S
Spyridon Bakas
Researcher at University of Pennsylvania
Publications - 161
Citations - 9711
Spyridon Bakas is an academic researcher from University of Pennsylvania. The author has contributed to research in topics: Computer science & Medicine. The author has an hindex of 22, co-authored 108 publications receiving 4477 citations. Previous affiliations of Spyridon Bakas include Kingston University & University of Houston.
Papers
More filters
Journal ArticleDOI
Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features
Spyridon Bakas,Hamed Akbari,Aristeidis Sotiras,Michel Bilello,Martin Rozycki,Justin Kirby,John Freymann,Keyvan Farahani,Christos Davatzikos +8 more
TL;DR: This set of labels and features should enable direct utilization of the TCGA/TCIA glioma collections towards repeatable, reproducible and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments, as well as performance evaluation of computer-aided segmentation methods.
Journal ArticleDOI
The Image Biomarker Standardization Initiative: Standardized Quantitative Radiomics for High-Throughput Image-based Phenotyping
Alex Zwanenburg,Alex Zwanenburg,Martin Vallières,Mahmoud A. Abdalah,Hugo J.W.L. Aerts,Hugo J.W.L. Aerts,Vincent Andrearczyk,Aditya Apte,Saeed Ashrafinia,Spyridon Bakas,Roelof J. Beukinga,Ronald Boellaard,Marta Bogowicz,Luca Boldrini,Irène Buvat,Gary Cook,Christos Davatzikos,Adrien Depeursinge,Marie-Charlotte Desseroit,Nicola Dinapoli,Cuong V. Dinh,Sebastian Echegaray,Issam El Naqa,Issam El Naqa,Andriy Fedorov,Roberto Gatta,Robert J. Gillies,Vicky Goh,Michael Götz,Matthias Guckenberger,Sung Min Ha,Mathieu Hatt,Fabian Isensee,Philippe Lambin,Stefan Leger,Stefan Leger,Ralph T.H. Leijenaar,Jacopo Lenkowicz,Fiona Lippert,Are Losnegård,Klaus H. Maier-Hein,Olivier Morin,Henning Müller,Sandy Napel,Christophe Nioche,Fanny Orlhac,Sarthak Pati,Elisabeth Pfaehler,Arman Rahmim,Arman Rahmim,Arvind Rao,Jonas Scherer,Muhammad Siddique,Nanna M. Sijtsema,Jairo Socarras Fernandez,Emiliano Spezi,Roel J H M Steenbakkers,Stephanie Tanadini-Lang,Daniela Thorwarth,Esther G.C. Troost,Esther G.C. Troost,Taman Upadhaya,Vincenzo Valentini,Lisanne V. van Dijk,Joost J. M. van Griethuysen,Floris H. P. van Velden,Philip Whybra,Christian Richter,Christian Richter,Steffen Löck,Steffen Löck +70 more
TL;DR: A set of 169 radiomics features was standardized, which enabled verification and calibration of different radiomics software and could be excellently reproduced.
Posted ContentDOI
Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge
Spyridon Bakas,Mauricio Reyes,Andras Jakab,Stefan Bauer,Markus Rempfler,Alessandro Crimi,Russell T. Shinohara,Christoph Berger,Sung Min Ha,Martin Rozycki,Marcel Prastawa,Esther Alberts,Jana Lipkova,John Freymann,John Freymann,Justin Kirby,Justin Kirby,Michel Bilello,Hassan M. Fathallah-Shaykh,Roland Wiest,Jan S. Kirschke,Benedikt Wiestler,Rivka R. Colen,Aikaterini Kotrotsou,Pamela LaMontagne,Daniel S. Marcus,Mikhail Milchenko,Arash Nazeri,Marc-André Weber,Abhishek Mahajan,Ujjwal Baid,Elizabeth R. Gerstner,Dongjin Kwon,Gagan Acharya,Manu Agarwal,M. S. Alam,Alberto Albiol,Antonio Albiol,F. Albiol,Varghese Alex,Nigel M. Allinson,Pedro H. A. Amorim,Abhijit Amrutkar,Ganesh Anand,Simon Andermatt,Tal Arbel,Pablo Arbeláez,Aaron Avery,Muneeza Azmat,B. Pranjal,Wenjia Bai,Subhashis Banerjee,Subhashis Banerjee,Bill Barth,Thomas Batchelder,Kayhan Batmanghelich,Enzo Battistella,Enzo Battistella,Andrew