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Breast mass regions classification from mammograms using convolutional neural networks and transfer learning.

Optica Acta: International Journal of Optics 2023年第10期70卷

作者： Yuliana Jiménez-Gaona María José Rodríguez-Álvarez Diana Carrión-Figueroa Darwin Castillo-Malla Vasudevan Lakshminarayanan a Departamento de Química y Ciencias Exactas Universidad Técnica Particular de Loja Loja Ecuadorb Instituto de Instrumentación para la Imagen Molecular i3M Universitat Politècnica de València (UPV)- Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spaind Theoretical and Experimental Epistemology Lab School of Optometry and Vision Science University of Waterloo Waterloo Canada b Instituto de Instrumentación para la Imagen Molecular i3M Universitat Politècnica de València (UPV)- Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain c Hospital Carlos Andrade Marín IESS Quito Ecuador d Theoretical and Experimental Epistemology Lab School of Optometry and Vision Science University of Waterloo Waterloo Canadae Department of Systems Design Engineering Physics and Electrical and Computer Engineering University of Waterloo Waterloo Canada

This study introduces a novel approach aimed at enhancing the quality of digital mammography images through pre-processing techniques, to improve breast cancer detection accuracy. The primary objective is to enhance image resolution, thus leading to more precise breast tissue segmentation and subsequent classification utilizing convolutional neural networks (CNNs). Three recognized public mammography databases: CBIS-DDSM, Mini-MIAS, and Inbreast were used as pre-processing data. Our statistical findings revealed that the EDSR method (PSNR = 39.05 dB/ SSIM = 0.90) consistently outperformed the visual quality of images when compared to SR-RDN (PSNR = 32.68 dB/SSIM = 0.82). Similarly, UNet demonstrated superior performance over SegNet, boasting an average Intersection over Union (IoU) of 0.862, an average Dice coefficient of 0.991, and an accuracy rate of 0.947 in Region of Interest (RoI) segmentation results. In conclusion, the ResNet model contributed to enhanced accuracy compared to conventional machine learning algorithms. However, it did not surpass state-of-the-art deep CNN-based classifiers, achieving an accuracy rate of 75%.Abbreviations:AUC: Area under curve; CAD: computer aided system; CC: Cranio caudal; CNN: Convolutional neural network; DNN: Deep neural network; DDSM: Digital Database for Screening Mammography; DM: Digital mammography; DL: Deep learning; EDSR: Enhanced Deep Residual Network; E2E: End to End; ESRGAN: Enhanced Super-Resolution Generative Adversarial Networks; ESPCN: Efficient sub-pixel convolutional neural network; GAN: Generative adversarial network; HR: High resolution; IoU: Intersection over Union; LR: Low resolution; MDSR: Multi-scale deep super-resolution; MLO: Mediolateral Oblique; PSNR: Peak signal to Noise Ratio; RoI: Region of interest; RDN: Residua Dense Network; RDB: Residual Dense Block; RNN: Recurrent Neural Network; ReLU: Rectified Linear Unit; SR-GAN: Super-Resolution Using a Generative Adversarial Network; SSIM: Structural Sim

关键词： Breast cancer classification convolutional neural network mammography images segmentation super resolution

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Toward the universal quantum cloner limit for designing compact photonic CNOT gate

arXiv

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arXiv 2019年

作者： Gueddana, Amor Lakshminarayanan, Vasudevan Green & Smart Communication Systems Lab Gres'Com Engineering School of Communication of Tunis Sup'Com University of Carthage Ghazela Technopark Ariana2083 Tunisia Theoretical & Experimental Epistemology Lab TEEL School of Optometry and Vision Science University of Waterloo 200 University Avenue West WaterlooONN2l 3G1 Canada Department of Physics Department of Electrical and Computer Engineering Department of Systems Design Engineering University of Waterloo 200 University Avenue West WaterlooONN2l 3G1 Canada

We suggest a near deterministic compact model of a photonic CNOT gate based on a quantum dot trapped in a double sided optical microcavity and a universal cloner. Our design surpasses the cloner optimal limit of 5/6 and we show that it provides fidelity around 91 % in the weak coupling regime. Copyright © 2019, The Authors. All rights reserved.

关键词： Semiconductor quantum dots

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A Modified Polynomial Chaos Modeling Approach for Uncertainty Quantification

A Modified Polynomial Chaos Modeling Approach for Uncertaint...

