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Signal-to-peak-interference ratio maximization with automatic interference weighting for threshold-based spike sorting of high-density neural probe data

Signal-to-peak-interference ratio maximization with automati...

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International IEEE/EMBS Conference on Neural Engineering, CNE

作者： Jasper Wouters Fabian Kloosterman Alexander Bertrand KU Leuven Electrical Engineering Dept. (ESAT) Stadius Center for Dynamical Systems Signal Processing and Data Analytics Leuven Belgium KU Leuven Brain & Cognition Research Unit Leuven Belgium

An innovative filter design method is proposed for threshold-based spike sorting of high-density neural recordings. Threshold-based spike sorting is the process of assigning each detected spike in an extracellular recording to its putative neuron, using only linear filters and simple thresholding operations. The low computational complexity of threshold-based spike sorting makes it interesting for real-time (hardware) implementations with potential applications in the field of brain-machine interfaces. The proposed method extends our earlier work on discriminative template matching and avoids the need for a prior heuristic definition of an interference covariance matrix. A new optimal filter design objective function is proposed, which automatically selects interference-dominated signal segments based on the output signal of the filter under design. This new method leads to filters that are signal-to-peak-interference ratio (SPIR) optimal. The method is validated on ground truth data recorded in-vivo.

关键词： Sorting Neurons Power generation Interference Design methodology Electrodes Probes

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A scalable method for probabilistic short-term forecasting of individual households consumption in low voltage grids

A scalable method for probabilistic short-term forecasting o...

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Grid Edge Technologies Conference & Exposition (Grid Edge), IEEE PES

作者： Lola Botman Jesus Lago Thijs Becker Oscar Mauricio Agudelo Koen Vanthournout Bart De Moor Research group STADIUS Center for Dynamical Systems Signal Processing and Data Analytics within the department of Electrical Engineering (ESAT) KU Leuven Belgium Amazon Amsterdam The Netherlands Unit Energietechnologie (ETE) VITO/EnergyVille Genk Belgium

Short-term individual household load forecasting is relevant for several applications and low voltage grid (LVG) stakeholders, e.g., for grid simulations, operation planning, congestion anticipation or advance payments. Electrical consumption at the household level is highly stochastic, point forecasting cannot capture this efficiently. To have insights about the uncertainty of the prediction, probabilistic methods should be developed. We propose a method to predict the half-hourly consumption of individual households one day ahead, based on a neural network, enhanced with empirical quantiles based on the point forecasts errors. The method is scalable thanks to its low computational requirements. Additionally, it requires only historical data and calendar features. Finally, the method is evaluated in a case study where it achieves state-of-the-art accuracy.

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Power aware scheme for water pipeline monitoring based on Wireless Sensor Networks

Power aware scheme for water pipeline monitoring based on Wi...

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International Conference on Intelligent Systems Design and Applications (ISDA)

作者： Manel Elleuchi Manel Boujelben Mohamed Abid Abdulfattah M. Obeid Mohammed S. BenSaleh Multimedia and Digital Data Processing (CETIC) National School of Engineers of Sfax ResearchCenter in Informatics Sfax Tunisia CES research unit National School of Engineers of Sfax Research Center in Informatics Multimedia and Digital Data Processing (CETIC) Technopark Sfax Tunisia National Center for Electronics Communications and Photonics King Abdulaziz City for Science and Technology Riyadh Kingdom of Saudi Arabi King Abdulaziz City for Science And Technology Riyadh Al Riyadh Province SA

ISBN: (纸本)9781467387101

Recently, using Wireless Sensor Networks (WSNs) is increasing in many areas, whether scientific, logistic, military, health and water monitoring. Water is among the vital material transported by pipeline systems. Any leakage in the pipe can cause major financial losses and possible environmental damages. Therefore, it is necessary to have a real time leak detection system. WSNs can play an important role to effectively detect the leak and minimize the water loss. Sensor size, however, is a significant limitation in terms of energy autonomy. In fact, the battery is very small and in general, it is not replaceable or rechargeable. Therefore, many studies are currently focusing on the management of the energy consumed by sensor nodes. In this paper, we propose a new energy efficient scheme for leak detection in water pipeline based on WSNs. The main goal of our proposal is to solve the problem of losing water and ameliorate network lifetime by reducing energy needs. The proposed scheme is composed of three tasks: deployment of sensors, routing and replacement of failed nodes. Simulations results validate the choice of the best cluster based routing protocol which will be executed in the second task of the proposed scheme.

关键词： Monitoring Routing Wireless sensor networks Logic gates Color Clustering algorithms Algorithm design and analysis

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Senext: Squeeze-and-Excitationnext for Single Image Super-Resolution

SSRN

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SSRN 2022年

作者： Muhammad, Wazir Aramvith, Supavadee Onoye, Takao Department of Electrical Engineering Faculty of Engineering Chulalongkorn University Bangkok10330 Thailand Multimedia Data Analytics and Processing Unit Department of Electrical Engineering Faculty of Engineering Chulalongkorn University Bangkok10330 Thailand Graduate School of Information Science and Technology Osaka University 1-5 Yamadaoka Suita565-0871 Japan

Recent research on single image super-resolution (SISR) using deep convolutional neural networks (CNNs) has shown significant development in the area computer vision-based tasks specially image and video processing. SISR seeks to reconstruct a visibly appealing high-quality / high-resolution (HR) output image from a low-quality / low-resolution (LR) input image as its primary goal. However, most existing CNN-based image super-resolution (SR) frameworks often use a deeper and broader network architecture that requires a sizeable computational resource, risk of overfitting, increases computational complexity, and more memory consumption, as well as takes more processing time during the evaluations. To resolve these problems, we propose a Squeeze-and-ExcitationNext for Single Image Super-Resolution concept named as SENext. In detail, the squeeze-and-excitation blocks (SEB) are used in our network architecture to reduce the computational cost and adopt the channel-wise feature mappings to adaptively recalibrate the features. Furthermore, local, sub-local and global skip connections are employed between each SEB to enable the feature reusability and stabilize training convergence smoothly. Instead of hand-designed bicubic upsampling at pre-processing step, we perform post-upsampling at the later end to reconstruct the high-resolution (HR) image. Extensive quantitative and qualitative experiments are performed on the benchmark test dataset, including Set5, Set14, BSDS100, Urban100, and Manga109. These experimental evaluations validate the superiority of the SENext over other deep CNN image SR methods in terms of PSNR/SSIM, FLOPs, Number of parameters, processing speed, and visually pleasing effect. © 2022, The Authors. All rights reserved.

关键词： Network architecture

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Machine Learning-Based Classification of Mental Health State Using the DASS-21 Profile

Machine Learning-Based Classification of Mental Health State...

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Biomedical Engineering International Conference (BMEiCON)

作者： Khanita Duangchaemkarn Patiphan Khammarew Supavadee Aramvith Department of Pharmacy Practice School of Pharmaceutical Sciences University of Phayao Phayao Thailand Pharmacy research extern under the Doctor of Pharmacy Program School of Pharmaceutical Sciences University of Phayao Phayao Thailand Multimedia Data Analytic and Processing Research Unit Department of Electrical Engineering Faculty of Engineering Chulalongkorn University Bangkok Thailand

ISBN: (数字)9798331505431

ISBN: (纸本)9798331505448

This study aimed to determine the most effective machine learning model for classifying emotional states of depression, anxiety, and stress based on the DASS-21 profile. Six machine learning models were developed and tested using 2,602 records from the University of Phayao Counselling Center, collected between 23 July and 16 August 2020. The results demonstrate that the deep learning model provided the highest accuracy and precision, exceeding 90% for all three emotional categories, with an AUC greater than 99%. These findings introduce an innovative approach for classifying emotional states of depression, anxiety, and stress using the DASS-21 profile as a benchmark. Incorporating additional features into the model could further enhance its utility in clinical decision-making, improving the accuracy of mental health screening and diagnosis.