Beers,Mikhail Belyaev,Martin Bendszus,Eze Benson,Jose Bernal,H. N. Bharath,George Biros,Sotirios Bisdas,James M. Brown,Mariano Cabezas,Shilei Cao,Jorge Cardoso,Eric Carver,Adrià Casamitjana,Laura Silvana Castillo,Marcel Catà,Philippe C. Cattin,Albert Cerigues,Vinicius S. Chagas,Siddhartha Chandra,Yi-Ju Chang,Shiyu Chang,Ken Chang,Joseph Chazalon,Shengcong Chen,Wei Chen,Jefferson W. Chen,Zhaolin Chen,Kun Cheng,Ahana Roy Choudhury,Roger Chylla,Albert Clèrigues,Steven Colleman,Ramiro German Rodriguez Colmeiro,Ramiro German Rodriguez Colmeiro,Marc Combalia,Anthony Costa,Xiaomeng Cui,Zhenzhen Dai,Lutao Dai,Laura Alexandra Daza,Eric Deutsch,Changxing Ding,Chao Dong,Shidu Dong,Wojciech Dudzik,Zach Eaton-Rosen,Gary F. Egan,Guilherme Escudero,Théo Estienne,Théo Estienne,Richard M. Everson,Jonathan Fabrizio,Yong Fan,Longwei Fang,Xue Feng,Enzo Ferrante,Lucas Fidon,Martin H. Fischer,Andrew P. French,Naomi Fridman,Huan Fu,David Fuentes,Yaozong Gao,Evan Gates,David T. Gering,Amir Gholami,Willi Gierke,Ben Glocker,Mingming Gong,Mingming Gong,Sandra González-Villà,Thomas Grosges,Yuanfang Guan,Sheng Guo,Sudeep Gupta,Woo-Sup Han,Il Song Han,Konstantin Harmuth,Huiguang He,Aura Hernández-Sabaté,Evelyn Herrmann,Naveen Himthani,Winston H. Hsu,Cheyu Hsu,Hu Xiaojun,Xiaobin Hu,Yan Hu,Yifan Hu,Rui Hua,Teng-Yi Huang,Weilin Huang,Sabine Van Huffel,Quan Huo,Vivek Hv,Khan M. Iftekharuddin,Fabian Isensee,Mobarakol Islam,Aaron S. Jackson,Sachin Jambawalikar,Andrew Jesson,Weijian Jian,Peter H. Jin,V Jeya Maria Jose,V Jeya Maria Jose,Alain Jungo,Bernhard Kainz,Konstantinos Kamnitsas,Po-Yu Kao,Ayush Karnawat,Thomas Kellermeier,Adel Kermi,Kurt Keutzer,Mohamed Tarek Khadir,Mahendra Khened,Philipp Kickingereder,Geena Kim,Nik King,Haley Knapp,Urspeter Knecht,Lisa Kohli,Deren Kong,Xiangmao Kong,Simon Koppers,Avinash Kori,Ganapathy Krishnamurthi,Egor Krivov,Piyush Kumar,Kaisar Kushibar,Dmitrii Lachinov,Dmitrii Lachinov,Tryphon Lambrou,Joon Lee,Chengen Lee,Yuehchou Lee,Matthew C. H. Lee,Szidónia Lefkovits,László Lefkovits,James Levitt,Tengfei Li,Hongwei Li,Wenqi Li,Wenqi Li,Hongyang Li,Xiaochuan Li,Yuexiang Li,Heng Li,Zhenye Li,Xiaoyu Li,Zeju Li,XiaoGang Li,Zheng-Shen Lin,Fengming Lin,Pietro Liò,C Liu,Boqiang Liu,Xiang Liu,Mingyuan Liu,Ju Liu,Luyan Liu,Xavier Lladó,Marc Moreno Lopez,Pablo Ribalta Lorenzo,Zhentai Lu,Lin Luo,Zhigang Luo,Jun Ma,Kai Ma,Thomas Mackie,Anant Madabushi,Issam Mahmoudi,Klaus H. Maier-Hein,Pradipta Maji,C. P. Mammen,Andreas Mang,B.S. Manjunath,M. Marcinkiewicz,Steven McDonagh,Stephen J. McKenna,Richard McKinley,Miriam Mehl,Sachin Mehta,Raghav Mehta,Raphael Meier,Christoph Meinel,Dorit Merhof,Craig H. Meyer,Robert F. Miller,Sushmita Mitra,Aliasgar Moiyadi,David Molina-García,Miguel Monteiro,Grzegorz Mrukwa,Andriy Myronenko,Jakub Nalepa,Thuyen Ngo,Dong Nie,Holly Ning,Chen Niu,Nicholas Nuechterlein,Eric K. Oermann,Arlindo L. Oliveira,Arlindo L. Oliveira,Diego D. C. Oliveira,Arnau Oliver,Alexander F. I. Osman,Yu-Nian Ou,Sebastien Ourselin,Nikos Paragios,Moo Sung Park,Brad Paschke,J. Gregory Pauloski,Kamlesh Pawar,Nick Pawlowski,Linmin Pei,Suting Peng,Silvio M. Pereira,Julián Pérez-Beteta,Víctor M. Pérez-García,Simon Pezold,Bao Pham,Ashish Phophalia,Gemma Piella,G. N. Pillai,Marie Piraud,Maxim Pisov,Anmol Popli,Michael P. Pound,Reza Pourreza,Prateek Prasanna,Vesna Prkovska,Tony P. Pridmore,Santi Puch,Elodie Puybareau,Buyue Qian,Xu Qiao,Martin Rajchl,Swapnil Rane,Michael Rebsamen,Hongliang