no code implementations • 19 Nov 2024 • Vishwesh Nath, Wenqi Li, Dong Yang, Andriy Myronenko, Mingxin Zheng, Yao Lu, Zhijian Liu, Hongxu Yin, Yee Man Law, Yucheng Tang, Pengfei Guo, Can Zhao, Ziyue Xu, Yufan He, Greg Heinrich, Stephen Aylward, Marc Edgar, Michael Zephyr, Pavlo Molchanov, Baris Turkbey, Holger Roth, Daguang Xu
In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models.
1 code implementation • 13 Sep 2024 • Pengfei Guo, Can Zhao, Dong Yang, Ziyue Xu, Vishwesh Nath, Yucheng Tang, Benjamin Simon, Mason Belue, Stephanie Harmon, Baris Turkbey, Daguang Xu
Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns.
no code implementations • 18 Jun 2024 • Alex Chen, Nathan Lay, Stephanie Harmon, Kutsev Ozyoruk, Enis Yilmaz, Brad J. Wood, Peter A. Pinto, Peter L. Choyke, Baris Turkbey
Prostate cancer is one of the most prevalent malignancies in the world.
1 code implementation • 7 Jun 2024 • Yufan He, Pengfei Guo, Yucheng Tang, Andriy Myronenko, Vishwesh Nath, Ziyue Xu, Dong Yang, Can Zhao, Benjamin Simon, Mason Belue, Stephanie Harmon, Baris Turkbey, Daguang Xu, Wenqi Li
The novel model design and training recipe represent a promising step toward developing a versatile medical image foundation model and will serve as a valuable foundation for CT image analysis.
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.
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.
no code implementations • 8 Feb 2024 • Pouria Yazdian Anari, Fiona Obiezu, Nathan Lay, Fatemeh Dehghani Firouzabadi, Aditi Chaurasia, Mahshid Golagha, Shiva Singh, Fatemeh Homayounieh, Aryan Zahergivar, Stephanie Harmon, Evrim Turkbey, Rabindra Gautam, Kevin Ma, Maria Merino, Elizabeth C. Jones, Mark W. Ball, W. Marston Linehan, Baris Turkbey, Ashkan A. Malayeri
The best primary model was then used to identify tumors in the remaining 861 patients and bounding box coordinates were generated on their scans using the model.
1 code implementation • 29 May 2023 • Bin Wang, Hongyi Pan, Armstrong Aboah, Zheyuan Zhang, Elif Keles, Drew Torigian, Baris Turkbey, Elizabeth Krupinski, Jayaram Udupa, Ulas Bagci
To our best knowledge, GazeGNN is the first work that adopts GNN to integrate image and eye-gaze data.
no code implementations • 6 Jan 2023 • Pouria Yazdian Anari, Nathan Lay, Aditi Chaurasia, Nikhil Gopal, Safa Samimi, Stephanie Harmon, Rabindra Gautam, Kevin Ma, Fatemeh Dehghani Firouzabadi, Evrim Turkbey, Maria Merino, Elizabeth C. Jones, Mark W. Ball, W. Marston Linehan, Baris Turkbey, Ashkan A. Malayeri
Our 2D U-Net achieved an average ccRCC lesion detection Area under the curve (AUC) of 0. 88 and DSC scores of 0. 78, 0. 40, and 0. 46 for segmentation of the kidney, cysts, and tumors, respectively.
no code implementations • 11 Oct 2022 • Xinrui Song, Xuanang Xu, Sheng Xu, Baris Turkbey, Bradford J. Wood, Thomas Sanford, Pingkun Yan
We then use the predicted landmarks to generate the affine transformation matrix, which outperforms the clinicians' manual rigid registration by a significant margin in terms of TRE.
no code implementations • 12 Mar 2022 • Pengfei Guo, Dong Yang, Ali Hatamizadeh, An Xu, Ziyue Xu, Wenqi Li, Can Zhao, Daguang Xu, Stephanie Harmon, Evrim Turkbey, Baris Turkbey, Bradford Wood, Francesca Patella, Elvira Stellato, Gianpaolo Carrafiello, Vishal M. Patel, Holger R. Roth
Federated learning (FL) is a distributed machine learning technique that enables collaborative model training while avoiding explicit data sharing.
1 code implementation • 9 Jul 2021 • Xinrui Song, Hengtao Guo, Xuanang Xu, Hanqing Chao, Sheng Xu, Baris Turkbey, Bradford J. Wood, Ge Wang, Pingkun Yan
In the past few years, convolutional neural networks (CNNs) have been proved powerful in extracting image features crucial for image registration.
no code implementations • 20 Apr 2021 • Yingda Xia, Dong Yang, Wenqi Li, Andriy Myronenko, Daguang Xu, Hirofumi Obinata, Hitoshi Mori, Peng An, Stephanie Harmon, Evrim Turkbey, Baris Turkbey, Bradford Wood, Francesca Patella, Elvira Stellato, Gianpaolo Carrafiello, Anna Ierardi, Alan Yuille, Holger Roth
In this work, we design a new data-driven approach, namely Auto-FedAvg, where aggregation weights are dynamically adjusted, depending on data distributions across data silos and the current training progress of the models.
no code implementations • 7 Apr 2021 • Ugur Demir, Ismail Irmakci, Elif Keles, Ahmet Topcu, Ziyue Xu, Concetto Spampinato, Sachin Jambawalikar, Evrim Turkbey, Baris Turkbey, Ulas Bagci
We provide an innovative visual explanation algorithm for general purpose and as an example application, we demonstrate its effectiveness for quantifying lesions in the lungs caused by the Covid-19 with high accuracy and robustness without using dense segmentation labels.
no code implementations • 23 Nov 2020 • Dong Yang, Ziyue Xu, Wenqi Li, Andriy Myronenko, Holger R. Roth, Stephanie Harmon, Sheng Xu, Baris Turkbey, Evrim Turkbey, Xiaosong Wang, Wentao Zhu, Gianpaolo Carrafiello, Francesca Patella, Maurizio Cariati, Hirofumi Obinata, Hitoshi Mori, Kaku Tamura, Peng An, Bradford J. Wood, Daguang Xu
To facilitate CT analysis, recent efforts have focused on computer-aided characterization and diagnosis, which has shown promising results.
no code implementations • 10 Jul 2020 • Liyue Shen, Wentao Zhu, Xiaosong Wang, Lei Xing, John M. Pauly, Baris Turkbey, Stephanie Anne Harmon, Thomas Hogue Sanford, Sherif Mehralivand, Peter Choyke, Bradford Wood, Daguang Xu
Multi-domain data are widely leveraged in vision applications taking advantage of complementary information from different modalities, e. g., brain tumor segmentation from multi-parametric magnetic resonance imaging (MRI).
1 code implementation • 11 May 2020 • Samira Masoudi, Syed M. Anwar, Stephanie A. Harmon, Peter L . Choyke, Baris Turkbey, Ulas Bagci
Abdominal fat quantification is critical since multiple vital organs are located within this region.
no code implementations • MIDL 2019 • Samira Masoudi, Stephanie A. Harmon, Stephanie Walker, Sherif Mehralivand, Ulas Bagci, Peter L. Choyke, Baris Turkbey
This work can considerably improve the quality of mpMRI combined assessment for prostate cancer detection.
no code implementations • MIDL 2019 • Stephanie A Harmon, Samira Masoudi, Thomas Sanford, Sherif Mehralivand, Stephanie Walker, Peter Choyke, Brad Wood, Peter Pinto, Jesse McKenney, Baris Turkbey
Current routine histopathologic evaluation of prostate cancer does not fully account for some individual morphology patterns associated with poor outcome.
1 code implementation • 7 Jun 2019 • Ling Zhang, Xiaosong Wang, Dong Yang, Thomas Sanford, Stephanie Harmon, Baris Turkbey, Holger Roth, Andriy Myronenko, Daguang Xu, Ziyue Xu
We rethink data augmentation for medical 3D images and propose a deep stacked transformations (DST) approach for domain generalization.
no code implementations • 17 Feb 2018 • Naji Khosravan, Haydar Celik, Baris Turkbey, Elizabeth Jones, Bradford Wood, Ulas Bagci
Computer aided diagnostic (CAD) tools are developed to help radiologists to compensate for some of these errors.
no code implementations • 22 Mar 2017 • Qikui Zhu, Bo Du, Baris Turkbey, Peter L . Choyke, Pingkun Yan
Prostate segmentation from Magnetic Resonance (MR) images plays an important role in image guided interven- tion.
no code implementations • 10 Aug 2016 • Naji Khosravan, Haydar Celik, Baris Turkbey, Ruida Cheng, Evan McCreedy, Matthew McAuliffe, Sandra Bednarova, Elizabeth Jones, Xinjian Chen, Peter L . Choyke, Bradford J. Wood, Ulas Bagci
During diagnostic assessment of lung CT scans, the radiologists' gaze information were used to create a visual attention map.