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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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Road Segmentation via Iterative Deep Analysis

Road Segmentation via Iterative Deep Analysis

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IEEE International Conference on robotics and Biomimetics

作者： Xiang Chen Yu Qiao Student at Shenzhen Key Laboratory of Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Address: 1068 Xueyuan Avenue Shenzhen University Town Shenzhen P.R.China Researcher at Shenzhen Key Laboratory of Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Address: 1068 Xueyuan Avenue Shenzhen University Town Shenzhen P.R.China

ISBN: (纸本)9781467396769

Nowadays, people are increasingly concerned about the safety of traffic systems. Road segmentation and recognition is a fundamental problem in perceiving traffic environments and serve as the basis for self-driving cars. In this paper, inspired by an iterative deep analysis thinking, we propose a novel method which is able to learning powerful features step by step, and solve the optimal precision by balancing local and global information to conduct pixel-level classification for road segmentation. Firstly, we introduce an iterative deep analysis thinking which shows that how to design a strong and robustness deep model from failure experience. Secondly, we choose a powerful global features learning network as basis to create a novel framework for our task. Meanwhile, we employ the patch and multi-scale pyramid as input to enhance local features learning. We conduct experiments on three datasets from KITTI vision Benchmark, namely UU, UM, UMM. The experimental results demonstrate that our proposed method obtains comparable performance with state-of-the-art methods on these datasets.

关键词： recognition fundamental datasets

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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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A novel feature extracting method for dynamic gesture recognition based on support vector machine

A novel feature extracting method for dynamic gesture recogn...

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International Conference on Information and Automation (ICIA)

作者： Yuanrong Xu Qianqian Wang Xiao Bai Yen-Lun Chen Xinyu Wu Shenzhen Key Lab for Computer Vision and Pattern Recognition Chinese Academy of Sciences University of Science and Technology of China Dept. Mechanical and Automation Engineering The Chinese University of Hong Kong Guangdong Provincial Key Laboratory of Robotics and Intelligent System Chinese Academy of Sciences

In this paper, we propose a method based on the SVM algorithm to recognize dynamic hand gestures. The information of motion trajectory is captured by a leap motion in three-dimension space. A new methodology of feature extracting is proposed to guarantee the length of samples being the same. The elements of feature vectors are ranged according to two different criteria: one is the amplitude of the variation of orientation angles, and the other criterion is the order of the appearance of features. Experimental results show that this method can classify the dynamic hand gestures effectively.

关键词： Vectors Trajectory Feature extraction Equations Mathematical model Hidden Markov models Automation

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Dynamic hand gesture early recognition based on Hidden Semi-Markov Models

Dynamic hand gesture early recognition based on Hidden Semi-...

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IEEE International Conference on robotics and Biomimetics

作者： Qianqian Wang Yuanrong Xu Yen-Lun Chen Yong Wang Xinyu Wu University of Science and Technology of China Shenzhen Key Lab for Computer Vision and Pattern Recognition Chinese Academy of Sciences Dept. Mechanical and Automation Engineering The Chinese University of Hong Kong. Guangdong Provincial Key Laboratory of Robotics and Intelligent System Chinese Academy of Sciences

ISBN: (纸本)9781479973989

Real-time performance can be greatly improved, if the early recognition is implemented. In this paper, a dynamic hand gesture early recognition system is proposed. The system can recognize the gesture before it is completed. Our method is based on the Hidden Semi-Markov Models. Three-dimensional information of the gesture trajectory collected by leapmotion is the main data we used. Experiments on the dataset which we established demonstrate the effectiveness of our method.

关键词： Hidden Markov models Gesture recognition Training Conferences Trajectory Arrays

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Rapid disparity prediction for dynamic scenes

Rapid disparity prediction for dynamic scenes

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9th International Symposium on Advances in Visual Computing, ISVC 2013

作者： Jiang, Jun Cheng, Jun Chen, Baowen Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences China Chinese University of Hong Kong Hong Kong Hong Kong Shsenzhen Institute of Information Technology China Guangdong Provincial Key Laboratory of Robotics and Intelligent System China Shenzhen Key Laboratory of Computer Vision and Pattern Recognition China

ISBN: (纸本)9783642419133

Real-time 3D sensing plays a critical role in robotic navigation, video surveillance and human-computer interaction, etc. When computing 3D structures of dynamic scenes from stereo sequences, spatiotemporal stereo and scene flow methods can produce temporally coherent disparity. However, most existing methods do not utilize the previous disparity map sufficiently to compute the next disparity map, and the searching space of correspondences limits the speed of disparity computation for each image pair. This paper proposes an effective scheme to predict disparity maps from stereo sequences. In particular, we apply a robust 3D registration algorithm based on the angular-invariant feature to estimate the ego-motion of the stereo rig between consecutive frames, and present the transformation between consecutive disparity maps. The scheme can produce a sequence of temporally coherent disparity maps rapidly. We apply the new scheme to real outdoor scenes, and thorough empirical studies indicate the effectiveness of the new scheme for practical applications. © 2013 Springer-Verlag.