Ren,Xuhua Ren,Karthik Revanuru,Mina Rezaei,Oliver Rippel,Luis Carlos Rivera,Charlotte Robert,Bruce R. Rosen,Daniel Rueckert,Mohammed Safwan,Mostafa Salem,Joaquim Salvi,Irina Sánchez,Heitor M. Santos,Emmett Sartor,Dawid Schellingerhout,Klaudius Scheufele,Matthew R. Scott,Artur A. Scussel,Sara Sedlar,Juan Pablo Serrano-Rubio,N. Jon Shah,Nameetha Shah,Mazhar Shaikh,B. Uma Shankar,Zeina A. Shboul,Haipeng Shen,Dinggang Shen,Linlin Shen,Haocheng Shen,Varun Shenoy,Feng Shi,Hyung Eun Shin,Hai Shu,Diana M. Sima,Matthew Sinclair,Örjan Smedby,James Snyder,Mohammadreza Soltaninejad,Guidong Song,Mehul Soni,Jean Stawiaski,Shashank Subramanian,Li Sun,Roger Sun,Roger Sun,Jiawei Sun,Kay Sun,Yu Sun,Guoxia Sun,Shuang Sun,Yannick Suter,László Szilágyi,Sanjay N. Talbar,Dacheng Tao,Zhongzhao Teng,Siddhesh Thakur,Meenakshi Thakur,Sameer Tharakan,Pallavi Tiwari,Guillaume Tochon,Tuan Tran,Yuhsiang M. Tsai,Kuan-Lun Tseng,Tran Anh Tuan,Vadim Turlapov,Nicholas J. Tustison,Maria Vakalopoulou,Sergi Valverde,Rami Vanguri,Evgeny Vasiliev,Jonathan Ventura,Luis Vera,Tom Vercauteren,Tom Vercauteren,C. A. Verrastro,Lasitha Vidyaratne,Verónica Vilaplana,Ajeet Vivekanandan,Guotai Wang,Guotai Wang,Qian Wang,Chiatse J. Wang,Weichung Wang,Duo Wang,Ruixuan Wang,Yuanyuan Wang,Chunliang Wang,Ning Wen,Xin Wen,Leon Weninger,Wolfgang Wick,Shaocheng Wu,Qiang Wu,Yihong Wu,Yong Xia,Yanwu Xu,Xiaowen Xu,Peiyuan Xu,Tsai-Ling Yang,Xiaoping Yang,Hao-Yu Yang,Junlin Yang,Haojin Yang,Guang Yang,Hongdou Yao,Xujiong Ye,Changchang Yin,Brett Young-Moxon,Jinhua Yu,Xiangyu Yue,Songtao Zhang,Angela Zhang,Kun Zhang,Xuejie Zhang,Lichi Zhang,Xiaoyue Zhang,Yazhuo Zhang,Lei Zhang,Jianguo Zhang,Xiang Zhang,Tianhao Zhang,Sicheng Zhao,Yu Zhao,Xiaomei Zhao,Liang Zhao,Liang Zhao,Yefeng Zheng,Liming Zhong,Chenhong Zhou,Xiaobing Zhou,Fan Zhou,Hongtu Zhu,Jin Zhu,Ying Zhuge,Weiwei Zong,Jayashree Kalpathy-Cramer,Keyvan Farahani,Christos Davatzikos,Koen Van Leemput,Koen Van Leemput,Bjoern H. Menze +438 more
TL;DR: This study assesses the state-of-the-art machine learning 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, and investigates the challenge of identifying the best ML algorithms for each of these tasks.
Journal ArticleDOI
The future of digital health with federated learning
Nicola Rieke,Nicola Rieke,Jonny Hancox,Wenqi Li,Fausto Milletari,Holger R. Roth,Shadi Albarqouni,Shadi Albarqouni,Spyridon Bakas,Mathieu N. Galtier,Bennett A. Landman,Klaus H. Maier-Hein,Klaus H. Maier-Hein,Sebastien Ourselin,Micah J. Sheller,Ronald M. Summers,Andrew Trask,Daguang Xu,Maximilian Baust,M. Jorge Cardoso +19 more
TL;DR: In this article, the authors consider key factors contributing to this issue, explore how federated learning may provide a solution for the future of digital health and highlight the challenges and considerations that need to be addressed.
Posted Content
A large annotated medical image dataset for the development and evaluation of segmentation algorithms
Amber L. Simpson,Michela Antonelli,Spyridon Bakas,Michel Bilello,Keyvan Farahani,Bram van Ginneken,Annette Kopp-Schneider,Bennett A. Landman,Geert Litjens,Bjoern H. Menze,Olaf Ronneberger,Ronald M. Summers,Patrick Bilic,Patrick Ferdinand Christ,Richard K. G. Do,Marc J. Gollub,Jennifer Golia-Pernicka,Stephan Heckers,William R. Jarnagin,Maureen McHugo,Sandy Napel,Eugene Vorontsov,Lena Maier-Hein,M. Jorge Cardoso +23 more
TL;DR: A large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain.