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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

引用

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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STP Approach to controlliability of Finite State Machines

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IFAC-PapersOnLine 2015年第28期48卷 138-143页

作者： Yongyi, Y.A.N. Zengqiang, C.H.E.N. Jumei, Y.U.E. College of Computer and Control Engineering Nankai University Zhejiang University Tianjin300071 China College of Agricultural Engineering Henan University of Science and Technology Henan471003 Taiwan

This work investigates the controllability of finite state machines with the help of the semi-tensor product of matrices (STP), which is a new matrix analysis tool proposed in recent years. Using the STP, the states and inputs of the machines are first converted to vector forms, and the transition function is then expressed in the form of matrices, Based on this algebraic description, a necessary and sufficient condition of controlliablility is established for checking whether a state is controllable to another one. Finally, the study of illustrative examples verifies the correctness of the results presented in this paper. © 2015

关键词： Matrix algebra controllability Finite automata Tensors Algebraic description Matrix analysis Matrix approach Semi tensor product of matrices Transition functions

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A comparison of robotic fish speed control based on analytical and empirical models

A comparison of robotic fish speed control based on analytic...

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Annual Conference of Industrial Electronics Society

作者： Saurab Verma Jian-Xin Xu Qinyuan Ren Wee Beng Tay Feng Lin Department of Electrical and Computer Engineering National University of Singapore Singapore College of Control Science and Engineering Zhejiang University China Temasek Laboratories National University of Singapore Singapore

In this paper, a comparative study of speed control efficiencies based on two dynamical models is presented. The common structure of dynamical models is developed using first principles of physics. The complex thrust mechanism is studied using two different techniques. First, we apply a novel data-driven approach to build up the non-linear mapping between tail angular motion and thrust generated, which is essential to specify the input gradient. Further, additional experiments are designed to acquire data necessary for modelling the input delay factor causing a time-delayed input to drive the system output. Second, analytically developed Lighthill's slender body theory is also employed to study thrust mechanism for comparative purposes. Though the theory has been used in robotic fish motion studies, it was originally formulated as an analytical tool for studying biological fish motion. Comparing the two theories help understand the predominant features in a robotic fish speed control. Lastly, because of the highly non-linear system dynamics, robust discrete-time Sliding Mode controllers (SMC) are developed with the two dynamical models as basis respectively. Experimental verifications confirm that SMC based on data-driven model performs superior to the SMC based on the Lighthill's theory, by efficiently controlling the robotic fish's speed to track the time-varying reference speeds.

关键词： Oscillators Force Robot kinematics Robot sensing systems Steady-state Drag

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Mining miRNAs2target genes interactions from biomedical literature

Mining miRNAs2target genes interactions from biomedical lite...

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2016 IEEE International Conference of Online Analysis and Computing science(ICOACS 2016)

作者： Lejun Gong Kaiyu Jiang Ronggen Yang Geng Yang Jiangsu High Technology Research Key Lab for Wireless Sensor Networks College of Computer Science & TechnologyNanjing University of Posts and Telecommunications College of Intelligent Science and Control Engineering Jinling Institute of Technology

This work describes an approach to mine miRNAs2 target genes interactions related to breast cancer from ***,the work obtain 53 miRNAs and 2130protein-coding genes regarding to the breast cancer,then using prior knowledge to extract the relationship between miRNAs and protein-coding genes,we achieved 2231 miRNAs2 target interactions *** also constructed a miRNAs2 target network,which could be used to clearly show the extracted miRNAs2 target interactions.

关键词： miRNA2target interaction breast cancer enrichment analysis relationship extraction

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Modeling and Reachability Analysis of A Class of Petri Nets via Semi-tensor Product of Matrices 34

Modeling and Reachability Analysis of A Class of Petri Nets ...

引用

第三十四届中国控制会议

作者： HAN Xiaoguang CHEN Zengqiang ZHANG Kuize LIU Zhongxin ZHANG Qing College of Computer and Control Engineering Nankai University College of Science Civil Aviation University of China College of Automation Harbin Engineering University

ISBN: (纸本)9781467374439

This paper investigates the matrix expression of state equation and reachability of a class of Petri nets(PNs) by using the semi-tensor product of matrices(STP). First, we get the formula for the number of states of the PNs based on the combinatorial mathematics method. The states and transitions of the PNs are expressed as vector forms, respectively, then the state equation of the PNs is established by using STP. Second, the transition-state adjacency matrix(TSAM) of the PNs is proposed, several necessary and sufficient conditions are obtained for the reachability of the PNs by using this state equation and TSAM. An algorithm is also designed to find all the firing sequences of any two reachable states. Finally, an example is presented to illustrate the theoretical results in this paper and shows that the new results are very effective in investigating the reachability of the PNs.

关键词： Petri nets,Semi-tensor product,Reachability,Transition-state transfer matrix,Transition-state adjacency matrix

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Vibration isolation system with a compact damping system for power recycling mirrors of KAGRA

arXiv

引用

arXiv 2019年

作者： Akiyama, Y. Akutsu, T. Ando, M. Arai, K. Arai, Y. Araki, S. Araya, A. Aritomi, N. Asada, H. Aso, Y. Bae, S. Baiotti, L. Barton, M.A. Cannon, K. Capocasa, E. Chen, C.-S. Chiu, T.-W. Cho, K. Chu, Y.-K. Craig, K. Dattilo, V. Doi, K. Enomoto, Y. Flaminio, R. Fujii, Y. Fujimoto, M.-K. Fukunaga, M. Fukushima, M. Furuhata, T. Haino, S. Hasegawa, K. Hashimoto, Y. Hashino, K. Hayama, K. Hirayama, T. Hirose, E. Hsieh, B.H. Huang, C.-Z. Ikenoue, B. Inoue, Y. Ioka, K. Itoh, Y. Izumi, K. Kaji, T. Kajita, T. Kakizaki, M. Kamiizumi, M. Kanbara, S. Kanda, N. Kanemura, S. Kang, G. Kasuya, J. Kawai, N. Kawasaki, T. Kim, C. Kim, W.S. Kim, J. Kim, J.C. Kimura, N. Kirii, S. Kitaoka, Y. Kitazawa, H. Kojima, Y. Kokeyama, K. Komori, K. Kong, A. Kotake, K. Kozu, R. Kumar, R. Kuo, H.-S. Kuroki, S. Kuroyanagi, S. Lee, H.K. Lee, H.M. Lee, H.W. Leonardi, M. Lin, C.-Y. Lin, F.-L. Liu, G.C. Marchio, M. Matsui, T. Michimura, Y. Mio, N. Miyakawa, O. Miyamoto, A. Miyoki, S. Morii, W. Morisaki, S. Moriwaki, Y. Musha, M. Nagano, S. Nagano, K. Nakamura, K. Nakamura, T. Nakano, H. Nakano, M. Narikawa, T. Quynh, L. Nguyen Ni, W.-T. Nishizawa, A. Obuchi, Y. Oh, J. Oh, S.H. Ohashi, M. Ohishi, N. Ohkawa, M. Okutomi, K. Ono, K. Oohara, K. Ooi, C.P. Pan, S.-S. Paoletti, F. Park, J. Passaquieti, R. Peña Arellano, F.E. Sago, N. Saito, S. Saito, Y. Sakai, K. Sakai, Y. Sasai, M. Sato, S. Sato, T. Sekiguchi, T. Sekiguchi, Y. Shibata, M. Shimoda, T. Shinkai, H. Shishido, T. Shoda, A. Someya, N. Somiya, K. Son, E.J. Suemasa, A. Suzuki, T. Suzuki, T. Tagoshi, H. Tahara, H. Takahashi, H. Takahashi, R. Takeda, H. Tanaka, H. Tanaka, K. Tanaka, T. Tanioka, S. San Martin, E.N. Tapia Tomaru, T. Tomura, T. Travasso, F. Tsubono, K. Tsuchida, S. Uchikata, N. Uchiyama, T. Uehara, T. Ueno, K. Uraguchi, F. Ushiba, T. van Putten, M.H.P.M. Vocca, H. Wakamatsu, T. Watanabe, Y. Xu, W.-R. Yamada, T. Yamamoto, K. Yamamoto, K. Yamamoto, S. Yamamoto, T. Yokogawa, K. Yokoyama, J. Yokozawa, T. Yoshioka, T. Yuzurihara, H. Zeidler, S. Zhu, Z.-H. Graduate School of Science and Engineering Hosei University TokyoKoganei184-8584 Japan National Astronomical Observatory of Japan TokyoMitaka181-8588 Japan Department of Physics University of Tokyo TokyoBunkyo113-0033 Japan University of Tokyo KashiwaChiba277-8582 Japan High Energy Accelerator Research Organization TsukubaIbaraki305-0801 Japan Earthquake Research Institute University of Tokyo TokyoBunkyo113-0032 Japan Department of Physics University of Tokyo TokyoBunkyo113-0033 Japan Department of Mathematics and Physics Hirosaki University AomoriHirosaki036-8561 Japan National Astronomical Observatory of Japan GifuHida506-1205 Japan Korea Institute of Science and Technology Information Yuseong Daejeon34141 Korea Republic of Department of Physics Osaka University ToyonakaOsaka560-0043 Japan University of Tokyo TokyoBunkyo113-0033 Japan Department of Physics National Taiwan Normal University Taipei116 Taiwan Department of Physics Sogang University Seoul121-742 Korea Republic of PisaCascinaI-56021 Italy Department of Physics University of Toyama ToyamaToyama930-8555 Japan Department of Astronomy University of Tokyo TokyoBunkyo113-0032 Japan Advanced Technology Center National Astronomical Observatory of Japan TokyoMitaka181-8588 Japan Institute of Physics Academia Sinica TaipeiNankang11529 Taiwan Department of Applied Physics Fukuoka University FukuokaJonan814-0180 Japan Yukawa Institute for Theoretical Physics Kyoto University KyotoSakyo606-8502 Japan Graduate School of Science Osaka City University OsakaSumiyosi558-8585 Japan Institute of Space and Astronautical Science Japan Aerospace Exploration Agency SagamiharaKanagawa252-5210 Japan University of Tokyo GifuHida506-1205 Japan Graduate Schoool of Science and Technology Tokyo Institute of Technology MeguroTokyo152-8551 Japan Department of Physics Ewha Womans University SeoulSeodaemun-gu03760 Korea Republic of National Institute for

A vibration isolation system called Type-Bp system used for power recycling mirrors has been developed for KAGRA, the interferometric gravitational-wave observatory in Japan. A suspension of the Type-Bp system passively isolates an optic from seismic vibration using three main pendulum stages equipped with two vertical vibration isolation systems. A compact reaction mass around each of the main stages allows for achieving sufficient damping performance with a simple feedback as well as vibration isolation ratio. Three Type-Bp systems were installed in KAGRA, and were proved to satisfy the requirements on the damping performance, and also on estimated residual displacement of the optics. Copyright © 2019, The Authors. All rights reserved.

关键词： Mirrors

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Naïve bayesian classifiers with continuous attributes using multi-smoothing parameters

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ICIC Express Letters 2016年第9期10卷 2135-2140页

作者： Han, Jinku Liu, Kehui Jia, Helin Zhang, Jianfei College of Computer and Control Engineering Qiqihar University No. 42 Wenhua Street Qiqihar161006 China Faculty of Information Technology Macau University of Science and Technology Macau999078 China

In this paper, we propose a method that can be used to construct Naïve Bayesian classifier with multi-smoothing parameters which can improve the classification performance of Naïve Bayesian classifier based on Gaussian kernel function. In the proposed approach, mean integrated square error (MISE) is taken into account, by which we can measure the error between estimated density and actual density. The optimal smoothing parameters can be determined by approximate calculation, so different smoothing parameters of attributes can be used to construct classifiers. The compared experiments results show the proposed method can achieve higher classifying accuracy. © 2016 ICIC International.

关键词： Surveying

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Improved low energy self-healing algorithm based on the anchor node selection strategy of tetrahedron similarity

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ICIC Express Letters 2016年第8期10卷 1857-1864页

作者： Wei, Liansuo Cai, Shaobin Dai, Xuefeng Department of Computer Science and Technology Harbin Engineering University No. 145 Nantong Ave. Nangang Dist. Harbin150001 China College of Computer Control Engineering Qiqihar University No. 42 Wenhua Ave. Qiqihar161006 China

In the network environment of underwater passive locating node, when the anchor nodes are always in a state of activation and keep corresponding with buoy nodes, the limited energy of the nodes will be exhausted rapidly and lead to some problems such as network fault and nodes death. Therefore a special improved low energy self-healing algorithm of selecting the best anchor node based on tetrahedron similarity was proposed in this paper. When a failure occurs, a new substitution anchor node will be selected in backup candidate nodes in real time. This substitution node will be aroused as a new node to choose the recovery path adaptively and ensure the smooth real-time transmission of the data. The simulation results show that this algorithm reduced the death number of the nodes and the rate of network faults. It shows good performance in terms of survival number of nodes, network traffic, and the prolongation of network lifetime. © 2016, ICIC Express Letters Office. All rights reserved.

关键词： Geometry

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Toward an architecture description language for dependability of internet-scaled software entities

Journal of Mechanical Engineering Research and Developments

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Journal of Mechanical engineering Research and Developments 2016年第2期39卷 529-535页

作者： Si, G.N. Yuan, L.Y. Xu, J. School of Information Science and Electrical Engineering Shandong Jiaotong University Jinan250357 China College of Computer and Control Engineering Nankai University Tianjin300071 China Shandong Provincial Key Laboratory of Software Engineering Jinan250014 China

Architecture Description Language (ADL) provides a conceptual framework for specific syntax and portray architecture allows the system developer can describe the architecture of their design, and the ability to use the tools provided many examples for analysis. ADL existing design problem solving systems, components or systems only consider reuse, and dependability among internal changes did not take into account the network configuration software system to protect the dependability of the various components and entities in the entity evolution of trust issues. Based on the analysis of network configuration software system architecture, based on the design of a formal description language entity credible case EDSADL, in order to describe the interactions between the entity and its internal components dependability of these changes on the real cause of the services provided affected.

关键词： computer software reusability

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A new-style decentralized nonlinear robust coordinated control of multiple static synchronous compensators

A new-style decentralized nonlinear robust coordinated contr...

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第35届中国控制会议

作者： Bangjun Lei Xiang Wu Shumin Fei Electrical Engineering College Guizhou Institute of Technology College of Mathmatics and Computer Science Guizhou Normal University Key Laboratory of Measurement and Control of Complex Systems of Engineering Ministry of EducationSchool of Automation Southeast University

ISBN: (纸本)9781509009107

Using the pseudo-generalized Hamiltonian method, this paper investigates the decentralized nonlinear robust coordinated control of multiple static synchronous compensators(STATCOMs) in multi-machine multiload power systems. First,the uncertain nonlinear differential algebraic equation model is constructed for the power system. Then, the dissipative pseudogeneralized Hamiltonian realization of the system is established by means of variable transformation and prefeedback ***, based on the obtained dissipative pseudo-generalized Hamiltonian realization, a new-style decentralized nonlinear robust coordinated controller is put forward. Simulation results demonstrate the effectiveness and robustness of the control scheme.

关键词： Pseudo-generalized Hamiltonian function method Uncertain nonlinear differential algebraic system Multimachine power systems Multiple STATCOMs Decentralized nonlinear robust coordinated control

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