no code implementations • 6 Jan 2025 • Xiwen Chen, Peijie Qiu, Wenhui Zhu, Huayu Li, Hao Wang, Aristeidis Sotiras, Yalin Wang, Abolfazl Razi
Since its introduction, the transformer has shifted the development trajectory away from traditional models (e. g., RNN, MLP) in time series forecasting, which is attributed to its ability to capture global dependencies within temporal tokens.
no code implementations • 29 Dec 2024 • Peijie Qiu, Wenhui Zhu, Sayantan Kumar, Xiwen Chen, Xiaotong Sun, Jin Yang, Abolfazl Razi, Yalin Wang, Aristeidis Sotiras
Previous attempts at multimodal VAEs approach this mainly through the lens of experts, aggregating unimodal inference distributions with a product of experts (PoE), a mixture of experts (MoE), or a combination of both.
1 code implementation • 10 Dec 2024 • Peijie Qiu, Satrajit Chakrabarty, Phuc Nguyen, Soumyendu Sekhar Ghosh, Aristeidis Sotiras
To validate the effectiveness of the proposed method, we conducted experiments on assessing its performance on evaluating the quality of two distinct segmentation tasks.
no code implementations • 3 Oct 2024 • Jin Yang, Daniel S. Marcus, Aristeidis Sotiras
In contrast, the DMSC module extracts features at different scales by employing convolutions with different kernel sizes and utilizing dynamic mechanisms to extract global contextual information.
1 code implementation • 4 Jul 2024 • Wenhui Zhu, Xiwen Chen, Peijie Qiu, Aristeidis Sotiras, Abolfazl Razi, Yalin Wang
Second, we propose two mechanisms to enforce the diversity among the global vectors to be more descriptive of the entire bag: (i) positive instance alignment and (ii) a novel, efficient, and theoretically guaranteed diversification learning paradigm.
1 code implementation • 21 Jun 2024 • Wenhui Zhu, Xiwen Chen, Peijie Qiu, Mohammad Farazi, Aristeidis Sotiras, Abolfazl Razi, Yalin Wang
Although numerous follow-up studies have also been dedicated to improving the performance of standard UNet, few have conducted in-depth analyses of the underlying interest pattern of UNet in medical image segmentation.
Ranked #14 on
Medical Image Segmentation
on Synapse multi-organ CT
2 code implementations • 6 May 2024 • Xiwen Chen, Peijie Qiu, Wenhui Zhu, Huayu Li, Hao Wang, Aristeidis Sotiras, Yalin Wang, Abolfazl Razi
Deep neural networks, including transformers and convolutional neural networks, have significantly improved multivariate time series classification (MTSC).
no code implementations • 4 Apr 2024 • Sayantan Kumar, Tom Earnest, Braden Yang, Deydeep Kothapalli, Andrew J. Aschenbrenner, Jason Hassenstab, Chengie Xiong, Beau Ances, John Morris, Tammie L. S. Benzinger, Brian A. Gordon, Philip Payne, Aristeidis Sotiras
An individual-level disease severity index (DSI) was calculated using both the spatial extent and magnitude of abnormal deviations across ATN.
1 code implementation • 29 Mar 2024 • Peijie Qiu, Jin Yang, Sayantan Kumar, Soumyendu Sekhar Ghosh, Aristeidis Sotiras
However, we argue that the current design of the vision transformer-based UNet (ViT-UNet) segmentation models may not effectively handle the heterogeneous appearance (e. g., varying shapes and sizes) of objects of interest in medical image segmentation tasks.
Ranked #2 on
Medical Image Segmentation
on ACDC
1 code implementation • 15 Mar 2024 • Jin Yang, Peijie Qiu, Yichi Zhang, Daniel S. Marcus, Aristeidis Sotiras
D-Net is able to effectively utilize a multi-scale large receptive field and adaptively harness global contextual information.
1 code implementation • 12 Mar 2024 • Jin Yang, Daniel S. Marcus, Aristeidis Sotiras
We evaluated Dynamic U-Net in two abdominal multi-organ segmentation benchmarks.
no code implementations • 2 Dec 2023 • Sayantan Kumar, Philip Payne, Aristeidis Sotiras
Normative models in neuroimaging learn the brain patterns of healthy population distribution and estimate how disease subjects like Alzheimer's Disease (AD) deviate from the norm.
