no code implementations • 8 Nov 2024 • Hongyi Pan, Ziliang Hong, Gorkem Durak, Elif Keles, Halil Ertugrul Aktas, Yavuz Taktak, Alpay Medetalibeyoglu, Zheyuan Zhang, Yury Velichko, Concetto Spampinato, Ivo Schoots, Marco J. Bruno, Pallavi Tiwari, Candice Bolan, Tamas Gonda, Frank Miller, Rajesh N. Keswani, Michael B. Wallace, Ziyue Xu, Ulas Bagci
In this study, we develop a federated learning framework for multi-center IPMN classification utilizing a comprehensive pancreas MRI dataset.
no code implementations • 29 Oct 2024 • Hongyi Pan, Gorkem Durak, Zheyuan Zhang, Yavuz Taktak, Elif Keles, Halil Ertugrul Aktas, Alpay Medetalibeyoglu, Yury Velichko, Concetto Spampinato, Ivo Schoots, Marco J. Bruno, Rajesh N. Keswani, Pallavi Tiwari, Candice Bolan, Tamas Gonda, Michael G. Goggins, Michael B. Wallace, Ziyue Xu, Ulas Bagci
Federated learning (FL) enables collaborative model training across institutions without sharing sensitive data, making it an attractive solution for medical imaging tasks.
no code implementations • 11 Aug 2024 • Koushik Biswas, Ridal Pal, Shaswat Patel, Debesh Jha, Meghana Karri, Amit Reza, Gorkem Durak, Alpay Medetalibeyoglu, Matthew Antalek, Yury Velichko, Daniela Ladner, Amir Borhani, Ulas Bagci
This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases.
no code implementations • 28 May 2024 • Maria Correia de Verdier, Rachit Saluja, Louis Gagnon, Dominic LaBella, Ujjwall Baid, Nourel Hoda Tahon, Martha Foltyn-Dumitru, Jikai Zhang, Maram Alafif, Saif Baig, Ken Chang, Gennaro D'Anna, Lisa Deptula, Diviya Gupta, Muhammad Ammar Haider, Ali Hussain, Michael Iv, Marinos Kontzialis, Paul Manning, Farzan Moodi, Teresa Nunes, Aaron Simon, Nico Sollmann, David Vu, Maruf Adewole, Jake Albrecht, Udunna Anazodo, Rongrong Chai, Verena Chung, Shahriar Faghani, Keyvan Farahani, Anahita Fathi Kazerooni, Eugenio Iglesias, Florian Kofler, Hongwei Li, Marius George Linguraru, Bjoern Menze, Ahmed W. Moawad, Yury Velichko, Benedikt Wiestler, Talissa Altes, Patil Basavasagar, Martin Bendszus, Gianluca Brugnara, Jaeyoung Cho, Yaseen Dhemesh, Brandon K. K. Fields, Filip Garrett, Jaime Gass, Lubomir Hadjiiski, Jona Hattangadi-Gluth, Christopher Hess, Jessica L. Houk, Edvin Isufi, Lester J. Layfield, George Mastorakos, John Mongan, Pierre Nedelec, Uyen Nguyen, Sebastian Oliva, Matthew W. Pease, Aditya Rastogi, Jason Sinclair, Robert X. Smith, Leo P. Sugrue, Jonathan Thacker, Igor Vidic, Javier Villanueva-Meyer, Nathan S. White, Mariam Aboian, Gian Marco Conte, Anders Dale, Mert R. Sabuncu, Tyler M. Seibert, Brent Weinberg, Aly Abayazeed, Raymond Huang, Sevcan Turk, Andreas M. Rauschecker, Nikdokht Farid, Philipp Vollmuth, Ayman Nada, Spyridon Bakas, Evan Calabrese, Jeffrey D. Rudie
Gliomas are the most common malignant primary brain tumors in adults and one of the deadliest types of cancer.
