Portrait de Julien Cohen-Adad

Julien Cohen-Adad

Membre académique associé
Professeur agrégé, Polytechnique Montréal, Département de génie électrique
Professeur asssocié, Université de Montréal, Département de neurosciences
Sujets de recherche
Apprentissage automatique médical

Biographie

Julien Cohen-Adad est professeur à Polytechnique Montréal et directeur associé de l'Unité de neuro-imagerie fonctionnelle de l'Université de Montréal. Il est également titulaire de la Chaire de recherche du Canada en imagerie par résonance magnétique quantitative. Ses recherches portent sur l'avancement des méthodes de neuro-imagerie avec l'aide de l'IA. Voici quelques exemples de ses projets :

- Formation multimodale pour les tâches d'imagerie médicale (segmentation des pathologies, diagnostic, etc.);

- Ajout d'un a priori issu de la physique de l'IRM pour améliorer la généralisation des modèles;

- Incorporation de mesures d'incertitude pour traiter la variabilité interévaluateurs;

- Stratégies d'apprentissage continu lorsque le partage des données est restreint;

- Introduction des méthodes d'IA dans la routine de la radiologie clinique par l’intermédiaire de solutions logicielles conviviales.

Le professeur Cohen-Adad dirige également de nombreux projets de logiciels libres qui profitent à la communauté scientifique et clinique. Plus de détails sur https://neuro.polymtl.ca/software.html.

En résumé, Julien aime : l'IRM avec des aimants puissants, la neuro-imagerie, la programmation et la science ouverte!

Étudiants actuels

Maîtrise recherche - Polytechnique
Co-superviseur⋅e :
Doctorat - Polytechnique
Co-superviseur⋅e :
Doctorat - Polytechnique
Maîtrise recherche - Polytechnique
Doctorat - Polytechnique
Doctorat - Polytechnique
Collaborateur·rice de recherche
Stagiaire de recherche - Polytechnique
Maîtrise recherche - UdeM
Maîtrise recherche - Polytechnique
Postdoctorat - Polytechnique

Publications

Pontomedullary junction as a reference for spinal cord cross-sectional area: validation across neck positions
Sandrine Bédard
Maxime Bouthillier
An 8‐channel Tx dipole and 20‐channel Rx loop coil array for MRI of the cervical spinal cord at 7 Tesla
Nibardo Lopez‐Rios
Kyle M. Gilbert
Daniel Papp
Gaspard Cereza
Alexandru Foias
Deshpande Rangaprakash
Markus W. May
Bastien Guerin
Lawrence L. Wald
Boris Keil
Jason P. Stockmann
Robert L. Barry
The quality of cervical spinal cord images can be improved by the use of tailored radiofrequency (RF) coil solutions for ultrahigh field ima… (voir plus)ging; however, very few commercial and research 7‐T RF coils currently exist for the spinal cord, and in particular, those with parallel transmission (pTx) capabilities. This work presents the design, testing, and validation of a pTx/Rx coil for the human neck and cervical/upper thoracic spinal cord. The pTx portion is composed of eight dipoles to ensure high homogeneity over this large region of the spinal cord. The Rx portion is made up of twenty semiadaptable overlapping loops to produce high signal‐to‐noise ratio (SNR) across the patient population. The coil housing is designed to facilitate patient positioning and comfort, while also being tight fitting to ensure high sensitivity. We demonstrate RF shimming capabilities to optimize B1+ uniformity, power efficiency, and/or specific absorption rate efficiency. B1+ homogeneity, SNR, and g‐factor were evaluated in adult volunteers and demonstrated excellent performance from the occipital lobe down to the T4‐T5 level. We compared the proposed coil with two state‐of‐the‐art head and head/neck coils, confirming its superiority in the cervical and upper thoracic regions of the spinal cord. This coil solution therefore provides a convincing platform for producing the high image quality necessary for clinical and research scanning of the upper spinal cord.
Dynamic shimming in the cervical spinal cord for multi-echo gradient-echo imaging at 3 T
Eva Alonso‐Ortiz
Daniel Papp
A. D'Astous
8-channel Tx dipole and 20-channel Rx loop coil array for MRI of the cervical spinal cord at 7 Tesla
Nibardo Lopez Rios
Kyle M. Gilbert
Daniel Papp
Gaspard Cereza
Alexandru Foias
D. Rangaprakash
Markus W. May
Bastien Guerin
Lawrence L. Wald
Boris Keil
Jason P. Stockmann
Robert L. Barry
Enhancing Medical Image Segmentation with TransCeption: A Multi-Scale Feature Fusion Approach
Reza Azad
Yiwei Jia
Ehsan Khodapanah Aghdam
Dorit Merhof
While CNN-based methods have been the cornerstone of medical image segmentation due to their promising performance and robustness, they suff… (voir plus)er from limitations in capturing long-range dependencies. Transformer-based approaches are currently prevailing since they enlarge the reception field to model global contextual correlation. To further extract rich representations, some extensions of the U-Net employ multi-scale feature extraction and fusion modules and obtain improved performance. Inspired by this idea, we propose TransCeption for medical image segmentation, a pure transformer-based U-shape network featured by incorporating the inception-like module into the encoder and adopting a contextual bridge for better feature fusion. The design proposed in this work is based on three core principles: (1) The patch merging module in the encoder is redesigned with ResInception Patch Merging (RIPM). Multi-branch transformer (MB transformer) adopts the same number of branches as the outputs of RIPM. Combining the two modules enables the model to capture a multi-scale representation within a single stage. (2) We construct an Intra-stage Feature Fusion (IFF) module following the MB transformer to enhance the aggregation of feature maps from all the branches and particularly focus on the interaction between the different channels of all the scales. (3) In contrast to a bridge that only contains token-wise self-attention, we propose a Dual Transformer Bridge that also includes channel-wise self-attention to exploit correlations between scales at different stages from a dual perspective. Extensive experiments on multi-organ and skin lesion segmentation tasks present the superior performance of TransCeption compared to previous work. The code is publicly available at https://github.com/mindflow-institue/TransCeption.
Label fusion and training methods for reliable representation of inter-rater uncertainty
Andreanne Lemay
Charley Gros
Enamundram Naga Karthik
HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation
Moein Heidari
Amirhossein Kazerouni
Milad Soltany
Reza Azad
Ehsan Khodapanah Aghdam
Dorit Merhof
Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation … (voir plus)in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, quantitative and qualitative results. Our code is publicly available at GitHub.
Contrast-agnostic deep learning–based registration pipeline: Validation in spinal cord multimodal MRI data
Biomedical image analysis competitions: The state of current participation practice
Matthias Eisenmann
Annika Reinke
Vivienn Weru
Minu Dietlinde Tizabi
Fabian Isensee
T. Adler
PATRICK GODAU
Veronika Cheplygina
Michal Kozubek
Sharib Ali
Anubha Gupta
Jan. Kybic
Alison Professor Noble
Carlos Ortiz de Sol'orzano
Samiksha Pachade
Caroline Petitjean
Daniel Sage
Donglai Wei
Elizabeth Wilden
Deepak Alapatt … (voir 334 de plus)
Vincent Andrearczyk
Ujjwal Baid
Spyridon Bakas
Niranjan Balu
Sophia Bano
Vivek Singh Bawa
Jorge Bernal
Sebastian Bodenstedt
Alessandro Casella
Jinwook Choi
Olivier Commowick
M. Daum
Adrien Depeursinge
Reuben Dorent
J. Egger
H. Eichhorn
Sandy Engelhardt
Melanie Ganz
Gabriel Girard
Lasse Donovan Hansen
Mattias Paul Heinrich
Nicholas Heller
Alessa Hering
Arnaud Huaulm'e
Hyunjeong Kim
Bennett Landman
Hongwei Bran Li
Jianning Li
Junfang Ma
Anne L. Martel
Carlos Mart'in-Isla
Bjoern Menze
Chinedu Innocent Nwoye
Valentin Oreiller
Nicolas Padoy
Sarthak Pati
Kelly Payette
Carole H. Sudre
K. V. Wijnen
Armine Vardazaryan
Tom Kamiel Magda Vercauteren
Martin Wagner
Chuanbo Wang
Moi Hoon Yap
Zeyun Yu
Chuner Yuan
Maximilian Zenk
Aneeq Zia
David Zimmerer
Rina Bao
Chanyeol Choi
Andrew Cohen
Oleh Dzyubachyk
Adrian Galdran
Tianyuan Gan
Tianqi Guo
Pradyumna Gupta
M. Haithami
Edward Ho
Ikbeom Jang
Zhili Li
Zheng Luo
Filip Lux
Sokratis Makrogiannis
Dominikus Muller
Young-Tack Oh
Subeen Pang
Constantin Pape
Görkem Polat
Charlotte Rosalie Reed
Kanghyun Ryu
Tim Scherr
Vajira L. Thambawita
Haoyu Wang
Xinliang Wang
Kele Xu
H.-I. Yeh
Doyeob Yeo
Yi Yuan
Yan Zeng
Xingwen Zhao
Julian Ronald Abbing
Jannes Adam
Nagesh Adluru
Niklas Agethen
S. Ahmed
Yasmina Al Khalil
Mireia Alenya
Esa J. Alhoniemi
C. An
Talha E Anwar
Tewodros Arega
Netanell Avisdris
D. Aydogan
Yi-Shi Bai
Maria Baldeon Calisto
Berke Doga Basaran
Marcel Beetz
Cheng Bian
Hao-xuan Bian
Kevin Blansit
Louise Bloch
Robert Bohnsack
Sara Bosticardo
J. Breen
Mikael Brudfors
Raphael Brungel
Mariano Cabezas
Alberto Cacciola
Zhiwei Chen
Yucong Chen
Dan Chen
Minjeong Cho
Min-Kook Choi
Chuantao Xie Chuantao Xie
Dana Cobzas
Jorge Corral Acero
Sujit Kumar Das
Marcela de Oliveira
Hanqiu Deng
Guiming Dong
Lars Doorenbos
Cory Efird
Di Fan
Mehdi Fatan Serj
Alexandre Fenneteau
Lucas Fidon
Patryk Filipiak
Ren'e Finzel
Nuno Renato Freitas
C. Friedrich
Mitchell J. Fulton
Finn Gaida
Francesco Galati
Christoforos Galazis
Changna Gan
Zheyao Gao
Sheng Gao
Matej Gazda
Beerend G. A. Gerats
Neil Getty
Adam Gibicar
Ryan J. Gifford
Sajan Gohil
Maria Grammatikopoulou
Daniel Grzech
Orhun Guley
Timo Gunnemann
Chun-Hai Guo
Sylvain Guy
Heonjin Ha
Luyi Han
Ilseok Han
Ali Hatamizadeh
Tianhai He
Ji-Wu Heo
Sebastian Hitziger
SeulGi Hong
Seungbum Hong
Rian Huang
Zi-You Huang
Markus Huellebrand
Stephan Huschauer
M. Hussain
Tomoo Inubushi
Ece Isik Polat
Mojtaba Jafaritadi
Seonghun Jeong
Bailiang Jian
Yu Jiang
Zhifan Jiang
Yu Jin
Smriti Joshi
A. Kadkhodamohammadi
R. A. Kamraoui
Inhak Kang
Jun-Su Kang
Davood Karimi
April Ellahe Khademi
Muhammad Irfan Khan
Suleiman A. Khan
Rishab Khantwal
Kwang-Ju Kim
Timothy Lee Kline
Satoshi Kondo
Elina Kontio
Adrian Krenzer
Artem Kroviakov
Hugo J. Kuijf
Satyadwyoom Kumar
Francesco La Rosa
Abhishek Lad
Doohee Lee
Minho Lee
Chiara Lena
Hao Li
Ling Li
Xingyu Li
F. Liao
Kuan-Ya Liao
Arlindo L. Oliveira
Chaonan Lin
Shanhai Lin
Akis Linardos
M. Linguraru
Han Liu
Tao Liu
Dian Liu
Yanling Liu
Joao Lourencco-Silva
Jing Lu
Jia Lu
Imanol Luengo
Christina Bach Lund
Huan Minh Luu
Yingqi Lv
Uzay Macar
Leon Maechler
L. SinaMansour
Kenji Marshall
Moona Mazher
Richard McKinley
Alfonso Medela
Felix Meissen
Mingyuan Meng
Dylan Bradley Miller
S. Mirjahanmardi
Arnab Kumar Mishra
Samir Mitha
Hassan Mohy-ud-Din
Tony C. W. Mok
Gowtham Krishnan Murugesan
Enamundram Naga Karthik
Sahil Nalawade
Jakub Nalepa
M. Naser
Ramin Nateghi
Hammad Naveed
Quang-Minh Nguyen
Cuong Nguyen Quoc
Brennan Nichyporuk
Bruno Oliveira
David Owen
Jimut Bahan Pal
Junwen Pan
W. Pan
Winnie Pang
Bogyu Park
Vivek G. Pawar
K. Pawar
Michael Peven
Lena Philipp
Tomasz Pieciak
Szymon S Płotka
Marcel Plutat
Fattane Pourakpour
Domen Prelovznik
K. Punithakumar
Abdul Qayyum
Sandro Queir'os
Arman Rahmim
Salar Razavi
Jintao Ren
Mina Rezaei
Jonathan Adam Rico
ZunHyan Rieu
Markus Rink
Johannes Roth
Yusely Ruiz-gonzalez
Numan Saeed
Anindo Saha
Mostafa M. Sami Salem
Ricardo Sanchez-matilla
Kurt G Schilling
Weizhen Shao
Zhiqiang Shen
Ruize Shi
Pengcheng Shi
Daniel Sobotka
Th'eodore Soulier
Bella Specktor Fadida
D. Stoyanov
Timothy Sum Hon Mun
Xiao-Fu Sun
Rong Tao
Franz Thaler
Antoine Th'eberge
Felix Thielke
Helena R. Torres
K. Wahid
Jiacheng Wang
Yifei Wang
W. Wang
Xiong Jun Wang
Jianhui Wen
Ning Wen
Marek Wodziński
Yehong Wu
Fangfang Xia
Tianqi Xiang
Cheng Xiaofei
Lizhang Xu
Tingting Xue
Yu‐Xia Yang
Lingxian Yang
Kai Yao
Huifeng Yao
Amirsaeed Yazdani
Michael Yip
Hwa-Seong Yoo
Fereshteh Yousefirizi
Shu-Fen Yu
Lei Yu
Jonathan Zamora
Ramy Ashraf Zeineldin
Dewen Zeng
Jianpeng Zhang
Bokai Zhang
Jiapeng Zhang
Fangxi Zhang
Huahong Zhang
Zhongchen Zhao
Zixuan Zhao
Jia Zhao
Can Zhao
Q. Zheng
Yuheng Zhi
Ziqi Zhou
Baosheng Zou
Klaus Maier-Hein
PAUL F. JÄGER
Annette Kopp-Schneider
Lena Maier-Hein
The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practic… (voir plus)e. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.
Biomedical image analysis competitions: The state of current participation practice
Matthias Eisenmann
Annika Reinke
Vivienn Weru
Minu Dietlinde Tizabi
Fabian Isensee
T. Adler
PATRICK GODAU
Veronika Cheplygina
Michal Kozubek
Sharib Ali
Anubha Gupta
Jan. Kybic
Alison Professor Noble
Carlos Ortiz de Sol'orzano
Samiksha Pachade
Caroline Petitjean
Daniel Sage
Donglai Wei
Elizabeth Wilden
Deepak Alapatt … (voir 334 de plus)
Vincent Andrearczyk
Ujjwal Baid
Spyridon Bakas
Niranjan Balu
Sophia Bano
Vivek Singh Bawa
Jorge Bernal
Sebastian Bodenstedt
Alessandro Casella
Jinwook Choi
Olivier Commowick
M. Daum
Adrien Depeursinge
Reuben Dorent
J. Egger
H. Eichhorn
Sandy Engelhardt
Melanie Ganz
Gabriel Girard
Lasse Donovan Hansen
Mattias Paul Heinrich
Nicholas Heller
Alessa Hering
Arnaud Huaulm'e
Hyunjeong Kim
Bennett Landman
Hongwei Bran Li
Jianning Li
Junfang Ma
Anne L. Martel
Carlos Mart'in-Isla
Bjoern Menze
Chinedu Innocent Nwoye
Valentin Oreiller
Nicolas Padoy
Sarthak Pati
Kelly Payette
Carole H. Sudre
K. V. Wijnen
Armine Vardazaryan
Tom Kamiel Magda Vercauteren
Martin Wagner
Chuanbo Wang
Moi Hoon Yap
Zeyun Yu
Chuner Yuan
Maximilian Zenk
Aneeq Zia
David Zimmerer
Rina Bao
Chanyeol Choi
Andrew Cohen
Oleh Dzyubachyk
Adrian Galdran
Tianyuan Gan
Tianqi Guo
Pradyumna Gupta
M. Haithami
Edward Ho
Ikbeom Jang
Zhili Li
Zheng Luo
Filip Lux
Sokratis Makrogiannis
Dominikus Muller
Young-Tack Oh
Subeen Pang
Constantin Pape
Görkem Polat
Charlotte Rosalie Reed
Kanghyun Ryu
Tim Scherr
Vajira L. Thambawita
Haoyu Wang
Xinliang Wang
Kele Xu
H.-I. Yeh
Doyeob Yeo
Yi Yuan
Yan Zeng
Xingwen Zhao
Julian Ronald Abbing
Jannes Adam
Nagesh Adluru
Niklas Agethen
S. Ahmed
Yasmina Al Khalil
Mireia Alenya
Esa J. Alhoniemi
C. An
Talha E Anwar
Tewodros Arega
Netanell Avisdris
D. Aydogan
Yi-Shi Bai
Maria Baldeon Calisto
Berke Doga Basaran
Marcel Beetz
Cheng Bian
Hao-xuan Bian
Kevin Blansit
Louise Bloch
Robert Bohnsack
Sara Bosticardo
J. Breen
Mikael Brudfors
Raphael Brungel
Mariano Cabezas
Alberto Cacciola
Zhiwei Chen
Yucong Chen
Dan Chen
Minjeong Cho
Min-Kook Choi
Chuantao Xie Chuantao Xie
Dana Cobzas
Jorge Corral Acero
Sujit Kumar Das
Marcela de Oliveira
Hanqiu Deng
Guiming Dong
Lars Doorenbos
Cory Efird
Di Fan
Mehdi Fatan Serj
Alexandre Fenneteau
Lucas Fidon
Patryk Filipiak
Ren'e Finzel
Nuno Renato Freitas
C. Friedrich
Mitchell J. Fulton
Finn Gaida
Francesco Galati
Christoforos Galazis
Changna Gan
Zheyao Gao
Sheng Gao
Matej Gazda
Beerend G. A. Gerats
Neil Getty
Adam Gibicar
Ryan J. Gifford
Sajan Gohil
Maria Grammatikopoulou
Daniel Grzech
Orhun Guley
Timo Gunnemann
Chun-Hai Guo
Sylvain Guy
Heonjin Ha
Luyi Han
Ilseok Han
Ali Hatamizadeh
Tianhai He
Ji-Wu Heo
Sebastian Hitziger
SeulGi Hong
Seungbum Hong
Rian Huang
Zi-You Huang
Markus Huellebrand
Stephan Huschauer
M. Hussain
Tomoo Inubushi
Ece Isik Polat
Mojtaba Jafaritadi
Seonghun Jeong
Bailiang Jian
Yu Jiang
Zhifan Jiang
Yu Jin
Smriti Joshi
A. Kadkhodamohammadi
R. A. Kamraoui
Inhak Kang
Jun-Su Kang
Davood Karimi
April Ellahe Khademi
Muhammad Irfan Khan
Suleiman A. Khan
Rishab Khantwal
Kwang-Ju Kim
Timothy Lee Kline
Satoshi Kondo
Elina Kontio
Adrian Krenzer
Artem Kroviakov
Hugo J. Kuijf
Satyadwyoom Kumar
Francesco La Rosa
Abhishek Lad
Doohee Lee
Minho Lee
Chiara Lena
Hao Li
Ling Li
Xingyu Li
F. Liao
Kuan-Ya Liao
Arlindo L. Oliveira
Chaonan Lin
Shanhai Lin
Akis Linardos
M. Linguraru
Han Liu
Tao Liu
Dian Liu
Yanling Liu
Joao Lourencco-Silva
Jing Lu
Jia Lu
Imanol Luengo
Christina Bach Lund
Huan Minh Luu
Yingqi Lv
Uzay Macar
Leon Maechler
L. SinaMansour
Kenji Marshall
Moona Mazher
Richard McKinley
Alfonso Medela
Felix Meissen
Mingyuan Meng
Dylan Bradley Miller
S. Mirjahanmardi
Arnab Kumar Mishra
Samir Mitha
Hassan Mohy-ud-Din
Tony C. W. Mok
Gowtham Krishnan Murugesan
Enamundram Naga Karthik
Sahil Nalawade
Jakub Nalepa
M. Naser
Ramin Nateghi
Hammad Naveed
Quang-Minh Nguyen
Cuong Nguyen Quoc
Brennan Nichyporuk
Bruno Oliveira
David Owen
Jimut Bahan Pal
Junwen Pan
W. Pan
Winnie Pang
Bogyu Park
Vivek G. Pawar
K. Pawar
Michael Peven
Lena Philipp
Tomasz Pieciak
Szymon S Płotka
Marcel Plutat
Fattane Pourakpour
Domen Prelovznik
K. Punithakumar
Abdul Qayyum
Sandro Queir'os
Arman Rahmim
Salar Razavi
Jintao Ren
Mina Rezaei
Jonathan Adam Rico
ZunHyan Rieu
Markus Rink
Johannes Roth
Yusely Ruiz-gonzalez
Numan Saeed
Anindo Saha
Mostafa M. Sami Salem
Ricardo Sanchez-matilla
Kurt G Schilling
Weizhen Shao
Zhiqiang Shen
Ruize Shi
Pengcheng Shi
Daniel Sobotka
Th'eodore Soulier
Bella Specktor Fadida
D. Stoyanov
Timothy Sum Hon Mun
Xiao-Fu Sun
Rong Tao
Franz Thaler
Antoine Th'eberge
Felix Thielke
Helena R. Torres
K. Wahid
Jiacheng Wang
Yifei Wang
W. Wang
Xiong Jun Wang
Jianhui Wen
Ning Wen
Marek Wodziński
Yehong Wu
Fangfang Xia
Tianqi Xiang
Cheng Xiaofei
Lizhang Xu
Tingting Xue
Yu‐Xia Yang
Lingxian Yang
Kai Yao
Huifeng Yao
Amirsaeed Yazdani
Michael Yip
Hwa-Seong Yoo
Fereshteh Yousefirizi
Shu-Fen Yu
Lei Yu
Jonathan Zamora
Ramy Ashraf Zeineldin
Dewen Zeng
Jianpeng Zhang
Bokai Zhang
Jiapeng Zhang
Fangxi Zhang
Huahong Zhang
Zhongchen Zhao
Zixuan Zhao
Jia Zhao
Can Zhao
Q. Zheng
Yuheng Zhi
Ziqi Zhou
Baosheng Zou
Klaus Maier-Hein
PAUL F. JÄGER
Annette Kopp-Schneider
Lena Maier-Hein
The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practic… (voir plus)e. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.
Biomedical image analysis competitions: The state of current participation practice
Matthias Eisenmann
Annika Reinke
Vivienn Weru
Minu Dietlinde Tizabi
Fabian Isensee
T. Adler
PATRICK GODAU
Veronika Cheplygina
Michal Kozubek
Sharib Ali
Anubha Gupta
Jan. Kybic
Alison Professor Noble
Carlos Ortiz de Sol'orzano
Samiksha Pachade
Caroline Petitjean
Daniel Sage
Donglai Wei
Elizabeth Wilden
Deepak Alapatt … (voir 334 de plus)
Vincent Andrearczyk
Ujjwal Baid
Spyridon Bakas
Niranjan Balu
Sophia Bano
Vivek Singh Bawa
Jorge Bernal
Sebastian Bodenstedt
Alessandro Casella
Jinwook Choi
Olivier Commowick
M. Daum
Adrien Depeursinge
Reuben Dorent
J. Egger
H. Eichhorn
Sandy Engelhardt
Melanie Ganz
Gabriel Girard
Lasse Donovan Hansen
Mattias Paul Heinrich
Nicholas Heller
Alessa Hering
Arnaud Huaulm'e
Hyunjeong Kim
Bennett Landman
Hongwei Bran Li
Jianning Li
Junfang Ma
Anne L. Martel
Carlos Mart'in-Isla
Bjoern Menze
Chinedu Innocent Nwoye
Valentin Oreiller
Nicolas Padoy
Sarthak Pati
Kelly Payette
Carole H. Sudre
K. V. Wijnen
Armine Vardazaryan
Tom Kamiel Magda Vercauteren
Martin Wagner
Chuanbo Wang
Moi Hoon Yap
Zeyun Yu
Chuner Yuan
Maximilian Zenk
Aneeq Zia
David Zimmerer
Rina Bao
Chanyeol Choi
Andrew Cohen
Oleh Dzyubachyk
Adrian Galdran
Tianyuan Gan
Tianqi Guo
Pradyumna Gupta
M. Haithami
Edward Ho
Ikbeom Jang
Zhili Li
Zheng Luo
Filip Lux
Sokratis Makrogiannis
Dominikus Muller
Young-Tack Oh
Subeen Pang
Constantin Pape
Görkem Polat
Charlotte Rosalie Reed
Kanghyun Ryu
Tim Scherr
Vajira L. Thambawita
Haoyu Wang
Xinliang Wang
Kele Xu
H.-I. Yeh
Doyeob Yeo
Yi Yuan
Yan Zeng
Xingwen Zhao
Julian Ronald Abbing
Jannes Adam
Nagesh Adluru
Niklas Agethen
S. Ahmed
Yasmina Al Khalil
Mireia Alenya
Esa J. Alhoniemi
C. An
Talha E Anwar
Tewodros Arega
Netanell Avisdris
D. Aydogan
Yi-Shi Bai
Maria Baldeon Calisto
Berke Doga Basaran
Marcel Beetz
Cheng Bian
Hao-xuan Bian
Kevin Blansit
Louise Bloch
Robert Bohnsack
Sara Bosticardo
J. Breen
Mikael Brudfors
Raphael Brungel
Mariano Cabezas
Alberto Cacciola
Zhiwei Chen
Yucong Chen
Dan Chen
Minjeong Cho
Min-Kook Choi
Chuantao Xie Chuantao Xie
Dana Cobzas
Jorge Corral Acero
Sujit Kumar Das
Marcela de Oliveira
Hanqiu Deng
Guiming Dong
Lars Doorenbos
Cory Efird
Di Fan
Mehdi Fatan Serj
Alexandre Fenneteau
Lucas Fidon
Patryk Filipiak
Ren'e Finzel
Nuno Renato Freitas
C. Friedrich
Mitchell J. Fulton
Finn Gaida
Francesco Galati
Christoforos Galazis
Changna Gan
Zheyao Gao
Sheng Gao
Matej Gazda
Beerend G. A. Gerats
Neil Getty
Adam Gibicar
Ryan J. Gifford
Sajan Gohil
Maria Grammatikopoulou
Daniel Grzech
Orhun Guley
Timo Gunnemann
Chun-Hai Guo
Sylvain Guy
Heonjin Ha
Luyi Han
Ilseok Han
Ali Hatamizadeh
Tianhai He
Ji-Wu Heo
Sebastian Hitziger
SeulGi Hong
Seungbum Hong
Rian Huang
Zi-You Huang
Markus Huellebrand
Stephan Huschauer
M. Hussain
Tomoo Inubushi
Ece Isik Polat
Mojtaba Jafaritadi
Seonghun Jeong
Bailiang Jian
Yu Jiang
Zhifan Jiang
Yu Jin
Smriti Joshi
A. Kadkhodamohammadi
R. A. Kamraoui
Inhak Kang
Jun-Su Kang
Davood Karimi
April Ellahe Khademi
Muhammad Irfan Khan
Suleiman A. Khan
Rishab Khantwal
Kwang-Ju Kim
Timothy Lee Kline
Satoshi Kondo
Elina Kontio
Adrian Krenzer
Artem Kroviakov
Hugo J. Kuijf
Satyadwyoom Kumar
Francesco La Rosa
Abhishek Lad
Doohee Lee
Minho Lee
Chiara Lena
Hao Li
Ling Li
Xingyu Li
F. Liao
Kuan-Ya Liao
Arlindo L. Oliveira
Chaonan Lin
Shanhai Lin
Akis Linardos
M. Linguraru
Han Liu
Tao Liu
Dian Liu
Yanling Liu
Joao Lourencco-Silva
Jing Lu
Jia Lu
Imanol Luengo
Christina Bach Lund
Huan Minh Luu
Yingqi Lv
Uzay Macar
Leon Maechler
L. SinaMansour
Kenji Marshall
Moona Mazher
Richard McKinley
Alfonso Medela
Felix Meissen
Mingyuan Meng
Dylan Bradley Miller
S. Mirjahanmardi
Arnab Kumar Mishra
Samir Mitha
Hassan Mohy-ud-Din
Tony C. W. Mok
Gowtham Krishnan Murugesan
Enamundram Naga Karthik
Sahil Nalawade
Jakub Nalepa
M. Naser
Ramin Nateghi
Hammad Naveed
Quang-Minh Nguyen
Cuong Nguyen Quoc
Brennan Nichyporuk
Bruno Oliveira
David Owen
Jimut Bahan Pal
Junwen Pan
W. Pan
Winnie Pang
Bogyu Park
Vivek G. Pawar
K. Pawar
Michael Peven
Lena Philipp
Tomasz Pieciak
Szymon S Płotka
Marcel Plutat
Fattane Pourakpour
Domen Prelovznik
K. Punithakumar
Abdul Qayyum
Sandro Queir'os
Arman Rahmim
Salar Razavi
Jintao Ren
Mina Rezaei
Jonathan Adam Rico
ZunHyan Rieu
Markus Rink
Johannes Roth
Yusely Ruiz-gonzalez
Numan Saeed
Anindo Saha
Mostafa M. Sami Salem
Ricardo Sanchez-matilla
Kurt G Schilling
Weizhen Shao
Zhiqiang Shen
Ruize Shi
Pengcheng Shi
Daniel Sobotka
Th'eodore Soulier
Bella Specktor Fadida
D. Stoyanov
Timothy Sum Hon Mun
Xiao-Fu Sun
Rong Tao
Franz Thaler
Antoine Th'eberge
Felix Thielke
Helena R. Torres
K. Wahid
Jiacheng Wang
Yifei Wang
W. Wang
Xiong Jun Wang
Jianhui Wen
Ning Wen
Marek Wodziński
Yehong Wu
Fangfang Xia
Tianqi Xiang
Cheng Xiaofei
Lizhang Xu
Tingting Xue
Yu‐Xia Yang
Lingxian Yang
Kai Yao
Huifeng Yao
Amirsaeed Yazdani
Michael Yip
Hwa-Seong Yoo
Fereshteh Yousefirizi
Shu-Fen Yu
Lei Yu
Jonathan Zamora
Ramy Ashraf Zeineldin
Dewen Zeng
Jianpeng Zhang
Bokai Zhang
Jiapeng Zhang
Fangxi Zhang
Huahong Zhang
Zhongchen Zhao
Zixuan Zhao
Jia Zhao
Can Zhao
Q. Zheng
Yuheng Zhi
Ziqi Zhou
Baosheng Zou
Klaus Maier-Hein
PAUL F. JÄGER
Annette Kopp-Schneider
Lena Maier-Hein
Biomedical image analysis competitions: The state of current participation practice
Matthias Eisenmann
Annika Reinke
Vivienn Weru
Minu Dietlinde Tizabi
Fabian Isensee
T. Adler
PATRICK GODAU
Veronika Cheplygina
Michal Kozubek
Sharib Ali
Anubha Gupta
Jan. Kybic
Alison Professor Noble
Carlos Ortiz de Sol'orzano
Samiksha Pachade
Caroline Petitjean
Daniel Sage
Donglai Wei
Elizabeth Wilden
Deepak Alapatt … (voir 334 de plus)
Vincent Andrearczyk
Ujjwal Baid
Spyridon Bakas
Niranjan Balu
Sophia Bano
Vivek Singh Bawa
Jorge Bernal
Sebastian Bodenstedt
Alessandro Casella
Jinwook Choi
Olivier Commowick
M. Daum
Adrien Depeursinge
Reuben Dorent
J. Egger
H. Eichhorn
Sandy Engelhardt
Melanie Ganz
Gabriel Girard
Lasse Donovan Hansen
Mattias Paul Heinrich
Nicholas Heller
Alessa Hering
Arnaud Huaulm'e
Hyunjeong Kim
Bennett Landman
Hongwei Bran Li
Jianning Li
Junfang Ma
Anne L. Martel
Carlos Mart'in-Isla
Bjoern Menze
Chinedu Innocent Nwoye
Valentin Oreiller
Nicolas Padoy
Sarthak Pati
Kelly Payette
Carole H. Sudre
K. V. Wijnen
Armine Vardazaryan
Tom Kamiel Magda Vercauteren
Martin Wagner
Chuanbo Wang
Moi Hoon Yap
Zeyun Yu
Chuner Yuan
Maximilian Zenk
Aneeq Zia
David Zimmerer
Rina Bao
Chanyeol Choi
Andrew Cohen
Oleh Dzyubachyk
Adrian Galdran
Tianyuan Gan
Tianqi Guo
Pradyumna Gupta
M. Haithami
Edward Ho
Ikbeom Jang
Zhili Li
Zheng Luo
Filip Lux
Sokratis Makrogiannis
Dominikus Muller
Young-Tack Oh
Subeen Pang
Constantin Pape
Görkem Polat
Charlotte Rosalie Reed
Kanghyun Ryu
Tim Scherr
Vajira L. Thambawita
Haoyu Wang
Xinliang Wang
Kele Xu
H.-I. Yeh
Doyeob Yeo
Yi Yuan
Yan Zeng