1 code implementation • 31 Oct 2023 • Peijie Qiu, Pan Xiao, Wenhui Zhu, Yalin Wang, Aristeidis Sotiras
Typical MIL methods include a feature embedding part, which embeds the instances into features via a pre-trained feature extractor, and an MIL aggregator that combines instance embeddings into predictions.
no code implementations • 1 Jun 2023 • Ahmed W. Moawad, Anastasia Janas, Ujjwal Baid, Divya Ramakrishnan, Rachit Saluja, Nader Ashraf, Nazanin Maleki, Leon Jekel, Nikolay Yordanov, Pascal Fehringer, Athanasios Gkampenis, Raisa Amiruddin, Amirreza Manteghinejad, Maruf Adewole, Jake Albrecht, Udunna Anazodo, Sanjay Aneja, Syed Muhammad Anwar, Timothy Bergquist, Veronica Chiang, Verena Chung, Gian Marco Conte, Farouk Dako, James Eddy, Ivan Ezhov, Nastaran Khalili, Keyvan Farahani, Juan Eugenio Iglesias, Zhifan Jiang, Elaine Johanson, Anahita Fathi Kazerooni, Florian Kofler, Kiril Krantchev, Dominic LaBella, Koen van Leemput, Hongwei Bran Li, Marius George Linguraru, Xinyang Liu, Zeke Meier, Bjoern H Menze, Harrison Moy, Klara Osenberg, Marie Piraud, Zachary Reitman, Russell Takeshi Shinohara, Chunhao Wang, Benedikt Wiestler, Walter Wiggins, Umber Shafique, Klara Willms, Arman Avesta, Khaled Bousabarah, Satrajit Chakrabarty, Nicolo Gennaro, Wolfgang Holler, Manpreet Kaur, Pamela Lamontagne, MingDe Lin, Jan Lost, Daniel S. Marcus, Ryan Maresca, Sarah Merkaj, Gabriel Cassinelli Pedersen, Marc von Reppert, Aristeidis Sotiras, Oleg Teytelboym, Niklas Tillmans, Malte Westerhoff, Ayda Youssef, Devon Godfrey, Scott Floyd, Andreas Rauschecker, Javier Villanueva-Meyer, Irada Pfluger, Jaeyoung Cho, Martin Bendszus, Gianluca Brugnara, Justin Cramer, Gloria J. Guzman Perez-Carillo, Derek R. Johnson, Anthony Kam, Benjamin Yin Ming Kwan, Lillian Lai, Neil U. Lall, Fatima Memon, Mark Krycia, Satya Narayana Patro, Bojan Petrovic, Tiffany Y. So, Gerard Thompson, Lei Wu, E. Brooke Schrickel, Anu Bansal, Frederik Barkhof, Cristina Besada, Sammy Chu, Jason Druzgal, Alexandru Dusoi, Luciano Farage, Fabricio Feltrin, Amy Fong, Steve H. Fung, R. Ian Gray, Ichiro Ikuta, Michael Iv, Alida A. Postma, Amit Mahajan, David Joyner, Chase Krumpelman, Laurent Letourneau-Guillon, Christie M. Lincoln, Mate E. Maros, Elka Miller, Fanny Moron, Esther A. Nimchinsky, Ozkan Ozsarlak, Uresh Patel, Saurabh Rohatgi, Atin Saha, Anousheh Sayah, Eric D. Schwartz, Robert Shih, Mark S. Shiroishi, Juan E. Small, Manoj Tanwar, Jewels Valerie, Brent D. Weinberg, Matthew L. White, Robert Young, Vahe M. Zohrabian, Aynur Azizova, Melanie Maria Theresa Bruseler, Mohanad Ghonim, Mohamed Ghonim, Abdullah Okar, Luca Pasquini, Yasaman Sharifi, Gagandeep Singh, Nico Sollmann, Theodora Soumala, Mahsa Taherzadeh, Philipp Vollmuth, Martha Foltyn-Dumitru, Ajay Malhotra, Aly H. Abayazeed, Francesco Dellepiane, Philipp Lohmann, Victor M. Perez-Garcia, Hesham Elhalawani, Maria Correia de Verdier, Sanaria Al-Rubaiey, Rui Duarte Armindo, Kholod Ashraf, Moamen M. Asla, Mohamed Badawy, Jeroen Bisschop, Nima Broomand Lomer, Jan Bukatz, Jim Chen, Petra Cimflova, Felix Corr, Alexis Crawley, Lisa Deptula, Tasneem Elakhdar, Islam H. Shawali, Shahriar Faghani, Alexandra Frick, Vaibhav Gulati, Muhammad Ammar Haider, Fatima Hierro, Rasmus Holmboe Dahl, Sarah Maria Jacobs, Kuang-chun Jim Hsieh, Sedat G. Kandemirli, Katharina Kersting, Laura Kida, Sofia Kollia, Ioannis Koukoulithras, Xiao Li, Ahmed Abouelatta, Aya Mansour, Ruxandra-Catrinel Maria-Zamfirescu, Marcela Marsiglia, Yohana Sarahi Mateo-Camacho, Mark McArthur, Olivia McDonnell, Maire McHugh, Mana Moassefi, Samah Mostafa Morsi, Alexander Munteanu, Khanak K. Nandolia, Syed Raza Naqvi, Yalda Nikanpour, Mostafa Alnoury, Abdullah Mohamed Aly Nouh, Francesca Pappafava, Markand D. Patel, Samantha Petrucci, Eric Rawie, Scott Raymond, Borna Roohani, Sadeq Sabouhi, Laura M. Sanchez-Garcia, Zoe Shaked, Pokhraj P. Suthar, Talissa Altes, Edvin Isufi, Yaseen Dhemesh, Jaime Gass, Jonathan Thacker, Abdul Rahman Tarabishy, Benjamin Turner, Sebastiano Vacca, George K. Vilanilam, Daniel Warren, David Weiss, Fikadu Worede, Sara Yousry, Wondwossen Lerebo, Alejandro Aristizabal, Alexandros Karargyris, Hasan Kassem, Sarthak Pati, Micah Sheller, Katherine E. Link, Evan Calabrese, Nourel Hoda Tahon, Ayman Nada, Yuri S. Velichko, Spyridon Bakas, Jeffrey D. Rudie, Mariam Aboian
Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing.
1 code implementation • 29 Mar 2023 • Pan Xiao, Peijie Qiu, Sungmin Ha, Abdalla Bani, Shuang Zhou, Aristeidis Sotiras
Several variants of variational autoencoders (VAEs) have been proposed to learn compact data representations by encoding high-dimensional data in a lower dimensional space.
no code implementations • 7 Oct 2022 • Satrajit Chakrabarty, Pamela Lamontagne, Joshua Shimony, Daniel S. Marcus, Aristeidis Sotiras
A 2. 5D hybrid convolutional neural network was proposed to simultaneously localize the tumor and classify its molecular status by leveraging imaging features from MR scans and prior knowledge features from clinical records and tumor location.
2 code implementations • 6 Oct 2022 • Satrajit Chakrabarty, Syed Amaan Abidi, Mina Mousa, Mahati Mokkarala, Isabelle Hren, Divya Yadav, Matthew Kelsey, Pamela Lamontagne, John Wood, Michael Adams, Yuzhuo Su, Sherry Thorpe, Caroline Chung, Aristeidis Sotiras, Daniel S. Marcus
Mean Dice scores were 0. 882 ($\pm$0. 244) and 0. 977 ($\pm$0. 04) for whole tumor segmentation for WUSM and MDA, respectively.
no code implementations • 13 Dec 2021 • Bhakti Baheti, Satrajit Chakrabarty, Hamed Akbari, Michel Bilello, Benedikt Wiestler, Julian Schwarting, Evan Calabrese, Jeffrey Rudie, Syed Abidi, Mina Mousa, Javier Villanueva-Meyer, Brandon K. K. Fields, Florian Kofler, Russell Takeshi Shinohara, Juan Eugenio Iglesias, Tony C. W. Mok, Albert C. S. Chung, Marek Wodzinski, Artur Jurgas, Niccolo Marini, Manfredo Atzori, Henning Muller, Christoph Grobroehmer, Hanna Siebert, Lasse Hansen, Mattias P. Heinrich, Luca Canalini, Jan Klein, Annika Gerken, Stefan Heldmann, Alessa Hering, Horst K. Hahn, Mingyuan Meng, Lei Bi, Dagan Feng, Jinman Kim, Ramy A. Zeineldin, Mohamed E. Karar, Franziska Mathis-Ullrich, Oliver Burgert, Javid Abderezaei, Aymeric Pionteck, Agamdeep Chopra, Mehmet Kurt, Kewei Yan, Yonghong Yan, Zhe Tang, Jianqiang Ma, Sahar Almahfouz Nasser, Nikhil Cherian Kurian, Mohit Meena, Saqib Shamsi, Amit Sethi, Nicholas J. Tustison, Brian B. Avants, Philip Cook, James C. Gee, Lin Tian, Hastings Greer, Marc Niethammer, Andrew Hoopes, Malte Hoffmann, Adrian V. Dalca, Stergios Christodoulidis, Theo Estiene, Maria Vakalopoulou, Nikos Paragios, Daniel S. Marcus, Christos Davatzikos, Aristeidis Sotiras, Bjoern Menze, Spyridon Bakas, Diana Waldmannstetter
Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance.
1 code implementation • 20 Oct 2021 • Junhao Wen, Cynthia H. Y. Fu, Duygu Tosun, Yogasudha Veturi, Zhijian Yang, Ahmed Abdulkadir, Elizabeth Mamourian, Dhivya Srinivasan, Jingxuan Bao, Guray Erus, Haochang Shou, Mohamad Habes, Jimit Doshi, Erdem Varol, Scott R Mackin, Aristeidis Sotiras, Yong Fan, Andrew J. Saykin, Yvette I. Sheline, Li Shen, Marylyn D. Ritchie, David A. Wolk, Marilyn Albert, Susan M. Resnick, Christos Davatzikos
We sought to delineate, cross-sectionally and longitudinally, disease-related heterogeneity in LLD linked to neuroanatomy, cognitive functioning, clinical symptomatology, and genetic profiles.
no code implementations • 10 Oct 2021 • Sayantan Kumar, Philip Payne, Aristeidis Sotiras
However, existing deep learning based normative models on multimodal MRI data use unimodal autoencoders with a single encoder and decoder that may fail to capture the relationship between brain measurements extracted from different MRI modalities.
no code implementations • 8 Sep 2021 • Gyujoon Hwang, Ahmed Abdulkadir, Guray Erus, Mohamad Habes, Raymond Pomponio, Haochang Shou, Jimit Doshi, Elizabeth Mamourian, Tanweer Rashid, Murat Bilgel, Yong Fan, Aristeidis Sotiras, Dhivya Srinivasan, John C. Morris, Daniel Marcus, Marilyn S. Albert, Nick R. Bryan, Susan M. Resnick, Ilya M. Nasrallah, Christos Davatzikos, David A. Wolk
First, a subset of AD patients and CN adults were selected based purely on clinical diagnoses to train SPARE-BA1 (regression of age using CN individuals) and SPARE-AD1 (classification of CN versus AD).
1 code implementation • 1 Jul 2020 • Junhao Wen, Erdem Varol, Ganesh Chand, Aristeidis Sotiras, Christos Davatzikos
There is a growing amount of clinical, anatomical and functional evidence for the heterogeneous presentation of neuropsychiatric and neurodegenerative diseases such as schizophrenia and Alzheimers Disease (AD).
4 code implementations • 9 Feb 2020 • Razvan V. Marinescu, Neil P. Oxtoby, Alexandra L. Young, Esther E. Bron, Arthur W. Toga, Michael W. Weiner, Frederik Barkhof, Nick C. Fox, Arman Eshaghi, Tina Toni, Marcin Salaterski, Veronika Lunina, Manon Ansart, Stanley Durrleman, Pascal Lu, Samuel Iddi, Dan Li, Wesley K. Thompson, Michael C. Donohue, Aviv Nahon, Yarden Levy, Dan Halbersberg, Mariya Cohen, Huiling Liao, Tengfei Li, Kaixian Yu, Hongtu Zhu, Jose G. Tamez-Pena, Aya Ismail, Timothy Wood, Hector Corrada Bravo, Minh Nguyen, Nanbo Sun, Jiashi Feng, B. T. Thomas Yeo, Gang Chen, Ke Qi, Shiyang Chen, Deqiang Qiu, Ionut Buciuman, Alex Kelner, Raluca Pop, Denisa Rimocea, Mostafa M. Ghazi, Mads Nielsen, Sebastien Ourselin, Lauge Sorensen, Vikram Venkatraghavan, Keli Liu, Christina Rabe, Paul Manser, Steven M. Hill, James Howlett, Zhiyue Huang, Steven Kiddle, Sach Mukherjee, Anais Rouanet, Bernd Taschler, Brian D. M. Tom, Simon R. White, Noel Faux, Suman Sedai, Javier de Velasco Oriol, Edgar E. V. Clemente, Karol Estrada, Leon Aksman, Andre Altmann, Cynthia M. Stonnington, Yalin Wang, Jianfeng Wu, Vivek Devadas, Clementine Fourrier, Lars Lau Raket, Aristeidis Sotiras, Guray Erus, Jimit Doshi, Christos Davatzikos, Jacob Vogel, Andrew Doyle, Angela Tam, Alex Diaz-Papkovich, Emmanuel Jammeh, Igor Koval, Paul Moore, Terry J. Lyons, John Gallacher, Jussi Tohka, Robert Ciszek, Bruno Jedynak, Kruti Pandya, Murat Bilgel, William Engels, Joseph Cole, Polina Golland, Stefan Klein, Daniel C. Alexander
TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease.