Tiwari, Pallavi
3D Nephrographic Image Synthesis in CT Urography with the Diffusion Model and Swin Transformer
Yu, Hongkun, Gardezi, Syed Jamal Safdar, Abel, E. Jason, Shapiro, Daniel, Lubner, Meghan G., Warner, Joshua, Smith, Matthew, Toia, Giuseppe, Mao, Lu, Tiwari, Pallavi, Wentland, Andrew L.
Purpose: This study aims to develop and validate a method for synthesizing 3D nephrographic phase images in CT urography (CTU) examinations using a diffusion model integrated with a Swin Transformer-based deep learning approach. Materials and Methods: This retrospective study was approved by the local Institutional Review Board. A dataset comprising 327 patients who underwent three-phase CTU (mean $\pm$ SD age, 63 $\pm$ 15 years; 174 males, 153 females) was curated for deep learning model development. The three phases for each patient were aligned with an affine registration algorithm. A custom deep learning model coined dsSNICT (diffusion model with a Swin transformer for synthetic nephrographic phase images in CT) was developed and implemented to synthesize the nephrographic images. Performance was assessed using Peak Signal-to-Noise Ratio (PSNR), Structural Similarity Index (SSIM), Mean Absolute Error (MAE), and Fr\'{e}chet Video Distance (FVD). Qualitative evaluation by two fellowship-trained abdominal radiologists was performed. Results: The synthetic nephrographic images generated by our proposed approach achieved high PSNR (26.3 $\pm$ 4.4 dB), SSIM (0.84 $\pm$ 0.069), MAE (12.74 $\pm$ 5.22 HU), and FVD (1323). Two radiologists provided average scores of 3.5 for real images and 3.4 for synthetic images (P-value = 0.5) on a Likert scale of 1-5, indicating that our synthetic images closely resemble real images. Conclusion: The proposed approach effectively synthesizes high-quality 3D nephrographic phase images. This model can be used to reduce radiation dose in CTU by 33.3\% without compromising image quality, which thereby enhances the safety and diagnostic utility of CT urography.
IPMN Risk Assessment under Federated Learning Paradigm
Pan, Hongyi, Hong, Ziliang, Durak, Gorkem, Keles, Elif, Aktas, Halil Ertugrul, Taktak, Yavuz, Medetalibeyoglu, Alpay, Zhang, Zheyuan, Velichko, Yury, Spampinato, Concetto, Schoots, Ivo, Bruno, Marco J., Tiwari, Pallavi, Bolan, Candice, Gonda, Tamas, Miller, Frank, Keswani, Rajesh N., Wallace, Michael B., Xu, Ziyue, Bagci, Ulas
Accurate classification of Intraductal Papillary Mucinous Neoplasms (IPMN) is essential for identifying high-risk cases that require timely intervention. In this study, we develop a federated learning framework for multi-center IPMN classification utilizing a comprehensive pancreas MRI dataset. This dataset includes 653 T1-weighted and 656 T2-weighted MRI images, accompanied by corresponding IPMN risk scores from 7 leading medical institutions, making it the largest and most diverse dataset for IPMN classification to date. We assess the performance of DenseNet-121 in both centralized and federated settings for training on distributed data. Our results demonstrate that the federated learning approach achieves high classification accuracy comparable to centralized learning while ensuring data privacy across institutions. This work marks a significant advancement in collaborative IPMN classification, facilitating secure and high-accuracy model training across multiple centers.
ResNCT: A Deep Learning Model for the Synthesis of Nephrographic Phase Images in CT Urography
Gardezi, Syed Jamal Safdar, Aronson, Lucas, Wawrzyn, Peter, Yu, Hongkun, Abel, E. Jason, Shapiro, Daniel D., Lubner, Meghan G., Warner, Joshua, Toia, Giuseppe, Mao, Lu, Tiwari, Pallavi, Wentland, Andrew L.
Purpose: To develop and evaluate a transformer-based deep learning model for the synthesis of nephrographic phase images in CT urography (CTU) examinations from the unenhanced and urographic phases. Materials and Methods: This retrospective study was approved by the local Institutional Review Board. A dataset of 119 patients (mean $\pm$ SD age, 65 $\pm$ 12 years; 75/44 males/females) with three-phase CT urography studies was curated for deep learning model development. The three phases for each patient were aligned with an affine registration algorithm. A custom model, coined Residual transformer model for Nephrographic phase CT image synthesis (ResNCT), was developed and implemented with paired inputs of non-contrast and urographic sets of images trained to produce the nephrographic phase images, that were compared with the corresponding ground truth nephrographic phase images. The synthesized images were evaluated with multiple performance metrics, including peak signal to noise ratio (PSNR), structural similarity index (SSIM), normalized cross correlation coefficient (NCC), mean absolute error (MAE), and root mean squared error (RMSE). Results: The ResNCT model successfully generated synthetic nephrographic images from non-contrast and urographic image inputs. With respect to ground truth nephrographic phase images, the images synthesized by the model achieved high PSNR (27.8 $\pm$ 2.7 dB), SSIM (0.88 $\pm$ 0.05), and NCC (0.98 $\pm$ 0.02), and low MAE (0.02 $\pm$ 0.005) and RMSE (0.042 $\pm$ 0.016). Conclusion: The ResNCT model synthesized nephrographic phase CT images with high similarity to ground truth images. The ResNCT model provides a means of eliminating the acquisition of the nephrographic phase with a resultant 33% reduction in radiation dose for CTU examinations.
Federated Learning Enables Big Data for Rare Cancer Boundary Detection
Pati, Sarthak, Baid, Ujjwal, Edwards, Brandon, Sheller, Micah, Wang, Shih-Han, Reina, G Anthony, Foley, Patrick, Gruzdev, Alexey, Karkada, Deepthi, Davatzikos, Christos, Sako, Chiharu, Ghodasara, Satyam, Bilello, Michel, Mohan, Suyash, Vollmuth, Philipp, Brugnara, Gianluca, Preetha, Chandrakanth J, Sahm, Felix, Maier-Hein, Klaus, Zenk, Maximilian, Bendszus, Martin, Wick, Wolfgang, Calabrese, Evan, Rudie, Jeffrey, Villanueva-Meyer, Javier, Cha, Soonmee, Ingalhalikar, Madhura, Jadhav, Manali, Pandey, Umang, Saini, Jitender, Garrett, John, Larson, Matthew, Jeraj, Robert, Currie, Stuart, Frood, Russell, Fatania, Kavi, Huang, Raymond Y, Chang, Ken, Balana, Carmen, Capellades, Jaume, Puig, Josep, Trenkler, Johannes, Pichler, Josef, Necker, Georg, Haunschmidt, Andreas, Meckel, Stephan, Shukla, Gaurav, Liem, Spencer, Alexander, Gregory S, Lombardo, Joseph, Palmer, Joshua D, Flanders, Adam E, Dicker, Adam P, Sair, Haris I, Jones, Craig K, Venkataraman, Archana, Jiang, Meirui, So, Tiffany Y, Chen, Cheng, Heng, Pheng Ann, Dou, Qi, Kozubek, Michal, Lux, Filip, Michálek, Jan, Matula, Petr, Keřkovský, Miloš, Kopřivová, Tereza, Dostál, Marek, Vybíhal, Václav, Vogelbaum, Michael A, Mitchell, J Ross, Farinhas, Joaquim, Maldjian, Joseph A, Yogananda, Chandan Ganesh Bangalore, Pinho, Marco C, Reddy, Divya, Holcomb, James, Wagner, Benjamin C, Ellingson, Benjamin M, Cloughesy, Timothy F, Raymond, Catalina, Oughourlian, Talia, Hagiwara, Akifumi, Wang, Chencai, To, Minh-Son, Bhardwaj, Sargam, Chong, Chee, Agzarian, Marc, Falcão, Alexandre Xavier, Martins, Samuel B, Teixeira, Bernardo C A, Sprenger, Flávia, Menotti, David, Lucio, Diego R, LaMontagne, Pamela, Marcus, Daniel, Wiestler, Benedikt, Kofler, Florian, Ezhov, Ivan, Metz, Marie, Jain, Rajan, Lee, Matthew, Lui, Yvonne W, McKinley, Richard, Slotboom, Johannes, Radojewski, Piotr, Meier, Raphael, Wiest, Roland, Murcia, Derrick, Fu, Eric, Haas, Rourke, Thompson, John, Ormond, David Ryan, Badve, Chaitra, Sloan, Andrew E, Vadmal, Vachan, Waite, Kristin, Colen, Rivka R, Pei, Linmin, Ak, Murat, Srinivasan, Ashok, Bapuraj, J Rajiv, Rao, Arvind, Wang, Nicholas, Yoshiaki, Ota, Moritani, Toshio, Turk, Sevcan, Lee, Joonsang, Prabhudesai, Snehal, Morón, Fanny, Mandel, Jacob, Kamnitsas, Konstantinos, Glocker, Ben, Dixon, Luke V M, Williams, Matthew, Zampakis, Peter, Panagiotopoulos, Vasileios, Tsiganos, Panagiotis, Alexiou, Sotiris, Haliassos, Ilias, Zacharaki, Evangelia I, Moustakas, Konstantinos, Kalogeropoulou, Christina, Kardamakis, Dimitrios M, Choi, Yoon Seong, Lee, Seung-Koo, Chang, Jong Hee, Ahn, Sung Soo, Luo, Bing, Poisson, Laila, Wen, Ning, Tiwari, Pallavi, Verma, Ruchika, Bareja, Rohan, Yadav, Ipsa, Chen, Jonathan, Kumar, Neeraj, Smits, Marion, van der Voort, Sebastian R, Alafandi, Ahmed, Incekara, Fatih, Wijnenga, Maarten MJ, Kapsas, Georgios, Gahrmann, Renske, Schouten, Joost W, Dubbink, Hendrikus J, Vincent, Arnaud JPE, Bent, Martin J van den, French, Pim J, Klein, Stefan, Yuan, Yading, Sharma, Sonam, Tseng, Tzu-Chi, Adabi, Saba, Niclou, Simone P, Keunen, Olivier, Hau, Ann-Christin, Vallières, Martin, Fortin, David, Lepage, Martin, Landman, Bennett, Ramadass, Karthik, Xu, Kaiwen, Chotai, Silky, Chambless, Lola B, Mistry, Akshitkumar, Thompson, Reid C, Gusev, Yuriy, Bhuvaneshwar, Krithika, Sayah, Anousheh, Bencheqroun, Camelia, Belouali, Anas, Madhavan, Subha, Booth, Thomas C, Chelliah, Alysha, Modat, Marc, Shuaib, Haris, Dragos, Carmen, Abayazeed, Aly, Kolodziej, Kenneth, Hill, Michael, Abbassy, Ahmed, Gamal, Shady, Mekhaimar, Mahmoud, Qayati, Mohamed, Reyes, Mauricio, Park, Ji Eun, Yun, Jihye, Kim, Ho Sung, Mahajan, Abhishek, Muzi, Mark, Benson, Sean, Beets-Tan, Regina G H, Teuwen, Jonas, Herrera-Trujillo, Alejandro, Trujillo, Maria, Escobar, William, Abello, Ana, Bernal, Jose, Gómez, Jhon, Choi, Joseph, Baek, Stephen, Kim, Yusung, Ismael, Heba, Allen, Bryan, Buatti, John M, Kotrotsou, Aikaterini, Li, Hongwei, Weiss, Tobias, Weller, Michael, Bink, Andrea, Pouymayou, Bertrand, Shaykh, Hassan F, Saltz, Joel, Prasanna, Prateek, Shrestha, Sampurna, Mani, Kartik M, Payne, David, Kurc, Tahsin, Pelaez, Enrique, Franco-Maldonado, Heydy, Loayza, Francis, Quevedo, Sebastian, Guevara, Pamela, Torche, Esteban, Mendoza, Cristobal, Vera, Franco, Ríos, Elvis, López, Eduardo, Velastin, Sergio A, Ogbole, Godwin, Oyekunle, Dotun, Odafe-Oyibotha, Olubunmi, Osobu, Babatunde, Shu'aibu, Mustapha, Dorcas, Adeleye, Soneye, Mayowa, Dako, Farouk, Simpson, Amber L, Hamghalam, Mohammad, Peoples, Jacob J, Hu, Ricky, Tran, Anh, Cutler, Danielle, Moraes, Fabio Y, Boss, Michael A, Gimpel, James, Veettil, Deepak Kattil, Schmidt, Kendall, Bialecki, Brian, Marella, Sailaja, Price, Cynthia, Cimino, Lisa, Apgar, Charles, Shah, Prashant, Menze, Bjoern, Barnholtz-Sloan, Jill S, Martin, Jason, Bakas, Spyridon
Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data. This is currently addressed by centrally sharing ample, and importantly diverse, data from multiple sites. However, such centralization is challenging to scale (or even not feasible) due to various limitations. Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here we present findings from the largest FL study to-date, involving data from 71 healthcare institutions across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, utilizing the largest dataset of such patients ever used in the literature (25, 256 MRI scans from 6, 314 patients). We demonstrate a 33% improvement over a publicly trained model to delineate the surgically targetable tumor, and 23% improvement over the tumor's entire extent. We anticipate our study to: 1) enable more studies in healthcare informed by large and diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further quantitative analyses for glioblastoma via performance optimization of our consensus model for eventual public release, and 3) demonstrate the effectiveness of FL at such scale and task complexity as a paradigm shift for multi-site collaborations, alleviating the need for data sharing.