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Common Limitations of image processing Metrics: A Picture Story

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arXiv 2021年

作者： Reinke, Annika Tizabi, Minu D. Sudre, Carole H. Eisenmann, Matthias Rädsch, Tim Baumgartner, Michael Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Bankhead, Peter Benis, Arriel Blaschko, Matthew Buettner, Florian Cardoso, M. Jorge Chen, Jianxu Cheplygina, Veronika Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Engelhardt, Sandy Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hamprecht, Fred Hashimoto, Daniel A. Heckmann-Nötzel, Doreen Hirsch, Peter Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kavur, A. Emre Kenngott, Hannes Kleesiek, Jens Kleppe, Andreas Koehler, Sven Kofler, Florian Kopp-Schneider, Annette Kooi, Thijs 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 Moher, David Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Noyan, M. Alican Petersen, Jens Polat, Gorkem Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Rieke, Nicola Riegler, Michael A. Rivaz, Hassan Saez-Rodriguez, Julio Sánchez, Clara I. Schroeter, Julien Saha, Anindo Selver, M. Alper Sharan, Lalith Shetty, Shravya Smeden, Maarten V.A.N. Stieltjes, Bram Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben V.A.N. Varoquaux, Gaël Wiesenfarth, Manuel Yaniv, Ziv R. Jäger, Paul Maier-Hein, Lena Division of Intelligent Medical Systems and HI Helmholtz Imaging Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Intelligent Medical Systems Heidelberg Germany NCT Heidelberg DKFZ University Medical Center Heidelberg 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 Division of Medical Image Computing Heidelberg Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal 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 Institute of Genetics and Cancer University of Edinburgh Edinburgh United Kingdom 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 Kasteelpark Arenberg 10 - box 2441 Leuven3001 Belgium Frankfurt/Mainz DKFZ UCT Frankfurt-Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany Frankfurt Cancer Insititute Germany Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for St

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide. © 2021, CC BY.

关键词： Medical imaging

STUDY OF DENSE NETWORK APPROACHES FOR SPEECH EMOTION RECOGNITION

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STUDY OF DENSE NETWORK APPROACHES FOR SPEECH EMOTION RECOGNI...

IEEE International Conference on Acoustics, Speech and signal processing

作者： Mohammed Abdelwahab Carlos Busso Multimodal Signal Processing (MSP) Laboratory Department of Electrical Computer Engineering The University of Texas at Dallas Richardson TX 75080 USA

ISBN: (纸本)9781538646595

Deep neural networks have been proven to be very effective in various classification problems and show great promise for emotion recognition from speech. Studies have proposed various architectures that further improve the performance of emotion recognition systems. However, there are still various open questions regarding the best approach to building a speech emotion recognition system. Would the system's performance improve if we have more labeled data? How much do we benefit from data augmentation? What activation and regularization schemes are more beneficial? How does the depth of the network affect the performance? We are collecting the MSP-Podcast corpus, a large dataset with over 30 hours of data, which provides an ideal resource to address these questions. This study explores various dense architectures to predict arousal, valence and dominance scores. We investigate varying the training set size, width, and depth of the network, as well as the activation functions used during training. We also study the effect of data augmentation on the network's performance. We find that bigger training set improves the performance. Batch normalization is crucial to achieving a good performance for deeper networks. We do not observe significant differences in the performance in residual networks compared to dense networks.

关键词： Speech emotion recognition Deep Neural Networks emotion recognition System performance Speech Network Activating function

NOVEL REALIZATIONS OF SPEECH-DRIVEN HEAD MOVEMENTS WITH GENERATIVE ADVERSARIAL NETWORKS

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NOVEL REALIZATIONS OF SPEECH-DRIVEN HEAD MOVEMENTS WITH GENE...