no code implementations • 28 May 2024 • Dominic LaBella, Katherine Schumacher, Michael Mix, Kevin Leu, Shan McBurney-Lin, Pierre Nedelec, Javier Villanueva-Meyer, Jonathan Shapey, Tom Vercauteren, Kazumi Chia, Omar Al-Salihi, Justin Leu, Lia Halasz, Yury Velichko, Chunhao Wang, John Kirkpatrick, Scott Floyd, Zachary J. Reitman, Trey Mullikin, Ulas Bagci, Sean Sachdev, Jona A. Hattangadi-Gluth, Tyler Seibert, Nikdokht Farid, Connor Puett, Matthew W. Pease, Kevin Shiue, Syed Muhammad Anwar, Shahriar Faghani, Muhammad Ammar Haider, Pranav Warman, Jake Albrecht, András Jakab, Mana Moassefi, Verena Chung, Alejandro Aristizabal, Alexandros Karargyris, Hasan Kassem, Sarthak Pati, Micah Sheller, Christina Huang, Aaron Coley, Siddharth Ghanta, Alex Schneider, Conrad Sharp, Rachit Saluja, Florian Kofler, Philipp Lohmann, Phillipp Vollmuth, Louis Gagnon, Maruf Adewole, Hongwei Bran Li, Anahita Fathi Kazerooni, Nourel Hoda Tahon, Udunna Anazodo, Ahmed W. Moawad, Bjoern Menze, Marius George Linguraru, Mariam Aboian, Benedikt Wiestler, Ujjwal Baid, Gian-Marco Conte, Andreas M. Rauschecker, Ayman Nada, Aly H. Abayazeed, Raymond Huang, Maria Correia de Verdier, Jeffrey D. Rudie, Spyridon Bakas, Evan Calabrese
The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aims to advance automated segmentation algorithms using the largest known multi-institutional dataset of radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or postoperative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery.
1 code implementation • 20 May 2024 • Zheyuan Zhang, Elif Keles, Gorkem Durak, Yavuz Taktak, Onkar Susladkar, Vandan Gorade, Debesh Jha, Asli C. Ormeci, Alpay Medetalibeyoglu, Lanhong Yao, Bin Wang, Ilkin Sevgi Isler, Linkai Peng, Hongyi Pan, Camila Lopes Vendrami, Amir Bourhani, Yury Velichko, Boqing Gong, Concetto Spampinato, Ayis Pyrros, Pallavi Tiwari, Derk C. F. Klatte, Megan Engels, Sanne Hoogenboom, Candice W. Bolan, Emil Agarunov, Nassier Harfouch, Chenchan Huang, Marco J. Bruno, Ivo Schoots, Rajesh N. Keswani, Frank H. Miller, Tamas Gonda, Cemal Yazici, Temel Tirkes, Baris Turkbey, Michael B. Wallace, Ulas Bagci
We also collected CT scans of 1, 350 patients from publicly available sources for benchmarking purposes.
no code implementations • 16 May 2024 • Dominic LaBella, Ujjwal Baid, Omaditya Khanna, Shan McBurney-Lin, Ryan McLean, Pierre Nedelec, Arif Rashid, Nourel Hoda Tahon, Talissa Altes, Radhika Bhalerao, Yaseen Dhemesh, Devon Godfrey, Fathi Hilal, Scott Floyd, Anastasia Janas, Anahita Fathi Kazerooni, John Kirkpatrick, Collin Kent, Florian Kofler, Kevin Leu, Nazanin Maleki, Bjoern Menze, Maxence Pajot, Zachary J. Reitman, Jeffrey D. Rudie, Rachit Saluja, Yury Velichko, Chunhao Wang, Pranav Warman, Maruf Adewole, Jake Albrecht, Udunna Anazodo, Syed Muhammad Anwar, Timothy Bergquist, Sully Francis Chen, Verena Chung, Gian-Marco Conte, Farouk Dako, James Eddy, Ivan Ezhov, Nastaran Khalili, Juan Eugenio Iglesias, Zhifan Jiang, Elaine Johanson, Koen van Leemput, Hongwei Bran Li, Marius George Linguraru, Xinyang Liu, Aria Mahtabfar, Zeke Meier, Ahmed W. Moawad, John Mongan, Marie Piraud, Russell Takeshi Shinohara, Walter F. Wiggins, Aly H. Abayazeed, Rachel Akinola, András Jakab, Michel Bilello, Maria Correia de Verdier, Priscila Crivellaro, Christos Davatzikos, Keyvan Farahani, John Freymann, Christopher Hess, Raymond Huang, Philipp Lohmann, Mana Moassefi, Matthew W. Pease, Phillipp Vollmuth, Nico