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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Shun-Cheng Chang Hsin-Pei Yu Yi-Hsien Hsieh Pochuang Wang Weichung Wang Tung-Hung Su Jia-Horng Kao Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taipei Taiwan Department of Computer Science and Information Engineering NTU Taipei Taiwan Institute of Applied Mathematical Sciences NTU Taipei Taiwan Department of Internal Medicine Division of Gastroenterology and Hepatology National Taiwan University Hospital Taipei Taiwan Department of Electrical Engineering NTU Taipei Taiwan Center for Advanced Computing and Imaging in Biomedicine NTU Taipei Taiwan Smart Medicine and Health Informatics Program NTU Taipei Taiwan

ISBN: (数字)9798350351552

ISBN: (纸本)9798350351569

Deep learning has revolutionized medical imaging, offering advanced methods for accurate diagnosis and treatment planning. The BCLC staging system is crucial for staging Hepatocellular Carcinoma (HCC), a high-mortality cancer. An automated BCLC staging system could significantly enhance diagnosis and treatment planning efficiency. However, we found that BCLC staging, which is directly related to the size and number of liver tumors, aligns well with the principles of the Multiple Instance Learning (MIL) framework. To effectively achieve this, we proposed a new preprocessing technique called Masked Cropping and Padding(MCP), which addresses the variability in liver volumes and ensures consistent input sizes. This technique preserves the structural integrity of the liver, facilitating more effective learning. Furthermore, we introduced Re ViT, a novel hybrid model that integrates the local feature extraction capabilities of Convolutional Neural Networks (CNNs) with the global context modeling of Vision Transformers (ViTs). Re ViT leverages the strengths of both architectures within the MIL framework, enabling a robust and accurate approach for BCLC staging. We will further explore the trade-off between performance and interpretability by employing TopK Pooling strategies, as our model focuses on the most informative instances within each bag.

关键词： Visualization Accuracy Three-dimensional displays Liver Transformers Planning Convolutional neural networks Context modeling Biomedical imaging Tumors

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Unbiased Approximations for Stationary Distributions of McKean-Vlasov SDEs

arXiv

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arXiv 2024年

作者： Awadelkarim, Elsiddig Chada, Neil K. Jasra, Ajay 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 Mathematics City University of Hong Kong Hong Kong School of Data Science The Chinese University of Hong Kong Shenzhen Shenzhen China

We consider the development of unbiased estimators, to approximate the stationary distribution of Mckean-Vlasov stochastic differential equations (MVSDEs). These are an important class of processes, which frequently appear in applications such as mathematical finance, biology and opinion dynamics. Typically the stationary distribution is unknown and indeed one cannot simulate such processes exactly. As a result one commonly requires a time-discretization scheme which results in a discretization bias and a bias from not being able to simulate the associated stationary distribution. To overcome this bias, we present a new unbiased estimator taking motivation from the literature on unbiased Monte Carlo. We prove the unbiasedness of our estimator, under assumptions. In order to prove this we require developing ergodicity results of various discrete time processes, through an appropriate discretization scheme, towards the invariant measure. Numerous numerical experiments are provided, on a range of MVSDEs, to demonstrate the effectiveness of our unbiased estimator. Such examples include the Currie-Weiss model, a 3D neuroscience model and a parameter estimation problem. © 2024, CC BY-NC-SA.

关键词： Stochastic systems

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(10$\bar{1}$3)-oriented semipolar GaN growth on (10$\bar{1}$0) m-plane ScAlMgO4 substrate

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Japanese Journal of Applied Physics 2024年第10期63卷 101001-101001页

作者： Mohammed A. Najmi Daisuke Iida Kazuhiro Ohkawa Electrical and Computer Engineering Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia

We report the growth of a GaN layer on a (10\bar{1}0)m-plane ScAlMgO4 (SAM) substrate. The GaN layer demonstrated (10\bar{1}3) preference growth orientation. The anisotropy of the crystalline quality was distinctly ob...

We report the growth of a GaN layer on a $$(10\bar<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAQAAAC1HAwCAAAAC0lEQVR42mNkYAAAAAYAAjCB0C8AAAAASUVORK5CYII=" data-src="https://***/journals/1347-4065/63/10/101001/revision2/***" style="max-width: 100%;" alt="$(10\bar{1}3)$" align="top">0)$ m-plane ScAlMgO₄ (SAM) substrate. The GaN layer demonstrated $(10\bar<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAQAAAC1HAwCAAAAC0lEQVR42mNkYAAAAAYAAjCB0C8AAAAASUVORK5CYII=" data-src="https://***/journals/1347-4065/63/10/101001/revision2/***" style="max-width: 100%;" alt="$(10\bar{1}3)$" align="top">3)$ preference growth orientation. The anisotropy of the crystalline quality was distinctly observed through an X-ray rocking curve (XRC) taken across the sample surface over various azimuths across the orthogonal directions [0001] and $[1\bar<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAQAAAC1HAwCAAAAC0lEQVR42mNkYAAAAAYAAjCB0C8AAAAASUVORK5CYII=" data-src="https://***/journals/1347-4065/63/10/101001/revision2/***" style="max-width: 100%;" alt="$[1\bar{2}10]$" align="top">10]$ of the SAM substrate. Notably, the crystalline quality exhibited gradual degradation as the substrate was rotated around its surface normal away from the c-direction

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Parameter Estimation for Partially Observed McKean-Vlasov Diffusions

arXiv

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arXiv 2024年

作者： Jasra, Ajay Maama, Mohamed Tempone, Raul School of Data Science The Chinese University of Hong Kong CN 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 Chair of Mathematics for Uncertainty Quantification RWTH Aachen University Aachen52062 Germany

In this article we consider likelihood-based estimation of static parameters for a class of partially observed McKean-Vlasov (POMV) diffusion process with discrete-time observations over a fixed time interval. In particular, using the framework of [5] we develop a new randomized multilevel Monte Carlo method for estimating the parameters, based upon Markovian stochastic approximation methodology. New Markov chain Monte Carlo algorithms for the POMV model are introduced facilitating the application of [5]. We prove, under assumptions, that the expectation of our estimator is biased, but with expected small and controllable bias. Our approach is implemented on several examples. Copyright © 2024, The Authors. All rights reserved.

关键词： Stochastic systems

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Cross-system biological image quality enhancement based on the generative adversarial network as a foundation for establishing a multi-institute microscopy cooperative network

arXiv

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arXiv 2024年

作者： Panek, Dominik Rząca, Carina Szczypior, Maksymilian Sorysz, Joanna Misztal, Krzysztof Baster, Zbigniew Rajfur, Zenon Doctoral School of Exact and Natural Sciences Jagiellonian University ul. Lojasiewicza 11 Kraków30-348 Poland Department of Molecular and Interfacial Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate Program in Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate program in Biomedical Engineering Faculty of Electrical Engineering Automatics Computer Science and Biomedical Engineering AGH University of Science and Technology Al. A. Mickiewicza 30 Building B-1 Kraków30-059 Poland Division of Computational Mathematics Faculty of Mathematics and Computer Science Jagiellonian University 6 Lojasiewicza St. Kraków Poland

High-quality fluorescence imaging of biological systems is limited by processes like photobleaching and phototoxicity, and also in many cases, by limited access to the latest generations of microscopes. Moreover, low temporal resolution can lead to a motion blur effect in living systems. Our work presents a deep learning (DL) generative-adversarial approach to the problem of obtaining high-quality (HQ) images based on their low-quality (LQ) equivalents. We propose a generative-adversarial network (GAN) for contrast transfer between two different separate microscopy systems: a confocal microscope (producing HQ images) and a wide-field fluorescence microscope (producing LQ images). Our model proves that such transfer is possible, allowing us to receive HQ-generated images characterized by low mean squared error (MSE) values, high structural similarity index (SSIM), and high peak signal-to-noise ratio (PSNR) values. For our best model in the case of comparing HQ-generated images and HQ-ground truth images, the median values of the metrics are 6·10-4, 0.9413, and 31.87, for MSE, SSIM, and PSNR, respectively. In contrast, in the case of comparison between LQ and HQ ground truth median values of the metrics are equal to 0.0071, 0.8304, and 21.48 for MSE, SSIM, and PSNR respectively. Therefore, we observe a significant increase ranging from 14% to 49% for SSIM and PSNR respectively. These results, together with other single-system cross-modality studies, provide proof of concept for further implementation of a cross-system biological image quality enhancement. © 2024, CC BY-SA.

关键词： Fluorescence imaging

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computer-Aided Lung Auscultation Screening and Radiographic Evaluation of Pediatric Pneumonia

Computer-Aided Lung Auscultation Screening and Radiographic ...

引用

Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Annapurna Kala Daniel Chong Abdullah H. Baqui Salahuddin Ahmed ASMD Ashraful Islam Nabid Chowdhury Arunangshu Roy Eric D. McCollum Mounya Elhilali Dpt. Electrical & Computer Engineering Lab. for Computational Audio Perception Johns Hopkins University Dpt. International Health Bloomberg School of Public Health Johns Hopkins University Projahnmo Research Foundation Dhaka Bangladesh Dpt. Pediatrics Global Program in Pediatric Respiratory Sciences Eudowood Division of Pediatric Respiratory Sciences Johns Hopkins School of Medicine Baltimore USA

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

While chest auscultations provide an accessible and low-cost tool for pediatric pneumonia diagnosis, its subjectivity and low reliability continues to hinder its inclusion in global pneumonia guidelines; eventhough more robust tools like chest radiography also suffer from cost and accessibility issues. Advances in computer-aided analytics is offering more robust tools for interpreting digital auscultation signals though little has been done to explore variations of lung sounds across different chest positions and the correspondence between auscultations and specific radiographic findings. The present study explores interpretation of lung auscultations across chest positions in a pediatric pneumonia population, using a deep neural network classification of normal and abnormal breathing patterns. The results reveal a strong alignment between computer-aided auscultation findings and radiographic interpretation not only in terms of presence of adventitious lung patterns, but also in terms of localizing the abnormality along the left or right lung. Though evaluated in a small clinical population, this research underscores the potential of computer-aided auscultation analysis as a cost-effective substitute for radiography in resource-limited settings.

关键词： Pneumonia Costs Lungs Artificial neural networks Reliability engineering in medicine and biology Diagnostic radiography Guidelines

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BENCHMARKING COMMUNITY DRUG RESPONSE PREDICTION MODELS: DATASETS, MODELS, TOOLS, AND METRICS FOR CROSS-DATASET GENERALIZATION ANALYSIS

arXiv

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arXiv 2025年

作者： Partin, Alexander Vasanthakumari, Priyanka Narykov, Oleksandr Wilke, Andreas Koussa, Natasha Jones, Sara E. Zhu, Yitan Overbeek, Jamie C. Jain, Rajeev Fernando, Gayara Demini Sanchez-Villalobos, Cesar Garcia-Cardona, Cristina Mohd-Yusof, Jamaludin Chia, Nicholas Wozniak, Justin M. Ghosh, Souparno Pal, Ranadip Brettin, Thomas S. Weil, M. Ryan Stevens, Rick L. Division of Data Science and Learning Argonne National Laboratory LemontIL United States Frederick National Laboratory for Cancer Research Cancer Data Science Initiatives Cancer Research Technology Program FrederickMD United States Department of Statistics University of Nebraska–Lincoln LincolnNE United States Department of Electrical & Computer Engineering Texas Tech University LubbockTX United States Division of Computer Computational and Statistical Sciences Los Alamos National Laboratory Los AlamosNM United States Department of Computer Science The University of Chicago ChicagoIL United States

