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Impact of scanner variability on lymph node segmentation in computational pathology

Journal of Pathology Informatics 2022年 13卷 100127-100127页

作者： Khan, Amjad Janowczyk, Andrew Müller, Felix Blank, Annika Nguyen, Huu Giao Abbet, Christian Studer, Linda Lugli, Alessandro Dawson, Heather Thiran, Jean-Philippe Zlobec, Inti Institute of Pathology University of Bern Murtenstrasse 31 Bern CH-3008 Switzerland Case Western Reserve University Department of Biomedical Engineering Cleveland 44106 OH United States Department of Oncology Lausanne University Hospital and Lausanne University Lausanne Switzerland Swiss Federal Institute of Technology Lausanne (EPFL) Signal Processing Laboratory (LTS5) Lausanne Switzerland Institute of Complex Systems (iCoSyS) University of Applied Sciences and Arts Western Switzerland Delémont Switzerland Document Image and Video Analysis (DIVA) Research Group Department of Informatics University of Fribourg Fribourg Switzerland Department of Radiology Lausanne University Hospital Lausanne University Centre d'Imagerie Biomédicale (CIBM) Lausanne Switzerland Institute of Pathology City Hospital Triemli Zürich Switzerland

Computer-aided diagnostics in histopathology are based on the digitization of glass slides. However, heterogeneity between the images generated by different slide scanners can unfavorably affect the performance of computational algorithms. Here, we evaluate the impact of scanner variability on lymph node segmentation due to its clinical importance in colorectal cancer diagnosis. 100 slides containing 276 lymph nodes were digitized using 4 different slide scanners, and 50 of the lymph nodes containing metastatic cancer cells. These 400 scans were subsequently annotated by 2 experienced pathologists to precisely label lymph node boundary. Three different segmentation methods were then applied and compared: Hematoxylin-channel-based thresholding (HCT), Hematoxylin-based active contours (HAC), and a convolution neural network (U-Net). Evaluation of U-Net trained from both a single scanner and an ensemble of all scanners was completed. Mosaic images based on representative tiles from a scanner were used as a reference image to normalize the new data from different test scanners to evaluate the performance of a pre-trained model. Fine-tuning was carried out by using weights of a model trained on one scanner to initialize model weights for other scanners. To evaluate the domain generalization, domain adversarial learning and stain mix-up augmentation were also implemented. Results show that fine-tuning and domain adversarial learning decreased the impact of scanner variability and greatly improved segmentation across scanners. Overall, U-Net with stain mix-up (Matthews correlation coefficient (MCC) = 0.87), domain adversarial learning (MCC = 0.86), and HAC (MCC = 0.87) were shown to outperform HCT (MCC = 0.81) for segmentation of lymph nodes when compared against the ground truth. The findings of this study should be considered for future algorithms applied in diagnostic routines. © 2022 The Author(s)

关键词： Colorectal cancer Computational pathology Domain generalization Fine tuning Lymph node Lymph node segmentation Scanner variability Whole slide image

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What's in a frequency: new tools for graph fourier transform visualization

arXiv

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arXiv 2019年

作者： Girault, Benjamin Ortega, Antonio Signal and Image Processing Institute Department of Electrical and Computer Engineering University of Southern California Los Angeles United States

Recent progress in graph signal processing (GSP) has addressed a number of problems, including sampling and filtering. Proposed methods have focused on generic graphs and defined signals with certain characteristics, e.g., bandlimited signals, based on the graph Fourier transform (GFT). However, the effect of GFT properties (e.g., vertex localization) on the behavior of such methods is not as well understood. In this paper, we propose novel GFT visualization tools and provide some examples to illustrate certain GFT properties and their impact on sampling or wavelet transforms. Copyright © 2019, The Authors. All rights reserved.

关键词： Visualization

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Robust variational autoencoder

arXiv

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arXiv 2019年

作者： Akrami, Haleh Joshi, Anand A. Li, Jian Leahy, Richard M. Signal and Image Processing Institute Ming Hsieh Department of Electrical and Computer Engineering University of Southern California Los AngelesCA United States

Machine learning methods often need a large amount of labeled training data. Since the training data is assumed to be the ground truth, outliers can severely degrade learned representations and performance of trained models. Here we apply concepts from robust statistics to derive a novel variational autoencoder that is robust to outliers in the training data. Variational autoencoders (VAEs) extract a lower dimensional encoded feature representation from which we can generate new data samples. Robustness of autoencoders to outliers is critical for generating a reliable representation of particular data types in the encoded space when using corrupted training data. Our robust VAE is based on beta-divergence rather than the standard Kullback-Leibler (KL) divergence. Our proposed model has the same computational complexity as the VAE, and contains a single tuning parameter to control the degree of robustness. We demonstrate performance of the betadivergence based autoencoder for a range of image data types, showing improved robustness to outliers both qualitatively and quantitatively. We also illustrate the use of the robust VAE for outlier detection. Copyright © 2019, The Authors. All rights reserved.

关键词： Statistics

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Performance prediction recipes for optical links

arXiv

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arXiv 2021年

作者： Agrell, Erik Secondini, Marco Alvarado, Alex Yoshida, Tsuyoshi The Department of Electrical Engineering Chalmers University of Technology Gothenburg41296 Sweden The Institute of Communication Information and Perception Technologies Scuola Superiore Sant'Anna Pisa Italy The National Laboratory of Photonic Networks CNIT Pisa Italy The Information and Communication Theory Lab Signal Processing Systems Group Department of Electrical Engineering Eindhoven University of Technology Eindhoven5600 MB Netherlands Information Technology R&D Center Mitsubishi Electric Corporation 5-1-1 Ofuna Kamakura247-8501 Japan Graduate School of Osaka University 2-1 Yamadaoka Suita565-0871 Japan

Although forward error-correction (FEC) coding is an essential part of modern fiber-optic communication systems, it is impractical to implement and evaluate FEC in transmission experiments and simulations. Therefore, it is desirable to accurately predict the end-to-end link performance including FEC from transmission data recorded without FEC. In this tutorial, we provide ready-to-implement "recipes" for such prediction techniques, which apply to arbitrary channels and require no knowledge of information or coding theory. The appropriate choice of recipe depends on properties of the FEC encoder and decoder. The covered metrics include bit error rate, symbol error rate, achievable information rate, and asymptotic information, in all cases computed using a mismatched receiver. Supplementary software implementations are available. © 2021, CC BY-SA.

关键词： Forward error correction

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Learning data-adaptive non-parametric kernels

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2020年第1期21卷 8590-8628页

作者： Fanghui Liu Xiaolin Huang Chen Gong Jie Yang Li Li Department of Electrical Engineering ESAT-STADIUS KU Leuven Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China PCA Lab Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology China and Department of Computing Hong Kong Polytechnic University Hong Kong SAR China Department of Automation BNRist Tsinghua University China

In this paper, we propose a data-adaptive non-parametric kernel learning framework in margin based kernel methods. In model formulation, given an initial kernel matrix, a data-adaptive matrix with two constraints is imposed in an entry-wise scheme. Learning this data-adaptive matrix in a formulation-free strategy enlarges the margin between classes and thus improves the model flexibility. The introduced two constraints are imposed either exactly (on small data sets) or approximately (on large data sets) in our model, which provides a controllable trade-off between model flexibility and complexity with theoretical demonstration. In algorithm optimization, the objective function of our learning framework is proven to be gradient-Lipschitz continuous. Thereby, kernel and classifier/regressor learning can be efficiently optimized in a unified framework via Nesterov's acceleration. For the scalability issue, we study a decomposition-based approach to our model in the large sample case. The effectiveness of this approximation is illustrated by both empirical studies and theoretical guarantees. Experimental results on various classification and regression benchmark data sets demonstrate that our non-parametric kernel learning framework achieves good performance when compared with other representative kernel learning based algorithms.

关键词： support vector machines non-parametric kernel learning gradient-Lipschitz continuous

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Understanding metric-related pitfalls in image analysis validation

arXiv

引用

arXiv 2023年

作者： Reinke, Annika Tizabi, Minu D. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Kavur, A. Emre Rädsch, Tim Sudre, Carole H. Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Buettner, Florian Cardoso, M. Jorge Cheplygina, Veronika Chen, Jianxu Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kleesiek, Jens Kofler, Florian Kooi, Thijs Kopp-Schneider, Annette Kozubek, Michal Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Riegler, Michael A. Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. van Calster, Ben Varoquaux, Gaël Yaniv, Ziv R. Jäger, Paul F. Maier-Hein, Lena Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany NCT Heidelberg A Partnership Between DKFZ University Medical Center Heidelberg Germany Heidelberg Division of Medical Image Computing Germany Heidelberg Division of Intelligent Medical Systems Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montreal Canada Division of Computational Pathology Dept of Pathology & Laboratory Medicine Indiana University School of Medicine IU Health Information and Translational Sciences Building Indianapolis United States University of Pennsylvania Richards Medical Research Laboratories FL7 PhiladelphiaPA United States Department of Digital Medical Technologies Holon Institute of Technology Holon Israel European Federation for Medical Informatics Le Mont-sur-Lausanne Switzerland Center for Processing Speech and Images Department of Electrical Engineering KU Leuven Leuven Belgium partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany and Frankfurt Cancer Insititute Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for Statistics in Medicine University of Oxford Oxford United Kingdom Center for Biomedical In

Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately. While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. While focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation. © 2023, CC BY.

关键词： Computer vision

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Graphene based functional devices: A short review

引用

Frontiers of physics 2019年第1期14卷 23-42页

作者： Rong Wang Xin-Gang Ren Ze Yan Li-Jun Jiang Wei E. I. Sha Guang-Cun Shan Department of Electrical and Electronic Engineering The University of Hong Kong Pokfulam Road Hong Kong China Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei 230039 China School of Instrumentation Science & Opto-electronics Engineering Beihang University Beijing 100191 China Key Laboratory of Micro-nano Electronic Devices and Smart Systems of Zhejiang Province College of Information Science & Electronic Engineering Zhejiang University Hangzhou 310027 China California NanoSystem Institute and Department of Chemistry & Biochemistry University of California Los Angeles CA 90095 USA

Graphene is an ideal 2D material system bridging electronic and photonic devices. It also breaks the fundamental speed and size limits by electronics and photonics, respectively. Graphene offers multiple functions of signal transmission, emission, modulation, and detection in a broad band, high speed, compact size, and low loss. Here, we have a brief view of graphene based functional devices at microwave, terahertz, and optical frequencies. Their fundamental physics and computational models were discussed as well.

关键词： graphene terahertz antenna microwave

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An interpretable compression and classification system: Theory and Applications

arXiv

引用

arXiv 2019年

作者： Tseng, Tzu-Wei Yang, Kai-Jiun Jay Kuo, C.-C. Tsai, Shang-Ho department of Electrical Engineering National Chiao Tung University Hsinchu Taiwan Industrial Technology Research Institute Zhudong31057 Taiwan department of Electrical Engineering Signal and Image Processing Institute University of Southern California Los Angeles United States

This study proposes a low-complexity interpretable classification system. The proposed system contains main modules including feature extraction, feature reduction, and classification. All of them are linear. Thanks to the linear property, the extracted and reduced features can be inversed to original data, like a linear transform such as Fourier transform, so that one can quantify and visualize the contribution of individual features towards the original data. Also, the reduced features and reversibility naturally endure the proposed system ability of data compression. This system can significantly compress data with a small percent deviation between the compressed and the original data. At the same time, when the compressed data is used for classification, it still achieves high testing accuracy. Furthermore, we observe that the extracted features of the proposed system can be approximated to uncorrelated Gaussian random variables. Hence, classical theory in estimation and detection can be applied for classification. This motivates us to propose using a MAP (maximum a posteriori) based classification method. As a result, the extracted features and the corresponding performance have statistical meaning and mathematically interpretable. Simulation results show that the proposed classification system not only enjoys significant reduced training and testing time but also high testing accuracy compared to the conventional schemes. Copyright © 2019, The Authors. All rights reserved.

关键词： Classification (of information)

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Locality in index coding for large min-rank

arXiv

引用

arXiv 2019年

作者： Natarajan, Lakshmi Dau, Hoang Krishnan, Prasad Lalitha, V. Department of Electrical Engineering Indian Institute of Technology Hyderabad Department of Electrical and Computer Systems Engineering Monash University Melbourne Australia Signal Processing & Communications Research Center International Institute of Information Technology Hyderabad India

An index code is said to be locally decodable if each receiver can decode its demand using its side information and by querying only a subset of the transmitted codeword symbols instead of observing the entire codeword. Local decodability can be a beneficial feature in some communication scenarios, such as when the receivers can afford to listen to only a part of the transmissions because of limited availability of power. The locality of an index code is the ratio of the maximum number of codeword symbols queried by a receiver to the message length. In this paper we analyze the optimum locality of linear codes for the family of index coding problems whose min-rank is one less than the number of receivers in the network. We first derive the optimal trade-off between the index coding rate and locality with vector linear coding when the side information graph is a directed cycle. We then provide the optimal trade-off achieved by scalar linear coding for a larger family of problems, viz., problems where the min-rank is only one less than the number of receivers. While the arguments used for achievability are based on known coding techniques, the converse arguments rely on new results on the structure of locally decodable index codes. Copyright © 2019, The Authors. All rights reserved.

关键词： Decoding

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A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

arXiv

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arXiv 2024年

作者： de la Rosa, Ezequiel Reyes, Mauricio Liew, Sook-Lei Hutton, Alexandre Wiest, Roland Kaesmacher, Johannes Hanning, Uta Hakim, Arsany Zubal, Richard Valenzuela, Waldo Robben, David Sima, Diana M. Anania, Vincenzo Brys, Arne Meakin, James A. Mickan, Anne Broocks, Gabriel Heitkamp, Christian Gao, Shengbo Liang, Kongming Zhang, Ziji Siddiquee, Md Mahfuzur Rahman Myronenko, Andriy Ashtari, Pooya Van Huffel, Sabine Jeong, Hyun-Su Yoon, Chi-Ho Kim, Chulhong Huo, Jiayu Ourselin, Sebastien Sparks, Rachel Clèrigues, Albert Oliver, Arnau Lladó, Xavier Chalcroft, Liam Pappas, Ioannis Bertels, Jeroen Heylen, Ewout Moreau, Juliette Hatami, Nima Frindel, Carole Qayyum, Abdul Mazher, Moona Puig, Domenec Lin, Shao-Chieh Juan, Chun-Jung Hu, Tianxi Boone, Lyndon Goubran, Maged Liu, Yi-Jui Wegener, Susanne Kofler, Florian Ezhov, Ivan Shit, Suprosanna Hernandez Petzsche, Moritz R. Menze, Bjoern Kirschke, Jan S. Wiestler, Benedikt Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Informatics Technical University Munich Germany Icometrix Leuven Belgium ARTORG Center for Biomedical Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Switzerland University of Bern Bern Switzerland Chan Division of Occupational Science and Occupational Therapy University of Southern California Los AngelesCA United States Stevens Neuroimaging and Informatics Institute Department of Neurology Keck School of Medicine University of Southern California United States University Institute of Diagnostic and Interventional Neuroradiology Inselspital Bern Switzerland University Institute of Diagnostic and Interventional Neuroradiology University Hospital Bern Inselspital University of Bern Bern Switzerland Department of Diagnostic and Interventional neuroradiology University Medical Center Hamburg-Eppendorf Hamburg Germany Department of Medical Imaging Radboud University Medical Center Institute for Health Sciences Nijmegen Netherlands Deepwise AI Lab Beijing China Beijing University of Posts and Telecommunications Bejing China School of Computing and Augmented Intelligence Arizona State University TempeAZ United States NVIDIA Santa ClaraCA United States STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Pohang Korea Republic of School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Institute of Computer Vision and Robotics University of Girona Spain Wellcome Centre for Human Neuroimaging University College London London United Kingdom Laboratory of Neuro Imaging Stevens Institute for Neuroimaging and Informatics Keck School of Medicine University of Southern California Los Angeles United States KU Leuven Leuven Belgium CREATIS Université Lyon1 CNRS UMR5220 INSERM U1206 INSA-Lyon Villeurbanne696

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES’22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. By assessing them against a hidden test set, we identified strengths, weaknesses, and potential biases. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model combines the individual algorithms’ strengths and achieved superior ischemic lesion detection and segmentation accuracy (median Dice score: 0.82, median lesion-wise F1 score: 0.86) on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers like lesion types and affected vascular territories. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm’s segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model’s generalizability (median Dice score: 0.82, median lesion-wise F1 score: 0.86). The algorithm’s outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)rad

关键词： Diagnosis

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