abundant and have many roles in our life. Studying bacteria is essential so that we can identify the bacteria that are needed for many industrial applications. However, the main problem is that majority of the bacteria are unculturable, hampering the exploration of bacteria from different environments. Metagenomics approach which employs Next Generation Sequencing technology could help study bacteria by utilizing 16S rRNA marker gene. This study aims to demonstrate data mining and bioinformatics approaches to analyze 16S rRNA sequencing data. The raw sequencing data of 16S rRNA was collected from biological database. Then, the data were trimmed, denoised, and clustered to generate Amplicon Sequence Variants (ASVs). Diversity (alpha and beta) and taxonomic analyses were then conducted to elucidate the bacterial diversity and taxonomic profile of ASVs. The results of this work showed that Shannon and PD indices in China's hot spring were higher than Singapore and the USA. Furthermore, a significant difference was observed in the PD index. The unweighted UniFrac distance also showed there was a significant difference of the bacterial communities between the three locations. In addition, the taxonomic investigation unveiled prevalent bacterial groups in the ecosystem, namely Proteobacteria, Chloroflexi, Cyanobacteria, and Crenarchaeota. The research outcomes have the potential to serve as a foundational resource for subsequent bacterial metagenomic research, particularly the hot spring environment.

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Med-IC: Fusing a Single Layer Involution with Convolutions for Enhanced Medical Image Classification and Segmentation

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arXiv 2024年

作者： Islam, Md. Farhadul Zabeen, Sarah Manab, Meem Arafat Mahin, Mohammad Rakibul Hasan Mondal, Joyanta Jyoti Reza, Md. Tanzim Hasan, Md Zahidul Haque, Munima Sadeque, Farig Noor, Jannatun Research Group Department of Computer Science and Engineering School of Data and Sciences BRAC University Dhaka Bangladesh Department of Computer Science and Engineering School of Data and Sciences BRAC University Dhaka Bangladesh Biotechnology Program Department of Mathematics and Natural Sciences School of Data and Sciences BRAC University Dhaka Bangladesh Department of Computer and Information Sciences University of Delaware United States School of Law and Government Dublin City University Ireland Gina Cody School of Engineering and Computer Science Concordia University Canada

The majority of medical images, especially those that resemble cells, have similar characteristics. These images, which occur in a variety of shapes, often show abnormalities in the organ or cell region. The convolution operation possesses a restricted capability to extract visual patterns across several spatial regions of an image. The involution process, which is the inverse operation of convolution, complements this inherent lack of spatial information extraction present in convolutions. In this study, we investigate how applying a single layer of involution prior to a convolutional neural network (CNN) architecture can significantly improve classification and segmentation performance, with a comparatively negligible amount of weight parameters. The study additionally shows how excessive use of involution layers might result in inaccurate predictions in a particular type of medical image. According to our findings from experiments, the strategy of adding only a single involution layer before a CNN-based model outperforms most of the previous *** Codes 68T45 © 2024, CC BY-NC-SA.

关键词： Convolutional neural networks

CVIT: CONTINUOUS VISION TRANSFORMER FOR OPERATOR LEARNING

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arXiv 2024年

作者： Wang, Sifan Seidman, Jacob H. Sankaran, Shyam Wang, Hanwen Pappas, George J. Perdikaris, Paris Institution for Foundation of Data Science Yale University United States Graduate Program in Applied Mathematics and Computational Science University of Pennsylvania United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania United States Department of Electrical and Systems Engineering University of Pennsylvania United States

Operator learning, which aims to approximate maps between infinite-dimensional function spaces, is an important area in scientific machine learning with applications across various physical domains. Here we introduce the Continuous Vision Transformer (CViT), a novel neural operator architecture that leverages advances in computer vision to address challenges in learning complex physical systems. CViT combines a vision transformer encoder, a novel grid-based coordinate embedding, and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. This design allows for flexible output representations and consistent evaluation at arbitrary resolutions. We demonstrate CViT’s effectiveness across a diverse range of partial differential equation (PDE) systems, including fluid dynamics, climate modeling, and reaction-diffusion processes. Our comprehensive experiments show that CViT achieves state-of-the-art performance on multiple benchmarks, often surpassing larger foundation models, even without extensive pretraining and roll-out fine-tuning. Taken together, CViT exhibits robust handling of discontinuous solutions, multi-scale features, and intricate spatio-temporal dynamics. Our contributions can be viewed as a significant step towards adapting advanced computer vision architectures for building more flexible and accurate machine learning models in the physical sciences. All data and code are publicly available at https://***/PredictiveIntelligenceLab/cvit. © 2024, CC BY-NC-SA.

关键词： Computer vision

A Bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

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A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Rudi Nirwantono Khoirunnisa Assidqi Alam Ahmad Hidayat Joko Pebrianto Trinugroho Bens Pardamean Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Food Biotechnology Research Center Bina Nusantara University Jakarta Indonesia Mathematics Departement School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site.

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Modeling of Measurement Error in Financial Returns data

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arXiv 2024年

作者： Jasra, Ajay Maama, Mohamed Mijatović, Aleksandar School of Data Science The Chinese University of Hong Kong Shenzhen China Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Statistics University of Warwick United Kingdom

In this paper we consider the modeling of measurement error for fund returns data. In particular, given access to a time-series of discretely observed log-returns and the associated maximum over the observation period, we develop a stochastic model which models the true log-returns and maximum via a Lévy process and the data as a measurement error there-of. The main technical difficulty of trying to infer this model, for instance Bayesian parameter estimation, is that the joint transition density of the return and maximum is seldom known, nor can it be simulated exactly. Based upon the novel stick breaking representation of [12] we provide an approximation of the model. We develop a Markov chain Monte Carlo (MCMC) algorithm to sample from the Bayesian posterior of the approximated posterior and then extend this to a multilevel MCMC method which can reduce the computational cost to approximate posterior expectations, relative to ordinary MCMC. We implement our methodology on several applications including for real data. Copyright © 2024, The Authors. All rights reserved.

关键词： Markov chains

Additive Poisson regression via forced categorical covariates and generalized fused Lasso 27

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Additive Poisson regression via forced categorical covariate...

27th International Conference on Knowledge Based and Intelligent Information and Engineering Sytems, KES 2023

作者： Yamamura, Mariko Ohishi, Mineaki Yanagihara, Hirokazu Department of Statistics Radiation Effects Research Foundation 5-2 Hijiyama Park Minami-ku Hiroshima732-0815 Japan Center for Data-driven Science and Artificial Intelligence Tohoku University 41 Kawauchi Aoba-ku Miyagi Sendai980-8576 Japan Mathematics Program Graduate School of Advanced Science and Engineering Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan

In this study, we use the log-linear link function and propose a generalized fused Lasso (GFL) Poisson regression model in which the nonlinear trend is discretely represented by categorical covariates in the additive model. We use the coordinate descent algorithm for the estimation and show that the optimal solution in a coordinate axis can be found explicitly. To demonstrate the proposed approach, we analyze Japanese crime data. Simulation results showed a fitness ratio for true fusion to be more than 90% in total, demonstrating the reliability of the estimates. © 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (https://***/licenses/by-nc-nd/4.0)

关键词： Additive Poisson regression Coordinate descent algorithm Generalized fused Lasso Spatio-temporal analysis