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International Applied Computational Electromagnetics Society Symposium

作者： Majid Ahadi Dolatsara Ambrish Varma Kumar Keshavan Madhavan Swaminathan School of Electrical and Computer Engineering Center for Co-Design of Chip Package System (C3PS) Georgia Institute of Technology Atlanta Ga Cadence Design Systems Inc. Chelmsford MA

ISBN: (纸本)9781728115184;9780996007887

Uncertainty quantification is a key element for modeling high speed circuits, which is often done with Monte Carlo analysis. However, because this method is computationally expensive, new approaches with higher efficiency have been developed. Many popular methods are based on the surrogate models developed with Polynomial Chaos theory. However, size of these models can be prohibitively large for realistic examples. Hence, this paper provides a novel methodology to use an ensemble of weaker models to improve efficiency. Finally, a numerical example with a DDR4 topology is provided.

关键词： DDR4 design space exploration Polynomial chaos theory Uncertainty quantification

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Optimal Power Allocation for Amplify and Forward Relaying with Finite Blocklength Codes and QoS Constraints

Optimal Power Allocation for Amplify and Forward Relaying wi...

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IEEE Conference on Vehicular Technology (VTC)

作者： Yulin Hu M. Cenk Gursoy Anke Schmeink Information Theory and Systematic Design of Communication Systems RWTH Aachen University Aachen Germany Department of Electrical Engineering and Computer Science Syracuse University Syracuse NY USA

In this work, motivated by emerging low-latency applications, we consider an amplify-and-forward relaying network operating with finite blocklength (FBL) codes subject to delay quality of service (QoS) constraints. Hence, we address both transmission delay (via FBL codes) and queueing delay (via delay QoS requirements). We first derive the QoS-constrained throughput of the network. Subsequently, we state a resource allocation problem aiming at allocating the power between the source and the relay to maximize the throughput. The convexity of the problem is proved and the optimal power allocation policy is provided. Via simulations, we confirm the accurateness of our analytical model. In addition, we provide interesting insights on the system behavior by characterizing the impact of the error probability, the QoS-exponent and coding blocklength on the throughput performance.

关键词： Quality of service Throughput Relays Resource management Error probability Encoding Delays

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The application of an extracellular vesicle-based biosensor in early diagnosis and prediction of chemoresponsiveness in ovarian cancer

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Cancer Letters 2024年 581卷 216533-216533页

作者： Tsang, Benjamin K. Asare-Werehene, Meshach Hunter, Rob Gerber, Emma Reunov, Arkadiy Brine, Isaiah Chang, Chia-Yu Chang, Chia-Ching Shieh, Dar-Bin Burger, Dylan Anis, Hanan Departments of Obstetrics & Gynecology and Cellular & Molecular Medicine Centre for Infection Immunity and Inflammation Interdisciplinary School of Health Sciences University of Ottawa Ottawa ON K1N 6N5 Canada Chronic Disease Program Ottawa Hospital Research Institute The Ottawa Hospital Ottawa ON K1Y 4E9 Canada Department of Biology St. Francis Xavier University 2320 Notre Dame Avenue Antigonish NS B2G 2W5 Canada School of Electrical Engineering and Computer Science Ottawa-Carleton Institute for Biomedical Engineering University of Ottawa Ottawa ON K1N 6N5 Canada Department of Biological Science and Department of Electrophysics Technology Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu 30068 Taiwan Institute of Basic Medical Science Institute of Oral Medicine and Department of Stomatology Advanced Optoelectronic Technology Center and Center for Micro/Nano Science and Technology National Cheng Kung University Hospital National Cheng Kung University Tainan 704 Taiwan Institute of Physics Academia Sinica Taipei 10529 Taiwan

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Inverse design Methods: Inverse design Strategies for 3D Surfaces Formed by Mechanically Guided Assembly (Adv. Mater. 14/2020)

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Advanced Materials 2020年第14期32卷

作者： Zhichao Fan Yiyuan Yang Fan Zhang Zheng Xu Hangbo Zhao Taoyi Wang Honglie Song Yonggang Huang John A. Rogers Yihui Zhang Applied Mechanics Laboratory Department of Engineering Mechanics Center for Flexible Electronics Technology Tsinghua University Beijing 100084 P. R. China Departments of Mechanical Engineering Northwestern University Evanston IL 60208 USA The State Key Laboratory for Manufacturing and Systems Engineering School of Mechanical Engineering Xi'an Jiaotong University Xi'an 710049 P. R. China Center for Bio‐Integrated Electronics Northwestern University Evanston IL 60208 USA Department of Physics Tsinghua University Beijing 100084 P. R. China Departments of Civil and Environmental Engineering Mechanical Engineering and Materials Science and Engineering Center for Bio‐Integrated Electronics Northwestern University Evanston IL 60208 USA Department of Materials Science and Engineering Biomedical Engineering Neurological Surgery Chemistry Mechanical Engineering Electrical Engineering and Computer Science Simpson Querrey Institute and Feinberg Medical School Center for Bio‐Integrated Electronics Northwestern University Evanston IL 60208 USA

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Eye tracking: empirical foundations for a minimal reporting guideline

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Behavior research methods 2023年第1期55卷 364-416页

作者： Kenneth Holmqvist Saga Lee Örbom Ignace T C Hooge Diederick C Niehorster Robert G Alexander Richard Andersson Jeroen S Benjamins Pieter Blignaut Anne-Marie Brouwer Lewis L Chuang Kirsten A Dalrymple Denis Drieghe Matt J Dunn Ulrich Ettinger Susann Fiedler Tom Foulsham Jos N van der Geest Dan Witzner Hansen Samuel B Hutton Enkelejda Kasneci Alan Kingstone Paul C Knox Ellen M Kok Helena Lee Joy Yeonjoo Lee Jukka M Leppänen Stephen Macknik Päivi Majaranta Susana Martinez-Conde Antje Nuthmann Marcus Nyström Jacob L Orquin Jorge Otero-Millan Soon Young Park Stanislav Popelka Frank Proudlock Frank Renkewitz Austin Roorda Michael Schulte-Mecklenbeck Bonita Sharif Frederick Shic Mark Shovman Mervyn G Thomas Ward Venrooij Raimondas Zemblys Roy S Hessels Department of Psychology Nicolaus Copernicus University Torun Poland. kenneth.holmqvist@ur.de. Department of Computer Science and Informatics University of the Free State Bloemfontein South Africa. kenneth.holmqvist@ur.de. Department of Psychology Regensburg University Regensburg Germany. kenneth.holmqvist@ur.de. Department of Psychology Regensburg University Regensburg Germany. Experimental Psychology Helmholtz Institute Utrecht University Utrecht The Netherlands. Lund University Humanities Lab and Department of Psychology Lund University Lund Sweden. Department of Ophthalmology SUNY Downstate Health Sciences University Brooklyn NY USA. Tobii Pro AB Danderyd Sweden. Social Health and Organizational Psychology Utrecht University Utrecht The Netherlands. Department of Computer Science and Informatics University of the Free State Bloemfontein South Africa. TNO Soesterberg The Netherlands. Department of Ergonomics Leibniz Institute for Working Environments and Human Factors Dortmund Germany. Institute of Informatics LMU Munich Munich Germany. Institute of Child Development University of Minnesota Minneapolis USA. School of Psychology University of Southampton Southampton UK. School of Optometry and Vision Sciences Cardiff University Cardiff UK. Department of Psychology University of Bonn Bonn Germany. Vienna University of Economics and Business Vienna Austria. Department of Psychology University of Essex Essex UK. Department of Neuroscience Erasmus MC Rotterdam The Netherlands. Machine Learning Group Department of Computer Science IT University of Copenhagen Copenhagen Denmark. SR Research Ltd Ottawa Canada. Human-Computer Interaction University of Tübingen Tübingen Germany. University of British Columbia Columbia Canada. Department of Eye and Vision Science Institute of Life Course and Medical Sciences University of Liverpool Liverpool UK. Department of Education and Pedagogy Division Education Faculty of Social and Behavioral Sciences Ut

In this paper, we present a review of how the various aspects of any study using an eye tracker (such as the instrument, methodology, environment, participant, etc.) affect the quality of the recorded eye-tracking data and the obtained eye-movement and gaze measures. We take this review to represent the empirical foundation for reporting guidelines of any study involving an eye tracker. We compare this empirical foundation to five existing reporting guidelines and to a database of 207 published eye-tracking studies. We find that reporting guidelines vary substantially and do not match with actual reporting practices. We end by deriving a minimal, flexible reporting guideline based on empirical research (Section "An empirically based minimal reporting guideline").

关键词： Data quality Eye movements Eye tracking Replicability Reporting guidelines Reporting practices Reporting standards Reproducibility

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Comparing LBP, HOG and Deep Features for Classification of Histopathology Images

arXiv

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arXiv 2018年

作者： Alhindi, Taha J. Kalra, Shivam Ng, Ka Hin Afrin, Anika Tizhoosh, Hamid R. Kimia Lab University of Waterloo Canada Dept. of Industrial Eng. King Abdulaziz Univ. Jeddah Saudi Arabia Systems Design Engineering University of Waterloo Canada Electrical and Computer Engineering University of Waterloo Canada

Medical image analysis has become a topic under the spotlight in recent years. There is a significant progress in medical image research concerning the usage of machine learning. However, there are still numerous questions and problems awaiting answers and solutions, respectively. In the present study, comparison of three classification models is conducted using features extracted using local binary patterns, the histogram of gradients, and a pre-trained deep network. Three common image classification methods, including support vector machines, decision trees, and artificial neural networks are used to classify feature vectors obtained by different feature extractors. We use KIMIA Path960, a publicly available dataset of 960 histopathology images extracted from 20 different tissue scans to test the accuracy of classification and feature extractions models used in the study, specifically for the histopathology images. SVM achieves the highest accuracy of 90.52% using local binary patterns as features which surpasses the accuracy obtained by deep features, namely 81.14%. Copyright © 2018, The Authors. All rights reserved.

关键词： Image classification

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From FAIR to CURE: Guidelines for Computational Models of Biological systems

arXiv

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arXiv 2025年

作者： Sauro, Herbert M. Agmon, Eran Blinov, Michael L. Gennari, John H. Hellerstein, Joe Heydarabadipour, Adel Hunter, Peter Jardine, Bartholomew E. May, Elebeoba Nickerson, David P. Smith, Lucian P. Bader, Gary D. Bergmann, Frank Boyle, Patrick M. Dräger, Andreas Faeder, James R. Feng, Song Freire, Juliana Fröhlich, Fabian Glazier, James A. Gorochowski, Thomas E. Helikar, Tomas Hoops, Stefan Imoukhuede, Princess Keating, Sarah M. Konig, Matthias Laubenbacher, Reinhard Loew, Leslie M. Lopez, Carlos F. Lytton, William W. McCulloch, Andrew Mendes, Pedro Myers, Chris J. Myers, Jerry G. Mulugeta, Lealem Niarakis, Anna van Niekerk, David D. Olivier, Brett G. Patrie, Alexander A. Quardokus, Ellen M. Radde, Nicole Rohwer, Johann M. Sahle, Sven Schaff, James C. Sego, T.J. Shin, Janis Snoep, Jacky L. Vadigepalli, Rajanikanth Wiley, H. Steve Waltemath, Dagmar Moraru, Ion Department of Bioengineering University of Washington SeattleWA98195-5061 United States Intelligent Systems Engineering and Biocomplexity Institute Indiana University Street BloomingtonIN47408 United States Center for Cardiovascular Biology University of Washington SeattleWA98195-5061 United States eScience Institute University of Washington SeattleWA98195-5061 United States Institute for Stem Cell and Regenerative Medicine University of Washington SeattleWA98195-5061 United States School of Biological Sciences University of Bristol 24 Tyndall Avenue BristolBS8 1TQ United Kingdom Departments of Physiology & Pharmacology Neurology Downstate Health Science University BrooklynNY11203 United States Department of Neurology Kings County Hospital BrooklynNY11203 United States NASA-John H. Glenn Research Center MS 110-3 21000 Brookpark Road ClevelandOH44135 United States Center for Cell Analysis and Modeling UConn Health 263 Farmington Avenue FarmingtonCT06030-6406 United States Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam1081 HZ Netherlands Department of Pathology and Genomic Medicine Thomas Jefferson University 1020 Locust St PhiladelphiaPA19107 United States Biological Sciences Division Pacific Northwest National Laboratory 902 Battelle Blvd RichlandWA99354 United States Auckland Bioengineering Institute University of Auckland Auckland1010 New Zealand Center of Integrative Biology University of Toulouse III-Paul Sabatier 165 Rue Marianne Grunberg-Manago Toulouse31400 France Lifeware Group Inria Building Alan Turing 1 Rue Honoré d’Estienne d’Orves Palaiseau91120 France Multiscale Modeling Group Altos Labs Redwood CityCA94065 United States partner site Tübingen Tübingen Germany Ottfried-Müller-Str. 37 Tübingen72076 Germany 06120 Germany Department of Computer Science Center for Data Science New York University New YorkNY11201 United States Department of Bi

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility;the clarity of model descriptions and annotations for understandability;adherence to standards and open science practices for reproducibility;and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible. © 2025, CC BY.

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Corrigendum to "A generalized predictive model for TiO2-Catalyzed photo-degradation rate constants of water contaminants through artificial neural network" [Environ. Res., 187, (2020), 109697]

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Environmental research 2020年 188卷 109850页

作者： Zhuoying Jiang Jiajie Hu Xijin Zhang Yihang Zhao Xudong Fan Shifa Zhong Huichun Zhang Xiong Yu Department of Civil and Environmental Engineering Case Western Reserve University 2104 Adelbert Road Cleveland OH 44106 USA. Gilmour Academy 34001 Cedar Road GatesMills OH 44040 USA. Department of Civil and Environmental Engineering Case Western Reserve University 2104 Adelbert Road Cleveland OH 44106 USA Departments of Computer and Data Sciences and Electrical Computer and Systems Engineering Case Western Reserve University 2104 Adelbert Road Cleveland OH 44106 USA. Electronic address: xxy21@case.edu.

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