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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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Robotic Software System for the Disaster Circumstances: System of Team KAIST in the DARPA robotics Challenge Finals

Robotic Software System for the Disaster Circumstances: Syst...

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IEEE-RAS International Conference on Humanoid Robots

作者： Jeongsoo Lim Inwook Shim Okkee Sim Hyunmin Joe Inhyeok Kim Jungho Lee Jun-Ho Oh Humanoid Research Center School of Mechanical Aerospace & Systems Engineering Department of Mechanical Engineering Korea Advanced Institute of Science and Technology Robotics and Computer Vision Laboratory Department of Electrical Engineering College of Information Science and Technology Korea Advanced Institute of Science and Technology Rainbow Co.

ISBN: (纸本)9781479968862

We developed a software system for operating the humanoid robot DRC-HUBO+ in disaster circumstances that the US Defense Advanced research Projects Agency suggested. This system was developed under the consideration of the stability of whole system, the systemic software environment for multiple developers, and the recovery routine when the system encounters a seriously abnormal situation. With these design goals, we devised our strategy for three domains: system, vision, and communication. Following the strategy we made two software frameworks (PODO and VPC) and one logical flow of data for remote process management. With this software system, we conducted all Tasks in the DARPA robotics Challenge Finals, and we won the competition.

关键词： Software systems DARPA design target robotics Disasters Religious Missions flow datas

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25th Annual Computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

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BMC NEUROSCIENCE 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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Control Strategies for a Humanoid Robot to Drive and then Egress a Utility Vehicle for Remote Approach

Control Strategies for a Humanoid Robot to Drive and then Eg...

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IEEE-RAS International Conference on Humanoid Robots

作者： Hyobin Jeong Jaesung Oh Mingeuk Kim Kyungdon Joo In So Kweon Jun-Ho Oh Humanoid Research Center School of Mechanical Aerospace & Systems Engineering Department of Mechanical Engineering Korea Advanced Institute of Science and Technology Robotics and Computer Vision Laboratory School of Mechanical Aerospace & Systems Engineering Department of Electrical Engineering Korea Advanced Institute of Science and Technology Department of Electrical Engineering KAIST

ISBN: (纸本)9781479968862

This paper proposes strategies for the driving and egress of a vehicle with a humanoid robot. To drive the vehicle, the RANSAC method was used to detect obstacles, and the Wagon model was used to control the steering and velocity of the vehicle with only a limited number of sensors which were installed on the humanoid robot. Additionally, a manual teleoperating method was used with the lane projection technique. For the egress motion, gain override and the Cartesian position/force control technique were used to interact with the vehicle structure. To overcome the disadvantages of a highly geared manipulator, a special technique was used that included modelled friction compensation and a non-complementary switching mode. DRC-HUBO+ used the proposed method to perform a vehicle driving and egress task in the DRC finals 2015.

关键词： Humanoid robots EGRESS vehicle Vehicle driving Automobile driving UTILITY VEHICLES control strategy friction compensation DRIVES Steering

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Pedestrian detection based on LIDAR-driven sliding window and relational parts-based detection

Pedestrian detection based on LIDAR-driven sliding window an...

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IEEE Symposium on Intelligent Vehicle

作者： Luciano Oliveira Urbano Nunes Intelligent Vision Research Laboratory Federal University Bahia Brazil Institute of Systems and Robotics Department of Electrical and Computer Engineering University of Coimbra Portugal

The most standard image object detectors are usually comprised of one or multiple feature extractors or classifiers within a sliding window framework. Nevertheless, this type of approach has demonstrated a very limited performance under datasets of cluttered scenes and real life situations. To tackle these issues, LIDAR space is exploited here in order to detect 2D objects in 3D space, avoiding all the inherent problems of regular sliding window techniques. Additionally, we propose a relational parts-based pedestrian detection in a probabilistic non-iid framework. With the proposed framework, we have achieved state-of-the-art performance in a pedestrian dataset gathered in a challenging urban scenario. The proposed system demonstrated superior performance in comparison with pure sliding-window-based image detectors.

关键词： Detectors Laser radar Feature extraction Support vector machines Training Probabilistic logic Vectors

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IEEE Transactions on Haptics: Editorial

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IEEE Transactions on Haptics 2008年第1期1卷 2-8页

作者： Edward Colgate, J. Lederman, Susan Prattichizzo, Domenico Barbagli, Federico Basdogan, Cagatay Buss, Martin Ernst, Marc Frisoli, Antonio Gillespie, Brent Grant, Danny Harders, Matthias Hayward, Vincent Jones, Lynette Kajimoto, Hiroyuki Kappers, Astrid Kheddar, Abderrahmane Lin, Ming C. MacLean, Karon Miller, Brian Noma, Haruo Okamura, Allison M. O'Malley, Mareia Ryu, Jeha Tan, Hong Z. Yokokohji, Yasuyoshi Department of Psychology School of Computing Queen's University Canada IEEE Robotics and Automation Society Tübingen Germany Stanford University's Computer Science Department Tübingen Germany Institute of Automatic Control Engineering Technische Universität München Germany Independent Research Group Multisensory Perception and Action Max Planck Institute for Biological Cybernetics Tübingen Germany Department of Applied Mechanics SSSA Japan Research Division Virtual Reality and Telerobotic Systems PERCRO Laboratory Japan Department of Mechanical Engineering Japan Department of Robotics McGill University Canada Computer Vision Lab ETH Zurich Japan Virtual Reality in Medicine Group Japan IEEE CS/RAS Technical Committee on Haptics Japan Department of Electrical and Computer Engineering McGill University Canada Department of Mechanical Engineering MIT Japan University of Electro-Communications Japan Department of Physics and Astronomy Utrecht University Netherlands University of Evry France Chapel Hill United States Department of Computer Science University of British Columbia Canada ATR Knowledge Science Lab United Kingdom Department of Mechanical Engineering Denmark Johns Hopkins University United States Laboratory for Computational Sensing and Robotics United Kingdom Engineering Research Center for Computer-Integrated Surgical Systems and Technology United States Mechanical Engineering and Materials Science Department Rice University United States Korea Republic of Department of Electrical and Computer Engineering Mechanical Engineering and Psychological Sciences Purdue University United States Department of Mechanical Engineering and Science Graduate School of Engineering Kyoto University Japan

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Visual Modules for Head Gesture Analysis in Intelligent Vehicle Systems

Visual Modules for Head Gesture Analysis in Intelligent Vehi...

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IEEE Symposium on Intelligent Vehicle

作者： Junwen Wu M.M. Trivedi Computer Vision and Robotics Research Laboratory Department of Electrical and Computer Engineering University of California San Diego CA USA

In this paper a coarse-to-fine system framework for analyzing the head gesture is presented. We discuss several important modules from computer vision aspects, including the pose-invariant face detection, face tracking, pose determination and high-resolution image reconstruction for eye pupils detection. Visual cues using intensity images obtained from in-car cameras are explored. A pose-invariant face detection algorithm is used to get the initial face area; afterwards face tracking and validation step is proposed to segment the face region for pose determination. The algorithm is tested on the drivers images under natural driving conditions. Experimental results show that the algorithm is robust to the head pose changes as well as the illumination changes. In this system framework, we propose that when coarse analysis utilizing the head pose alone is not sufficient for driver's behavior analysis, a finer analysis based on the eye gaze tracking is used, which requires images with sufficient resolution. A novel super-resolution reconstruction algorithm is proposed to help reveal more facial details, so as to facilitate the pupil detection. Experiment on the synthesis data shows the effectiveness of the super-resolution reconstruction algorithm

关键词： Intelligent vehicles Face detection Head Image analysis Reconstruction algorithms computer vision Image reconstruction Cameras Image segmentation Testing

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A Regression Model in TensorPCA Subspace for Face Image Super-resolution Reconstruction

A Regression Model in TensorPCA Subspace for Face Image Supe...

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International Conference on Pattern Recognition

作者： Junwen Wu M.M. Trivedi Computer Vision and Robotics Research Laboratory Department of Electrical and Computer Engineering University of California San Diego CA USA

ISBN: (纸本)0769525210

A regression model in the tensorPCA subspace is proposed in this paper for face super-resolution reconstruction. An approximate conditional probability model is used for the tensor subspace coefficients and maximum-likelihood estimator gives a linear regression model. The approximation is corrected by adding non-linear component from a RBF-type regressor. Experiments on face images from FERET database validate the algorithm. Although each projection coefficient is estimated by a local estimator, tensorPCA subspace analysis is still a global descriptor, which makes the algorithm have certain ability to deal with partially occluded images

关键词： Image resolution Image reconstruction Tensile stress Spatial resolution Principal component analysis Face detection Image analysis computer vision Robot vision systems Laboratories

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A binary tree for probability learning in eye detection

A binary tree for probability learning in eye detection

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2005 IEEE computer Society Conference on computer vision and Pattern Recognition, CVPR 2005 - Workshops

作者： Wu, Junwen Trivedi, Mohan M. Computer Vision and Robotics Research Laboratory Department of Electrical and Computer Engineering University of California San DiegoCA92037 United States

ISBN: (纸本)0769526608

In this paper we proposed to solve the eye detection and localization problem under a general statistical model based object detection framework. A binary tree representation is used to discover the objects' underlying statistical structure. Tree structures enable us to describe the object local statistical structure in a coarse-to-fine fashion. Each subtree explains the statistics for certain local *** tree is built in a top-down fashion. Subsets with negligible conditional independency are found by k-means clustering using mutual information. The conditionally independent features are separated into different subtrees, while more dependent features are tended to appear close in the tree. The distribution of the object can be learned accordingly. Gaussian mixture in the independent component analysis (ICA) subspace is used to model the distribution of each high dependent feature subset, where each independent component explains the local substructure. The use of tree structure enables us to learn the distribution recursively by applying Bayesian criterion. Substantial experiments were done to evaluate the performance over the eyes detection accuracy as well as the localization ability. Experimental results show a better detection accuracy than the Viisage system with a reasonable localization ability, which validate the algorithm. © 2005 IEEE computer Society. All rights reserved.

关键词： Object detection

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