Xingwen Zhao
Julian Ronald Abbing
Jannes Adam
Nagesh Adluru
Niklas Agethen
S. Ahmed
Yasmina Al Khalil
Mireia Alenya
Esa J. Alhoniemi
C. An
Talha E Anwar
Tewodros Arega
Netanell Avisdris
D. Aydogan
Yi-Shi Bai
Maria Baldeon Calisto
Berke Doga Basaran
Marcel Beetz
Cheng Bian
Hao-xuan Bian
Kevin Blansit
Louise Bloch
Robert Bohnsack
Sara Bosticardo
J. Breen
Mikael Brudfors
Raphael Brungel
Mariano Cabezas
Alberto Cacciola
Zhiwei Chen
Yucong Chen
Dan Chen
Minjeong Cho
Min-Kook Choi
Chuantao Xie Chuantao Xie
Dana Cobzas
Jorge Corral Acero
Sujit Kumar Das
Marcela de Oliveira
Hanqiu Deng
Guiming Dong
Lars Doorenbos
Cory Efird
Di Fan
Mehdi Fatan Serj
Alexandre Fenneteau
Lucas Fidon
Patryk Filipiak
Ren'e Finzel
Nuno Renato Freitas
C. Friedrich
Mitchell J. Fulton
Finn Gaida
Francesco Galati
Christoforos Galazis
Changna Gan
Zheyao Gao
Sheng Gao
Matej Gazda
Beerend G. A. Gerats
Neil Getty
Adam Gibicar
Ryan J. Gifford
Sajan Gohil
Maria Grammatikopoulou
Daniel Grzech
Orhun Guley
Timo Gunnemann
Chun-Hai Guo
Sylvain Guy
Heonjin Ha
Luyi Han
Ilseok Han
Ali Hatamizadeh
Tianhai He
Ji-Wu Heo
Sebastian Hitziger
SeulGi Hong
Seungbum Hong
Rian Huang
Zi-You Huang
Markus Huellebrand
Stephan Huschauer
M. Hussain
Tomoo Inubushi
Ece Isik Polat
Mojtaba Jafaritadi
Seonghun Jeong
Bailiang Jian
Yu Jiang
Zhifan Jiang
Yu Jin
Smriti Joshi
A. Kadkhodamohammadi
R. A. Kamraoui
Inhak Kang
Jun-Su Kang
Davood Karimi
April Ellahe Khademi
Muhammad Irfan Khan
Suleiman A. Khan
Rishab Khantwal
Kwang-Ju Kim
Timothy Lee Kline
Satoshi Kondo
Elina Kontio
Adrian Krenzer
Artem Kroviakov
Hugo J. Kuijf
Satyadwyoom Kumar
Francesco La Rosa
Abhishek Lad
Doohee Lee
Minho Lee
Chiara Lena
Hao Li
Ling Li
Xingyu Li
F. Liao
Kuan-Ya Liao
Arlindo L. Oliveira
Chaonan Lin
Shanhai Lin
Akis Linardos
M. Linguraru
Han Liu
Tao Liu
Dian Liu
Yanling Liu
Joao Lourencco-Silva
Jing Lu
Jia Lu
Imanol Luengo
Christina Bach Lund
Huan Minh Luu
Yingqi Lv
Uzay Macar
Leon Maechler
L. SinaMansour
Kenji Marshall
Moona Mazher
Richard McKinley
Alfonso Medela
Felix Meissen
Mingyuan Meng
Dylan Bradley Miller
S. Mirjahanmardi
Arnab Kumar Mishra
Samir Mitha
Hassan Mohy-ud-Din
Tony C. W. Mok
Gowtham Krishnan Murugesan
Enamundram Naga Karthik
Sahil Nalawade
Jakub Nalepa
M. Naser
Ramin Nateghi
Hammad Naveed
Quang-Minh Nguyen
Cuong Nguyen Quoc
Brennan Nichyporuk
Bruno Oliveira
David Owen
Jimut Bahan Pal
Junwen Pan
W. Pan
Winnie Pang
Bogyu Park
Vivek G. Pawar
K. Pawar
Michael Peven
Lena Philipp
Tomasz Pieciak
Szymon S Płotka
Marcel Plutat
Fattane Pourakpour
Domen Prelovznik
K. Punithakumar
Abdul Qayyum
Sandro Queir'os
Arman Rahmim
Salar Razavi
Jintao Ren
Mina Rezaei
Jonathan Adam Rico
ZunHyan Rieu
Markus Rink
Johannes Roth
Yusely Ruiz-gonzalez
Numan Saeed
Anindo Saha
Mostafa M. Sami Salem
Ricardo Sanchez-matilla
Kurt G Schilling
Weizhen Shao
Zhiqiang Shen
Ruize Shi
Pengcheng Shi
Daniel Sobotka
Th'eodore Soulier
Bella Specktor Fadida
D. Stoyanov
Timothy Sum Hon Mun
Xiao-Fu Sun
Rong Tao
Franz Thaler
Antoine Th'eberge
Felix Thielke
Helena R. Torres
K. Wahid
Jiacheng Wang
Yifei Wang
W. Wang
Xiong Jun Wang
Jianhui Wen
Ning Wen
Marek Wodziński
Yehong Wu
Fangfang Xia
Tianqi Xiang
Cheng Xiaofei
Lizhang Xu
Tingting Xue
Yu‐Xia Yang
Lingxian Yang
Kai Yao
Huifeng Yao
Amirsaeed Yazdani
Michael Yip
Hwa-Seong Yoo
Fereshteh Yousefirizi
Shu-Fen Yu
Lei Yu
Jonathan Zamora
Ramy Ashraf Zeineldin
Dewen Zeng
Jianpeng Zhang
Bokai Zhang
Jiapeng Zhang
Fangxi Zhang
Huahong Zhang
Zhongchen Zhao
Zixuan Zhao
Jia Zhao
Can Zhao
Q. Zheng
Yuheng Zhi
Ziqi Zhou
Baosheng Zou
Klaus Maier-Hein
PAUL F. JÄGER
Annette Kopp-Schneider
Lena Maier-Hein
The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practic… (voir plus)e. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.