关键词： Human computer interaction

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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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ONLINE ADAPTIVE DICTIONARY LEARNING AND WEIGHTED SPARSE CODING FOR ABNORMALITY DETECTION

ONLINE ADAPTIVE DICTIONARY LEARNING AND WEIGHTED SPARSE CODI...

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IEEE International Conference on Image Processing

作者： Sheng Han Ruiqing Fu Suzhen Wang Xinyu Wu Shenzhen Key Lab for Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Guangdong Provincial Key Lab of Robotics and Intelligent System Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences The Chinese University of Hong Kong

ISBN: (纸本)9781479923427

This paper focuses mainly on adaptive dictionary updating and abnormality detection via weighted space coding in video surveillance. Generally, abnormality analysis conducted on a large amount of video data is very complicated, time-consuming and time-variant. However, our dictionary is very efficient at following up on shifted contents in video and abandoning old inactive information in time. The adaptability characteristic also helps reduce the dictionary's size to a small scale, since it only needs to keep recent or active information. We also introduce a simple, but effective, judgement criterion for abnormal detection based on sparse coding over weighted bases. Because of the condensed dictionary and the simplified judgment criterion, our algorithm performs online learning and online detection with a high speed and a high accuracy in various scenes.

关键词： Dictionary Learning Adaptive Learning Sparse Coding Abnormality Detection Sparse coding anomaly detection video data Dictionaries as Topic video monitoring

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Compressed sensing ensemble classifier for human detection

Compressed sensing ensemble classifier for human detection

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4th International Conference on Intelligence Science and Big Data Engineering, IScIDE 2013

作者： Zhang, Baochang Liu, Juan Gao, Yongsheng Liu, Jianzhuang Science and Technology on Aircraft Control Laboratory School of Automation Science and Electrical Engineering BeiHang University Beijing 100191 China School of Engineering Griffith University Australia Shenzhen Key Lab for Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences China Department of Information Engineering Chinese University of Hong Kong Hong Kong Hong Kong

ISBN: (纸本)9783642420566

This paper proposes a novel Compressed Sensing Ensemble Classifier (CSEC) for human detection. The proposed CSEC employs the compressed sensing technique to get a more sparse model with a more reasonable selection of base classifiers. The major contributions of this paper are: 1) a novel principled framework for ensemble classifier design based on compressed sensing;2) a new concept of considering both the simplicity of ensemble classifier and irrelevance of base classifiers towards optimal classifier design;and 3) a quadratic function for CSEC optimization which includes a new optimizable positive semi-definite relevance matrix to simultaneously select appropriate base classifiers with minimized relevance. Experimental results on INRIA and SDL databases show that the performance of CSEC is better than two most popular classifiers SVM and AdaBoost, as well as a most recent method CLML. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Compressed sensing

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Online non-feedback image re-ranking via dominant data selection

Online non-feedback image re-ranking via dominant data selec...

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20th ACM International Conference on Multimedia, MM 2012

作者： Cao, Chen Chen, Shifeng Li, Yuhong Liu, Jianzhuang Shenzhen Key Laboratory for Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China Department of Information Engineering Chinese University of Hong Kong Hong Kong Media Lab. Huawei Technologies Co. Ltd. China

ISBN: (纸本)9781450310895

Image re-ranking aims at improving the precision of keyword-based image retrieval, mainly by introducing visual features to re-rank. Many existing approaches require offline training for every keyword, which are unsuitable for online image search. Other real-time approaches demand user interaction, which are inappropriate for large-scale image collection. To improve the accuracy of web image retrieval in a practicable manner, we propose a novel re-ranking algorithm to explore the cluster information of the image set. First, we build spectral graph on images that retrieved bysearch engine, and remove isolated nodes as noisy images. Then, we select positive samples from the most dominant cluster in initial top-ranked images, and the samples are used for semi-supervised learning and ranking. Our algorithm is online and non-feedback. Experiments on two public databases demonstrate that our algorithm outperforms the state-of-the-art approaches. © 2012 ACM.

关键词： Supervised learning

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