no code implementations • 29 Feb 2024 • Shruti P. Gadewar, Alyssa H. Zhu, Iyad Ba Gari, Sunanda Somu, Sophia I. Thomopoulos, Paul M. Thompson, Talia M. Nir, Neda Jahanshad
For one case-control study, we used a generative adversarial model for style-based harmonization to generate site-specific controls.
no code implementations • 18 Nov 2023 • Vladimir Belov, Tracy Erwin-Grabner, Ling-Li Zeng, Christopher R. K. Ching, Andre Aleman, Alyssa R. Amod, Zeynep Basgoze, Francesco Benedetti, Bianca Besteher, Katharina Brosch, Robin Bülow, Romain Colle, Colm G. Connolly, Emmanuelle Corruble, Baptiste Couvy-Duchesne, Kathryn Cullen, Udo Dannlowski, Christopher G. Davey, Annemiek Dols, Jan Ernsting, Jennifer W. Evans, Lukas Fisch, Paola Fuentes-Claramonte, Ali Saffet Gonul, Ian H. Gotlib, Hans J. Grabe, Nynke A. Groenewold, Dominik Grotegerd, Tim Hahn, J. Paul Hamilton, Laura K. M. Han, Ben J Harrison, Tiffany C. Ho, Neda Jahanshad, Alec J. Jamieson, Andriana Karuk, Tilo Kircher, Bonnie Klimes-Dougan, Sheri-Michelle Koopowitz, Thomas Lancaster, Ramona Leenings, Meng Li, David E. J. Linden, Frank P. MacMaster, David M. A. Mehler, Susanne Meinert, Elisa Melloni, Bryon A. Mueller, Benson Mwangi, Igor Nenadić, Amar Ojha, Yasumasa Okamoto, Mardien L. Oudega, Brenda W. J. H. Penninx, Sara Poletti, Edith Pomarol-Clotet, Maria J. Portella, Elena Pozzi, Joaquim Radua, Elena Rodríguez-Cano, Matthew D. Sacchet, Raymond Salvador, Anouk Schrantee, Kang Sim, Jair C. Soares, Aleix Solanes, Dan J. Stein, Frederike Stein, Aleks Stolicyn, Sophia I. Thomopoulos, Yara J. Toenders, Aslihan Uyar-Demir, Eduard Vieta, Yolanda Vives-Gilabert, Henry Völzke, Martin Walter, Heather C. Whalley, Sarah Whittle, Nils Winter, Katharina Wittfeld, Margaret J. Wright, Mon-Ju Wu, Tony T. Yang, Carlos Zarate, Dick J. Veltman, Lianne Schmaal, Paul M. Thompson, Roberto Goya-Maldonado
Based on the hypothesis that integration of vertex-wise cortical features can improve classification performance, we evaluated the classification of a DenseNet and a Support Vector Machine (SVM), with the expectation that the former would outperform the latter.
no code implementations • 9 Sep 2023 • Nikhil J. Dhinagar, Amit Singh, Saket Ozarkar, Ketaki Buwa, Sophia I. Thomopoulos, Conor Owens-Walton, Emily Laltoo, Yao-Liang Chen, Philip Cook, Corey McMillan, Chih-Chien Tsai, J-J Wang, Yih-Ru Wu, Paul M. Thompson
The resulting pre-trained models can be adapted to a range of downstream neuroimaging tasks, even when training data for the target task is limited.
no code implementations • 25 May 2023 • Reza Shirkavand, Liang Zhan, Heng Huang, Li Shen, Paul M. Thompson
Especially in studies of brain diseases, research cohorts may include both neuroimaging data and genetic data, but for practical clinical diagnosis, we often need to make disease predictions only based on neuroimages.
no code implementations • 1 May 2023 • Shruti P. Gadewar, Elnaz Nourollahimoghadam, Ravi R. Bhatt, Abhinaav Ramesh, Shayan Javid, Iyad Ba Gari, Alyssa H. Zhu, Sophia Thomopoulos, Paul M. Thompson, Neda Jahanshad
A quality control algorithm is also built-in, trained on the midCC shape features.
no code implementations • 31 Mar 2023 • Jianfeng Wu, Yi Su, Yanxi Chen, Wenhui Zhu, Eric M. Reiman, Richard J. Caselli, Kewei Chen, Paul M. Thompson, Junwen Wang, Yalin Wang
Objective: To build a surface-based model to 1) detect differences between APOE subgroups in patterns of tau deposition and hippocampal atrophy, and 2) use the extracted surface-based features to predict cognitive decline.
no code implementations • 14 Mar 2023 • Nikhil J. Dhinagar, Vignesh Santhalingam, Katherine E. Lawrence, Emily Laltoo, Paul M. Thompson
Inspired by the effectiveness of meta-learning for optimizing a model across multiple tasks, here we propose a framework to adapt it to learn across multiple sites.
no code implementations • 14 Mar 2023 • Nikhil J. Dhinagar, Sophia I. Thomopoulos, Emily Laltoo, Paul M. Thompson
In our experiments, two vision transformer architecture variants achieved an AUC of 0. 987 for sex and 0. 892 for AD classification, respectively.