Deep learning (DL) and machine learning (ML) models have shown promise in drug response prediction (DRP), yet their ability to generalize across datasets remains an open question, raising concerns about their real-world applicability. Due to the lack of standardized benchmarking approaches, model evaluations and comparisons often rely on inconsistent datasets and evaluation criteria, making it difficult to assess true predictive capabilities. In this work, we introduce a benchmarking framework for evaluating cross-dataset prediction generalization in DRP models. Our framework incorporates five publicly available drug screening datasets, six standardized DRP models, and a scalable workflow for systematic evaluation. To assess model generalization, we introduce a set of evaluation metrics that quantify both absolute performance (e.g., predictive accuracy across datasets) and relative performance (e.g., performance drop compared to within-dataset results), enabling a more comprehensive assessment of model transferability. Our results reveal substantial performance drops when models are tested on unseen datasets, underscoring the importance of rigorous generalization assessments. While several models demonstrate relatively strong cross-dataset generalization, no single model consistently outperforms across all datasets. Furthermore, we identify CTRPv2 as the most effective source dataset for training, yielding higher generalization scores across target datasets. By sharing this standardized evaluation framework with the community, our study aims to establish a rigorous foundation for model comparison, and accelerate the development of robust DRP models for real-world applications. © 2025, CC BY.

关键词： Prediction models

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Parallel Approximations for High-Dimensional Multivariate Normal Probability Computation in Confidence Region Detection Applications

arXiv

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arXiv 2024年

作者： Zhang, Xiran Abdulah, Sameh Cao, Jian Ltaief, Hatem Sun, Ying Genton, Marc G. Keyes, David E. Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Saudi Arabia Statistics Program King Abdullah University of Science and Technology Saudi Arabia Extreme Computing Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Mathematics The University of Houston HoustonTX United States

Addressing the statistical challenge of computing the multivariate normal (MVN) probability in high dimensions holds significant potential for enhancing various applications. For example, the critical task of detecting confidence regions where a process probability surpasses a specific threshold is essential in diverse applications, such as pinpointing tumor locations in magnetic resonance imaging (MRI) scan images, determining hydraulic parameters in groundwater flow issues, and forecasting regional wind power to optimize wind turbine placement, among numerous others. One common way to compute high-dimensional MVN probabilities is the Separation-of- Variables (SOV) algorithm. This algorithm is known for its high computational complexity of O(n3) and space complexity of O(n2), mainly due to a Cholesky factorization operation for an n × n covariance matrix, where n represents the dimensionality of the MVN problem. This work proposes a high-performance computing framework that allows scaling the SOV algorithm and, subsequently, the confidence region detection algorithm. The framework leverages parallel linear algebra algorithms with a task-based programming model to achieve performance scalability in computing process probabilities, especially on largescale systems. In addition, we enhance our implementation by incorporating Tile Low-Rank (TLR) approximation techniques to reduce algorithmic complexity without compromising the necessary accuracy. To evaluate the performance and accuracy of our framework, we conduct assessments using simulated data and a wind speed dataset. Our proposed implementation effectively handles high-dimensional multivariate normal (MVN) probability computations on shared and distributed-memory systems using finite precision arithmetics and TLR approximation computation. Performance results show a significant speedup of up to 20X in solving the MVN problem using TLR approximation compared to the reference dense solution without sacrificing the

关键词： Statistics

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Time-domain methods for quantifying dynamic cerebral blood flow autoregulation: Review and recommendations. A white paper from the Cerebrovascular Research Network (CARNet)

引用

Journal of Cerebral Blood Flow and Metabolism 2024年第9期44卷 1480-1514页

作者： Kostoglou, Kyriaki Bello-Robles, Felipe Brassard, Patrice Chacon, Max Claassen, Jurgen AHR Czosnyka, Marek Elting, Jan-Willem Hu, Kun Labrecque, Lawrence Liu, Jia Marmarelis, Vasilis Z Payne, Stephen J Shin, Dae Cheol Simpson, David Smirl, Jonathan Panerai, Ronney B Mitsis, Georgios D Department of Electrical and Computer Engineering McGill University Montreal QC Canada Institute of Neural Engineering Graz University of Technology Graz Austria Departamento de Ingeniería Informática Universidad de Santiago de Chile Santiago Chile Department of Kinesiology Faculty of Medicine Université Laval QC Canada Research Center of the Institut universitaire de cardiologie et de pneumologie de Québec Quebec QC Canada Department of Geriatrics Radboud University Medical Center Research Institute for Medical Innovation and Donders Institute Nijmegen Netherlands Cerebral Haemodynamics in Ageing and Stroke Medicine (CHiASM) Department of Cardiovascular Sciences University of Leicester Leicester United Kingdom Department of Clinical Neurosciences Neurosurgery Department University of Cambridge Cambridge United Kingdom Department of Neurology and Clinical Neurophysiology University Medical Center Groningen Groningen Netherlands Medical Biodynamics Program Division of Sleep and Circadian Disorders Brigham and Women's Hospital Harvard Medical School Boston MA United States Division of Sleep Medicine Harvard Medical School Boston MA United States Laboratory for Engineering and Scientific Computing Institute of Advanced Computing and Digital Engineering Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Guangdong Shenzhen China Department Biomedical Engineering Viterbi School of Engineering University of Southern California Los Angeles CA United States Institute of Applied Mechanics National Taiwan University Taipei Taiwan Institute of Sound and Vibration Research University of Southampton Southampton United Kingdom Cerebrovascular Concussion Laboratory Faculty of Kinesiology University of Calgary Calgary AB Canada Sport Injury Prevention Research Centre Faculty of Kinesiology University of Calgary Calgary AB Canada Hotchkiss Brain Institute University of Calgary Calgary AB Canada NIHR Leicester Biomedical Research Centre Bri

Cerebral Autoregulation (CA) is an important physiological mechanism stabilizing cerebral blood flow (CBF) in response to changes in cerebral perfusion pressure (CPP). By maintaining an adequate, relatively constant supply of blood flow, CA plays a critical role in brain function. Quantifying CA under different physiological and pathological states is crucial for understanding its implications. This knowledge may serve as a foundation for informed clinical decision-making, particularly in cases where CA may become impaired. The quantification of CA functionality typically involves constructing models that capture the relationship between CPP (or arterial blood pressure) and experimental measures of CBF. Besides describing normal CA function, these models provide a means to detect possible deviations from the latter. In this context, a recent white paper from the Cerebrovascular Research Network focused on Transfer Function Analysis (TFA), which obtains frequency domain estimates of dynamic CA. In the present paper, we consider the use of time-domain techniques as an alternative approach. Due to their increased flexibility, time-domain methods enable the mitigation of measurement/physiological noise and the incorporation of nonlinearities and time variations in CA dynamics. Here, we provide practical recommendations and guidelines to support researchers and clinicians in effectively utilizing these techniques to study CA. © The Author(s) 2024.

关键词： CARNet cerebral autoregulation cerebral blood flow time-domain methods white paper

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Diabetes Prediction Model for Better Clarification by using Machine Learning

Diabetes Prediction Model for Better Clarification by using ...

引用

International Conference on Inventive Computation Technologies (ICICT)

作者： J. Lysa Eben R. Jayasudha S. Ramya S. Kaliappan Shobha Aswal Khalid Ali Salem Al-Salehi Department of Computer Applications School of Computing Sciences Vels Institute of Science Technology and Advanced Studies Chennai Tamilnadu India Department of Mathematics Dr.N.G.P.Institute of Technology Coimbatore India Department of Computer Science and Engineering Kongu Engineering College Erode Tamilnadu India Division of Research and Development Lovely Professional University Phagwara Punjab India School of Computing Graphic Era Hill University Dehradun India Biomedical engineering study program faculty of science and technology Airlangga University Surabaya Indonesia

Diabetes mellitus is one of the most pressing health concerns because so many people are afflicted by its disabling symptoms. Factors such as age, excess body fat, insufficient physical activity, a history of diabetes in one's family, a sedentary lifestyle, an unhealthy diet, hypertension, etc., all increase the likelihood of developing diabetes mellitus. Health complications are more common in people with diabetes, including cardiovascular disease, renal failure, stroke, blindness, and nerve injury. To validate a diagnosis of diabetes, hospitals typically perform a battery of procedures on the patient. Big data analytics has many vital applications in the healthcare sector. Numerous large computer systems are used in the healthcare sector. With the help of big data analytics, researchers can sift through mountains of data in search of previously unseen patterns and insights. Current techniques have a poor degree of precision in classification and forecast. While previous research has focused on factors such as glucose, body mass index, age, insulin, etc., the proposed model takes these into account and also the other factors that may be more relevant to the development of diabetes. The newer sample is superior to the older one based on categorization accuracy. A workflow algorithm for diabetes prognosis is also required to improve the accuracy.

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