IEEE International Conference on Acoustics, Speech and signal processing

作者： Najmeh Sadoughi Carlos Busso Multimodal Signal Processing (MSP) Laboratory Department of Electrical and Computer Engineering The University of Texas at Dallas Richardson TX 75080 USA

ISBN: (纸本)9781538646595

Head movement is an integral part of face-to-face communications. It is important to investigate methodologies to generate naturalistic movements for conversational agents (CAs). The predominant method for head movement generation is using rules based on the meaning of the message. However, the variations of head movements by these methods are bounded by the predefined dictionary of gestures. Speech-driven methods offer an alternative approach, learning the relationship between speech and head movements from real recordings. However, previous studies do not generate novel realizations for a repeated speech signal. Conditional generative adversarial network (GAN) provides a framework to generate multiple realizations of head movements for each speech segment by sampling from a conditioned distribution. We build a conditional GAN with bidirectional long-short term memory (BLSTM), which is suitable for capturing the long-short term dependencies of time-continuous signals. This model learns the distribution of head movements conditioned on speech prosodic features. We compare this model with a dynamic Bayesian network (DBN) and BLSTM models optimized to reduce mean squared error (MSE) or to increase concordance correlation. The objective evaluations and subjective evaluations of the results showed better performance for the conditional GAN model compared with these baseline systems.

关键词： Head movements synthesis speech-driven animation conditional generative adversarial networks Head Movements Speech Head Conditional Voice signal Mean square error

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Publisher Correction: Brain imaging with portable low-field MRI

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Nature Reviews Bioengineering

Nature Reviews Bioengineering 2023年 680页

作者： W. Taylor Kimberly Annabel J. Sorby-Adams Andrew G. Webb Ed X. Wu Rachel Beekman Kevin N. Sheth Ritvij Bowry Steven J. Schiff Adam de Havenon Francis X. Shen Gordon Sze Pamela Schaefer Juan Eugenio Iglesias Matthew S. Rosen Department of Neurology and the Center for Genomic Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA Department of Radiology Leiden University Medical Center Leiden The Netherlands Laboratory of Biomedical Imaging and Signal Processing Department of Electrical and Electronic Engineering The University of Hong Kong Hong Kong SAR China Division of Neurocritical Care and Emergency Neurology Department of Neurology Yale New Haven Hospital and Yale School of Medicine Yale Center for Brain & Mind Health New Haven CT USA Departments of Neurosurgery and Neurology McGovern Medical School University of Texas Health Neurosciences Houston TX USA Department of Neurosurgery Yale School of Medicine New Haven CT USA Division of Vascular Neurology Department of Neurology Yale New Haven Hospital and Yale School of Medicine New Haven CT USA Harvard Medical School Center for Bioethics Harvard law School Boston MA USA Department of Psychiatry Massachusetts General Hospital Boston MA USA Department of Radiology Yale New Haven Hospital and Yale School of Medicine New Haven CT USA Division of Neuroradiology Department of Radiology Massachusetts General Hospital and Harvard Medical School Boston MA USA Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology Massachusetts General Hospital and Harvard Medical School Boston MA USA Centre for Medical Image Computing University College London London UK Computer Science and AI Laboratory Massachusetts Institute of Technology Boston MA USA

Forecasting of jump arrivals in stock prices: New attention-based network architecture using limit order book data

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arXiv 2018年

作者： Mäkinen, Milla Kanniainen, Juho Gabbouj, Moncef Iosifidis, Alexandros Laboratory of Signal Processing Tampere University of Technology Finland Laboratory of Industrial and Information Management Tampere University of Technology Finland Department of Engineering Electrical and Computer Engineering Aarhus University Denmark

The existing literature provides evidence that limit order book data can be used to predict short-term price movements in stock markets. This paper proposes a new neural network architecture for predicting return jump arrivals in equity markets with high-frequency limit order book data. This new architecture, based on Convolutional Long Short-Term Memory with Attention, is introduced to apply time series representation learning with memory and to focus the prediction attention on the most important features to improve performance. The data set consists of order book data on five liquid U.S. stocks. The use of the attention mechanism makes it possible to analyze the importance of the inclusion limit order book data and other input variables. By using this mechanism, we provide evidence that the use of limit order book data was found to improve the performance of the proposed model in jump prediction, either clearly or marginally, depending on the underlying stock. This suggests that path-dependence in limit order book markets is a stock specific feature. Moreover, we find that the proposed approach with an attention mechanism outperforms the multi-layer perceptron network as well as the convolutional neural network and Long Short-Term memory model. Copyright © 2018, The Authors. All rights reserved.

关键词： Long short-term memory

GazeGAN: A robust generative adversarial saliency model based on invariance analysis of human gaze during scene free viewing

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arXiv 2019年

作者： Che, Zhaohui Borji, Ali Zhai, Guangtao Min, Xiongkuo Guo, Guodong Le Callet, Patrick Institute of Image Communication and Network Engineering Shanghai Key Laboratory of Digital Media Processing and Transmissions Shanghai Jiao Tong University Shanghai200240 China MarkableAI United States Institute of Deep Learning Baidu Research Department of Computer Science and Electrical Engineering West Virginia University MorgantownWV United States Equipe Image Perception et Interaction Laboratoire des Sciences du Numérique de Nantes Université de Nantes France

—Data size is the bottleneck for developing deep saliency models, because collecting eye-movement data is very time-consuming and expensive. Most of current studies on human attention and saliency modeling have used high-quality stereotype stimuli. In real world, however, captured images undergo various types of transformations. Can we use these transformations to augment existing saliency datasets? Here, we first create a novel saliency dataset including fixations of 10 observers over 1900 images degraded by 19 types of transformations. Second, by analyzing eye movements, we find that observers look at different locations over transformed versus original images. Third, we utilize the new data over transformed images, called data augmentation transformation (DAT), to train deep saliency models. We find that label-preserving DATs with negligible impact on human gaze boost saliency prediction, whereas some other DATs that severely impact human gaze degrade the performance. These label-preserving valid augmentation transformations provide a solution to enlarge existing saliency datasets. Finally, we introduce a novel saliency model based on generative adversarial network (dubbed GazeGAN). A modified U-Net is proposed as the generator of the GazeGAN, which combines classic "skip connections" with a novel "center-surround connection (CSC)", in order to leverage multi-level features. We also propose a histogram loss based on Alternative Chi-Square Distance (ACS HistLoss) to refine the saliency map in terms of luminance distribution. Extensive experiments and comparisons over 3 datasets indicate that GazeGAN achieves the best performance in terms of popular saliency evaluation metrics, and is more robust to various perturbations. We also provide a comprehensive quantitative comparison of 22 state-of-the-art saliency models on distorted images, which contributes a robustness benchmark for saliency community. Our code and data are available at: https://***/CZHQuality/

关键词： Luminance

Neural signatures of motor skill in the resting brain

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arXiv 2019年

作者： Özdenizci, Ozan Meyer, Timm Wichmann, Felix Peters, Jan Schölkopf, Bernhard Çetin, Müjdat Grosse-Wentrup, Moritz Department of Electrical and Computer Engineering Northeastern University BostonMA United States Signal Processing and Information Systems Laboratory Faculty of Engineering and Natural Sciences Sabancı University Istanbul Turkey Max Planck Institute for Intelligent Systems Tübingen Germany Faculty of Science University of Tübingen Bernstein Center for Computational Neuroscience Tübingen Tübingen Germany FG Intelligente Autonome Systeme Technische Universität Darmstadt Darmstadt Germany Department of Electrical and Computer Engineering University of Rochester RochesterNY United States Research Group Neuroinformatics Faculty of Computer Science University of Vienna Vienna Austria

Stroke-induced disturbances of large-scale cortical networks are known to be associated with the extent of motor deficits. We argue that identifying brain networks representative of motor behavior in the resting brain would provide significant insights for current neurorehabilitation approaches. Particularly, we aim to investigate the global configuration of brain rhythms and their relation to motor skill, instead of learning performance as broadly studied. We empirically approach this problem by conducting a three-dimensional physical space visuomotor learning experiment during electroencephalographic (EEG) data recordings with thirty-seven healthy participants. We demonstrate that across-subjects variations in average movement smoothness as the quantified measure of subjects' motor skills can be predicted from the global configuration of resting-state EEG alpha-rhythms (8-14 Hz) recorded prior to the experiment. Importantly, this neural signature of motor skill was found to be orthogonal to (independent of) task- as well as to learning-related changes in alpha-rhythms, which we interpret as an organizing principle of the brain. We argue that disturbances of such configurations in the brain may contribute to motor deficits in stroke, and that reconfiguring stroke patients' brain rhythms by neurofeedback may enhance post-stroke neurorehabilitation. Copyright © 2019, The Authors. All rights reserved.

关键词： Electroencephalography

AI-based volumetric six-tissue body composition quantification from CT cardiac attenuation scans for mortality prediction: a multicentre study

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The Lancet. Digital health 2025年第5期7卷 100862页

作者： Jirong Yi Anna M Marcinkiewicz Aakash Shanbhag Robert J H Miller Jolien Geers Wenhao Zhang Aditya Killekar Nipun Manral Mark Lemley Mikolaj Buchwald Jacek Kwiecinski Jianhang Zhou Paul B Kavanagh Joanna X Liang Valerie Builoff Terrence D Ruddy Andrew J Einstein Attila Feher Edward J Miller Albert J Sinusas Daniel S Berman Damini Dey Piotr J Slomka Departments of Medicine (Division of Artificial Intelligence in Medicine) Biomedical Sciences and Imaging Cedars-Sinai Medical Center Los Angeles CA USA. Departments of Medicine (Division of Artificial Intelligence in Medicine) Biomedical Sciences and Imaging Cedars-Sinai Medical Center Los Angeles CA USA Center of Radiological Diagnostics National Medical Institute of the Ministry of the Interior and Administration Warsaw Poland. Signal and Image Processing Institute Ming Hsieh Department of Electrical and Computer Engineering University of Southern California Los Angeles CA USA. Department of Cardiac Sciences University of Calgary Calgary AB Canada. Department of Cardiology Centrum voor Hart-en Vaatziekten (CHVZ) Universitair Ziekenhuis Brussel (UZ Brussel) Vrije Universiteit Brussel (VUB) Brussels Belgium. Department of Interventional Cardiology and Angiology Institute of Cardiology Warsaw Poland. Division of Cardiology University of Ottawa Heart Institute Ottawa ON Canada. Division of Cardiology Department of Medicine and Department of Radiology Columbia University Irving Medical Center and New York-Presbyterian Hospital New York NY USA. Section of Cardiovascular Medicine Department of Internal Medicine Yale University School of Medicine New Haven CT USA. Departments of Medicine (Division of Artificial Intelligence in Medicine) Biomedical Sciences and Imaging Cedars-Sinai Medical Center Los Angeles CA USA. Electronic address: piotr.slomka@***.

BACKGROUND:CT attenuation correction (CTAC) scans are routinely obtained during cardiac perfusion imaging, but currently only used for attenuation correction and visual calcium estimation. We aimed to develop a novel artificial intelligence (AI)-based approach to obtain volumetric measurements of chest body composition from CTAC scans and to evaluate these measures for all-cause mortality risk stratification. METHODS:We applied AI-based segmentation and image-processing techniques on CTAC scans from a large international image-based registry at four sites (Yale University, University of Calgary, Columbia University, and University of Ottawa), to define the chest rib cage and multiple tissues. Volumetric measures of bone, skeletal muscle, subcutaneous adipose tissue, intramuscular adipose tissue (IMAT), visceral adipose tissue (VAT), and epicardial adipose tissue (EAT) were quantified between automatically identified T5 and T11 vertebrae. The independent prognostic value of volumetric attenuation and indexed volumes were evaluated for predicting all-cause mortality, adjusting for established risk factors and 18 other body composition measures via Cox regression models and Kaplan-Meier curves. FINDINGS:The end-to-end processing time was less than 2 min per scan with no user interaction. Between 2009 and 2021, we included 11 305 participants from four sites participating in the REFINE SPECT registry, who underwent single-photon emission computed tomography cardiac scans. After excluding patients who had incomplete T5-T11 scan coverage, missing clinical data, or who had been used for EAT model training, the final study group comprised 9918 patients. 5451 (55%) of 9918 participants were male and 4467 (45%) of 9918 participants were female. Median follow-up time was 2·48 years (IQR 1·46-3·65), during which 610 (6%) patients died. High VAT, EAT, and IMAT attenuation were associated with an increased all-cause mortality risk (adjusted hazard ratio 2·39, 95% CI 1·92-2·96; p<

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