1 code implementation • 2 Mar 2023 • Umang Gupta, Tamoghna Chattopadhyay, Nikhil Dhinagar, Paul M. Thompson, Greg Ver Steeg, the Alzheimer's Disease Neuroimaging Initiative
Transfer learning has remarkably improved computer vision.
no code implementations • 27 Feb 2023 • Nikhil J. Dhinagar, Conor Owens-Walton, Emily Laltoo, Christina P. Boyle, Yao-Liang Chen, Philip Cook, Corey McMillan, Chih-Chien Tsai, J-J Wang, Yih-Ru Wu, Ysbrand van der Werf, Paul M. Thompson
There is great interest in developing radiological classifiers for diagnosis, staging, and predictive modeling in progressive diseases such as Parkinson's disease (PD), a neurodegenerative disease that is difficult to detect in its early stages.
no code implementations • 28 Oct 2022 • Jianfeng Wu, Yi Su, Wenhui Zhu, Negar Jalili Mallak, Natasha Lepore, Eric M. Reiman, Richard J. Caselli, Paul M. Thompson, Kewei Chen, Yalin Wang
Experimental results suggest that amyloid/tau measurements predicted with our PASCP-MP representations are closer to the real values than the measures derived from other approaches, such as hippocampal surface area, volume, and shape morphometry features based on spherical harmonics (SPHARM).
no code implementations • 16 Jun 2022 • Vladimir Belov, Tracy Erwin-Grabner, Ali Saffet Gonul, Alyssa R. Amod, Amar Ojha, Andre Aleman, Annemiek Dols, Anouk Scharntee, Aslihan Uyar-Demir, Ben J Harrison, Benson M. Irungu, Bianca Besteher, Bonnie Klimes-Dougan, Brenda W. J. H. Penninx, Bryon A. Mueller, Carlos Zarate, Christopher G. Davey, Christopher R. K. Ching, Colm G. Connolly, Cynthia H. Y. Fu, Dan J. Stein, Danai Dima, David E. J. Linden, David M. A. Mehler, Edith Pomarol-Clotet, Elena Pozzi, Elisa Melloni, Francesco Benedetti, Frank P. MacMaster, Hans J. Grabe, Henry Völzke, Ian H. Gotlib, Jair C. Soares, Jennifer W. Evans, Kang Sim, Katharina Wittfeld, Kathryn Cullen, Liesbeth Reneman, Mardien L. Oudega, Margaret J. Wright, Maria J. Portella, Matthew D. Sacchet, Meng Li, Moji Aghajani, Mon-Ju Wu, Natalia Jaworska, Neda Jahanshad, Nic J. A. van der Wee, Nynke Groenewold, Paul J. Hamilton, Philipp Saemann, Robin Bülow, Sara Poletti, Sarah Whittle, Sophia I. Thomopoulos, Steven J. A. van, der Werff, Sheri-Michelle Koopowitz, Thomas Lancaster, Tiffany C. Ho, Tony T. Yang, Zeynep Basgoze, Dick J. Veltman, Lianne Schmaal, Paul M. Thompson, Roberto Goya-Maldonado
Machine learning (ML) techniques have gained popularity in the neuroimaging field due to their potential for classifying neuropsychiatric disorders.
no code implementations • 11 May 2022 • Dimitris Stripelis, Umang Gupta, Hamza Saleem, Nikhil Dhinagar, Tanmay Ghai, Rafael Chrysovalantis Anastasiou, Armaghan Asghar, Greg Ver Steeg, Srivatsan Ravi, Muhammad Naveed, Paul M. Thompson, Jose Luis Ambite
Each site trains the neural network over its private data for some time, then shares the neural network parameters (i. e., weights, gradients) with a Federation Controller, which in turn aggregates the local models, sends the resulting community model back to each site, and the process repeats.
no code implementations • 20 Oct 2021 • Jianfeng Wu, Wenhui Zhu, Yi Su, Jie Gui, Natasha Lepore, Eric M. Reiman, Richard J. Caselli, Paul M. Thompson, Kewei Chen, Yalin Wang
We evaluate our framework on 925 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI).
no code implementations • 7 Aug 2021 • Dimitris Stripelis, Hamza Saleem, Tanmay Ghai, Nikhil Dhinagar, Umang Gupta, Chrysovalantis Anastasiou, Greg Ver Steeg, Srivatsan Ravi, Muhammad Naveed, Paul M. Thompson, Jose Luis Ambite
Federated learning (FL) enables distributed computation of machine learning models over various disparate, remote data sources, without requiring to transfer any individual data to a centralized location.
no code implementations • 6 May 2021 • Umang Gupta, Dimitris Stripelis, Pradeep K. Lam, Paul M. Thompson, José Luis Ambite, Greg Ver Steeg
In particular, we show that it is possible to infer if a sample was used to train the model given only access to the model prediction (black-box) or access to the model itself (white-box) and some leaked samples from the training data distribution.
2 code implementations • 8 Feb 2021 • Umang Gupta, Pradeep K. Lam, Greg Ver Steeg, Paul M. Thompson
Deep Learning for neuroimaging data is a promising but challenging direction.
no code implementations • 18 Nov 2020 • Pradeep Lam, Alyssa H. Zhu, Iyad Ba Gari, Neda Jahanshad, Paul M. Thompson
Building on a 3D convolutional neural network, we added two attention modules at different layers of abstraction, so that features learned are spatially related to the global features for the task.
no code implementations • MIDL 2019 • Daniel Moyer, Greg Ver Steeg, Paul M. Thompson
Pooled imaging data from multiple sources is subject to bias from each source.
no code implementations • 10 Apr 2019 • Daniel Moyer, Greg Ver Steeg, Chantal M. W. Tax, Paul M. Thompson
Purpose: In the present work we describe the correction of diffusion-weighted MRI for site and scanner biases using a novel method based on invariant representation.
no code implementations • 19 Oct 2018 • Santiago Silva, Boris Gutman, Eduardo Romero, Paul M. Thompson, Andre Altmann, Marco Lorenzi
At this moment, databanks worldwide contain brain images of previously unimaginable numbers.
no code implementations • 12 Jun 2018 • Daniel Moyer, Paul M. Thompson, Greg Ver Steeg
In the present work, we use information theory to understand the empirical convergence rate of tractography, a widely-used approach to reconstruct anatomical fiber pathways in the living brain.
no code implementations • 14 Oct 2017 • Nikita Mokrov, Maxim Panov, Boris A. Gutman, Joshua I. Faskowitz, Neda Jahanshad, Paul M. Thompson
This paper considers the problem of brain disease classification based on connectome data.
no code implementations • 26 May 2017 • Dajiang Zhu, Brandalyn C. Riedel, Neda Jahanshad, Nynke A. Groenewold, Dan J. Stein, Ian H. Gotlib, Matthew D. Sacchet, Danai Dima, James H. Cole, Cynthia H. Y. Fu, Henrik Walter, Ilya M. Veer, Thomas Frodl, Lianne Schmaal, Dick J. Veltman, Paul M. Thompson
Within each iteration, the classification result and the selected features are collected to update the weighting parameters for each feature.
no code implementations • 27 Apr 2017 • Qingyang Li, Dajiang Zhu, Jie Zhang, Derrek Paul Hibar, Neda Jahanshad, Yalin Wang, Jieping Ye, Paul M. Thompson, Jie Wang
Then we select the relevant group features by performing the group Lasso feature selection process in a sequence of parameters.
1 code implementation • 2 Mar 2017 • Daniel Moyer, Boris A. Gutman, Neda Jahanshad, Paul M. Thompson
One of the primary objectives of human brain mapping is the division of the cortical surface into functionally distinct regions, i. e. parcellation.
no code implementations • 18 Nov 2016 • Daniel Moyer, Boris A. Gutman, Joshua Faskowitz, Neda Jahanshad, Paul M. Thompson
In the present work we demonstrate the use of a parcellation free connectivity model based on Poisson point processes.
no code implementations • 19 Aug 2016 • Qingyang Li, Tao Yang, Liang Zhan, Derrek Paul Hibar, Neda Jahanshad, Yalin Wang, Jieping Ye, Paul M. Thompson, Jie Wang
To the best of our knowledge, this is the first successful run of the computationally intensive model selection procedure to learn a consistent model across different institutions without compromising their privacy while ranking the SNPs that may collectively affect AD.