关键词： Deep learning Employee welfare Adaptation models Accuracy Anxiety disorders Decision making Mental health Depression Reliability engineering data models

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OC09.06: Building gestational age independent features for first trimester viability prediction

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Ultrasound in Obstetrics & Gynecology 2020年 56卷 27-27页

作者： T. Vaulet M. Al‐Memar H. Fourie S. Bobdiwala S. Saso J. Farren B. De Moor C. Stalder P. Bennett D. Timmerman T. Bourne ESAT‐STADIUS Stadius Centre for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Early Pregnancy and Acute Gynecology Unit Tommy's National Centre for Miscarriage Research Queen Charlotte's and Chelsea Hospital Imperial College London London United Kingdom Department of Development and Regeneration KU Leuven Leuven Belgium

A key predictor of first trimester miscarriage is the discrepancy between observed and expected fetal development. The later requires a certain date of last menstruation period (LMP). However, a significant proportion of women are unsure of their LMP. This lack of gestational age (GA) absolute reference makes those patients ineligible for first trimester predictive model where GA adjustment is required. In this study, we assessed the use of relative references to build GA independent *** studied 4 different predictors ‐ MSD, CRL, progesterone and bhCG ‐ based on data from 105 women with first trimester miscarriage and 1022 with viable pregnancies, prospectively recruited from a single centre from March 2014‐ May 2019. Using the subset of viable pregnancies with certain date of LMP, we first modelled the relationship to GA by LMP, and assessed the GA correlation. Estimated GA were then derived for all pregnancies. Doing so, the transformed predictor now demonstrates a constant growth rate in viable pregnancies, making its rate GA‐independent. We computed the ROC AUC with 95% CI as predictive performance of those GA independent *** was time‐independent in the viable cohort and could be used without reference to GA with decent performance (AUC 0.799; 95% CI 0.730‐0.869). MSD was linear in terms of GA, no specific transformation were needed to achieve constant rate (AUC 0.696; 95% CI 0.668‐0.718.) For early pregnancies, using empirical CRL growth rate was acceptable without correction for the quadratic behaviour (AUC 0.852; 95% CI 0.813‐0.891). Due to the large variability in bhCG concentration, obtaining accurate GA was more challenging, preventing the use of a growth rate method. However, using a combination of bhCG absolute and rate values, we were able to create a proxy variable with decent correlation to GA by LMP (R2 : 0.692), independent of the ultrasound‐based *** have demonstrated that it is possible to derive meaningful predictor in

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Methods for Evaluating Medical Tests and Biomarkers

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Diagnostic and Prognostic research 2017年第1期1卷 1-34页

作者： Gowri Gopalakrishna Miranda Langendam Patrick Bossuyt Mariska Leeflang Rob Scholten Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Marie Westwood Jos Kleinen Richard Riley Gary Collins Hans Reitsma Karel Moons Antonia Zapf Katharina Kramer Annika Hoyer Oliver Kuss J. Ensor R. D. Riley J. J. Deeks E. C. Martin Gerta Rücker Martin Schumacher Susanne Steinhauser Joie Ensor Kym Snell Brian Willis Jon Deeks Thomas Debray Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A. Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Sabine Van Huffel Jan Verbakel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O’Sullivan Rafael Perera Brian Nicholson Hannah L. Bromley Tracy E. Roberts Adele Francis Denniis Petrie G. Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G. Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Peter Selby Doug Altman William Rosenberg Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Johannes Reitsma Anne Rutjes Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Bavo De Cock Daan Nieboer Ewout W. Steyerberg Micael J. Pencina Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Zoe Plummer Barnaby Reeves Chris Rogers Andrew Mumford Kurtis Lee Veerle Verheyden Gianni D. Angelini Gavin J. Murphy Jeremy Huddy Melody Ni George Hanna Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands Department of Clinical Epidemiology and Biostatistics Academic Medical Center University of Amsterdam Amsterdam Netherlands Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK EPPI-Centre Department of Social Science University College London London UK Division of Health and Social Care Research King’s College London London UK College of Computer and Information Science Northeastern University Boston USA University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK Institute of Applied Health Research University of Birmingham Birmingham UK School of Social and Community Medicine University of Bristol Bristol UK Kleijnen Systematic Reviews Ltd York UK Research Institute for Primary Care and Health Sciences Keele University Keele UK Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Cochrane Netherlands University Medical Center Utrecht Utrecht The Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands Department of Medical Statistics University Medical Center Göttingen Göttingen Germany Institute for Biometry and Epidemiology German Diabetes Center Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf Germany Manchester Pharmacy School University of Manchester Manchester UK Institute for Medical Biometry and Statistics Faculty of Medicine and Medical Center – University of Freiburg Stefan-Meier-Str. 26 79104 Freiburg Germany

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Why is the Winner the Best?

Why is the Winner the Best?

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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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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