Sollmann, David Diffley, Khanak K. Nandolia, Daniel I. Warren, Ali Hussain, Pascal Fehringer, Yulia Bronstein, Lisa Deptula, Evan G. Stein, Mahsa Taherzadeh, Eduardo Portela de Oliveira, Aoife Haughey, Marinos Kontzialis, Luca Saba, Benjamin Turner, Melanie M. T. Brüßeler, Shehbaz Ansari, Athanasios Gkampenis, David Maximilian Weiss, Aya Mansour, Islam H. Shawali, Nikolay Yordanov, Joel M. Stein, Roula Hourani, Mohammed Yahya Moshebah, Ahmed Magdy Abouelatta, Tanvir Rizvi, Klara Willms, Dann C. Martin, Abdullah Okar, Gennaro D'Anna, Ahmed Taha, Yasaman Sharifi, Shahriar Faghani, Dominic Kite, Marco Pinho, Muhammad Ammar Haider, Alejandro Aristizabal, Alexandros Karargyris, Hasan Kassem, Sarthak Pati, Micah Sheller, Michelle Alonso-Basanta, Javier Villanueva-Meyer, Andreas M. Rauschecker, Ayman Nada, Mariam Aboian, Adam E. Flanders, Benedikt Wiestler, Spyridon Bakas, Evan Calabrese
The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0. 976, 0. 976, and 0. 964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0. 899, 0. 904, and 0. 871, respectively.
no code implementations • 10 May 2024 • Debesh Jha, Nikhil Kumar Tomar, Koushik Biswas, Gorkem Durak, Matthew Antalek, Zheyuan Zhang, Bin Wang, Md Mostafijur Rahman, Hongyi Pan, Alpay Medetalibeyoglu, Yury Velichko, Daniela Ladner, Amir Borhani, Ulas Bagci
Each decoder network is connected to a different part of the encoder via a multi-scale feature enhancement dilated block.
no code implementations • 2 May 2024 • Abhijit Das, Debesh Jha, Vandan Gorade, Koushik Biswas, Hongyi Pan, Zheyuan Zhang, Daniela P. Ladner, Yury Velichko, Amir Borhani, Ulas Bagci
Computer-aided segmentation methods can assist medical personnel in improving diagnostic outcomes.
1 code implementation • 25 Apr 2024 • Ziliang Hong, Debesh Jha, Koushik Biswas, Zheyuan Zhang, Yury Velichko, Cemal Yazici, Temel Tirkes, Amir Borhani, Baris Turkbey, Alpay Medetalibeyoglu, Gorkem Durak, Ulas Bagci
Identifying peri-pancreatic edema is a pivotal indicator for identifying disease progression and prognosis, emphasizing the critical need for accurate detection and assessment in pancreatitis diagnosis and management.
1 code implementation • 8 Mar 2024 • Xin Zhu, Hongyi Pan, Yury Velichko, Adam B. Murphy, Ashley Ross, Baris Turkbey, Ahmet Enis Cetin, Ulas Bagci
Random samples drawn from latent space are then incorporated with a prototypical corrected image to generate multiple plausible images.
1 code implementation • 17 Jan 2024 • Debesh Jha, Nikhil Kumar Tomar, Koushik Biswas, Gorkem Durak, Alpay Medetalibeyoglu, Matthew Antalek, Yury Velichko, Daniela Ladner, Amir Borhani, Ulas Bagci
Accurate liver segmentation from CT scans is essential for effective diagnosis and treatment planning.
Ranked #5 on
Liver Segmentation
on LiTS2017
no code implementations • 29 Nov 2023 • Koushik Biswas, Debesh Jha, Nikhil Kumar Tomar, Gorkem Durak, Alpay Medetalibeyoglu, Matthew Antalek, Yury Velichko, Daniela Ladner, Amir Bohrani, Ulas Bagci
We apply this new activation function to two important and commonly used general tasks in medical image analysis: automatic disease diagnosis and organ segmentation in CT and MRI.
1 code implementation • 22 Nov 2023 • Amirhossein Kazerouni, Sanaz Karimijafarbigloo, Reza Azad, Yury Velichko, Ulas Bagci, Dorit Merhof
Semantic segmentation, a crucial task in computer vision, often relies on labor-intensive and costly annotated datasets for training.
1 code implementation • 21 Nov 2023 • Afshin Bozorgpour, Bobby Azad, Reza Azad, Yury Velichko, Ulas Bagci, Dorit Merhof
In addition, we introduce a skeletal loss term to reinforce the model's geometric dependence on the spine.
no code implementations • 21 Nov 2023 • Sanaz Karimijafarbigloo, Reza Azad, Yury Velichko, Ulas Bagci, Dorit Merhof
Current 3D semi-supervised segmentation methods face significant challenges such as limited consideration of contextual information and the inability to generate reliable pseudo-labels for effective unsupervised data use.
no code implementations • 2 Oct 2023 • Ariana M. Familiar, Anahita Fathi Kazerooni, Hannah Anderson, Aliaksandr Lubneuski, Karthik Viswanathan, Rocky Breslow, Nastaran Khalili, Sina Bagheri, Debanjan Haldar, Meen Chul Kim, Sherjeel Arif, Rachel Madhogarhia, Thinh Q. Nguyen, Elizabeth A. Frenkel, Zeinab Helili, Jessica Harrison, Keyvan Farahani, Marius George Linguraru, Ulas Bagci, Yury Velichko, Jeffrey Stevens, Sarah Leary, Robert M. Lober, Stephani Campion, Amy A. Smith, Denise Morinigo, Brian Rood, Kimberly Diamond, Ian F. Pollack, Melissa Williams, Arastoo Vossough, Jeffrey B. Ware, Sabine Mueller, Phillip B. Storm, Allison P. Heath, Angela J. Waanders, Jena V. Lilly, Jennifer L. Mason, Adam C. Resnick, Ali Nabavizadeh
Pediatric brain and spinal cancers remain the leading cause of cancer-related death in children.
1 code implementation • 31 Aug 2023 • Sanaz Karimijafarbigloo, Reza Azad, Amirhossein Kazerouni, Yury Velichko, Ulas Bagci, Dorit Merhof
Accurate medical image segmentation is of utmost importance for enabling automated clinical decision procedures.
1 code implementation • 31 Aug 2023 • Reza Azad, Leon Niggemeier, Michael Huttemann, Amirhossein Kazerouni, Ehsan Khodapanah Aghdam, Yury Velichko, Ulas Bagci, Dorit Merhof
To address these challenges, we introduce the concept of \textbf{Deformable Large Kernel Attention (D-LKA Attention)}, a streamlined attention mechanism employing large convolution kernels to fully appreciate volumetric context.
1 code implementation • 31 Aug 2023 • Reza Azad, Amirhossein Kazerouni, Babak Azad, Ehsan Khodapanah Aghdam, Yury Velichko, Ulas Bagci, Dorit Merhof
Vision Transformer (ViT) models have demonstrated a breakthrough in a wide range of computer vision tasks.
no code implementations • 12 May 2023 • Dominic LaBella, Maruf Adewole, Michelle Alonso-Basanta, Talissa Altes, Syed Muhammad Anwar, Ujjwal Baid, Timothy Bergquist, Radhika Bhalerao, Sully Chen, Verena Chung, Gian-Marco Conte, Farouk Dako, James Eddy, Ivan Ezhov, Devon Godfrey, Fathi Hilal, Ariana Familiar, Keyvan Farahani, Juan Eugenio Iglesias, Zhifan Jiang, Elaine Johanson, Anahita Fathi Kazerooni, Collin Kent, John Kirkpatrick, Florian Kofler, Koen van Leemput, Hongwei Bran Li, Xinyang Liu, Aria Mahtabfar, Shan McBurney-Lin, Ryan McLean, Zeke Meier, Ahmed W Moawad, John Mongan, Pierre Nedelec, Maxence Pajot, Marie Piraud, Arif Rashid, Zachary Reitman, Russell Takeshi Shinohara, Yury Velichko, Chunhao Wang, Pranav Warman, Walter Wiggins, Mariam Aboian, Jake Albrecht, Udunna Anazodo, Spyridon Bakas, Adam Flanders, Anastasia Janas, Goldey Khanna, Marius George Linguraru, Bjoern Menze, Ayman Nada, Andreas M Rauschecker, Jeff Rudie, Nourel Hoda Tahon, Javier Villanueva-Meyer, Benedikt Wiestler, Evan Calabrese
Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality.