Publications

Journal Publications

  • Cui H, Dai W, Zhu Y, Kan X, Gu AAC, Lukemire J, Zhan L, He L, Guo Y, Yang C. BrainGB: A Benchmark for Brain Network Analysis With Graph Neural Networks. IEEE Trans Med Imaging. 2023 Feb;42(2):493-506. doi: 10.1109/TMI.2022.3218745. Epub 2023 Feb 2. PMID: 36318557; PMCID: PMC10079627.
  • Tang H, Ma G, Guo L, Fu X, Huang H, Zhan L. Contrastive Brain Network Learning via Hierarchical Signed Graph Pooling Model. IEEE Trans Neural Netw Learn Syst. 2022 Nov 14;PP:10.1109/TNNLS.2022.3220220. doi: 10.1109/TNNLS.2022.3220220. Epub ahead of print. PMID: 36374890; PMCID: PMC10183052.
  • Bashyam VM, Erus G, Doshi J, Habes M, Nasrallah I, Truelove-Hill M, Srinivasan D, Mamourian L, Pomponio R, Fan Y, Launer LJ, Masters CL, Maruff P, Zhuo C, Völzke H, Johnson SC, Fripp J, Koutsouleris N, Satterthwaite TD, Wolf D, Gur RE, Gur RC, Morris J, Albert MS, Grabe HJ, Resnick S, Bryan RN, Wolk DA, Shou H, Davatzikos C. MRI signatures of brain age and disease over the lifespan based on a deep brain network and 14 468 individuals worldwide. Brain. 2020 Jul 1;143(7):2312-2324. doi: 10.1093/brain/awaa160. Erratum in: Brain. 2021 Feb 12;144(1):e12. PMID: 32591831; PMCID: PMC7364766.
  • Beer JC, Tustison NJ, Cook PA, Davatzikos C, Sheline YI, Shinohara RT, Linn KA; Alzheimer’s Disease Neuroimaging Initiative. Longitudinal ComBat: A method for harmonizing longitudinal multi-scanner imaging data. Neuroimage. 2020 Oct 15;220:117129. doi: 10.1016/j.neuroimage.2020.117129. Epub 2020 Jul 5. PMID: 32640273; PMCID: PMC7605103.
  • Srinivasan D, Erus G, Doshi J, Wolk DA, Shou H, Habes M, Davatzikos C; Alzheimer’s Disease Neuroimaging Initiative; BLSA; iSTAGING. A comparison of Freesurfer and multi-atlas MUSE for brain anatomy segmentation: Findings about size and age bias, and inter-scanner stability in multi-site aging studies. Neuroimage. 2020 Dec;223:117248. doi: 10.1016/j.neuroimage.2020.117248. Epub 2020 Aug 27. PMID: 32860881.
  • Peng B, Yao X, Risacher SL, Saykin AJ, Shen L, Ning X; ADNI. Cognitive biomarker prioritization in Alzheimer’s Disease using brain morphometric data. BMC Med Inform Decis Mak. 2020 Dec 2;20(1):319. doi: 10.1186/s12911-020-01339-z. PMID: 33267852; PMCID: PMC7709267.
  • Choi SE, Mukherjee S, Gibbons LE, Sanders RE, Jones RN, Tommet D, Mez J, Trittschuh EH, Saykin A, Lamar M, Rabin L, Foldi NS, Sikkes S, Jutten RJ, Grandoit E, Mac Donald C, Risacher S, Groot C, Ossenkoppele R; Alzheimer’s Disease Neuroimaging Initiative, Crane PK. Development and validation of language and visuospatial composite scores in ADNI. Alzheimers Dement (N Y). 2020 Dec 5;6(1):e12072. doi: 10.1002/trc2.12072. PMID: 33313380; PMCID: PMC7718716.
  • Jo T, Nho K, Risacher SL, Saykin AJ; Alzheimer’s Neuroimaging Initiative. Deep learning detection of informative features in tau PET for Alzheimer’s disease classification. BMC Bioinformatics. 2020 Dec 28;21(Suppl 21):496. doi: 10.1186/s12859-020-03848-0. PMID: 33371874; PMCID: PMC7768646.
  • Kim M, Bao J, Liu K, Park BY, Park H, Baik JY, Shen L. A structural enriched functional network: An application to predict brain cognitive performance. Med Image Anal. 2021 Jul;71:102026. doi: 10.1016/j.media.2021.102026. Epub 2021 Mar 4. PMID: 33848962; PMCID: PMC8184595.
  • Wu J, Dong Q, Gui J, Zhang J, Su Y, Chen K, Thompson PM, Caselli RJ, Reiman EM, Ye J, Wang Y. Predicting Brain Amyloid Using Multivariate Morphometry Statistics, Sparse Coding, and Correntropy: Validation in 1,101 Individuals From the ADNI and OASIS Databases. Front Neurosci. 2021 Aug 6;15:669595. doi: 10.3389/fnins.2021.669595. PMID: 34421510; PMCID: PMC8377280.
  • Bashyam VM, Doshi J, Erus G, Srinivasan D, Abdulkadir A, Singh A, Habes M, Fan Y, Masters CL, Maruff P, Zhuo C, Völzke H, Johnson SC, Fripp J, Koutsouleris N, Satterthwaite TD, Wolf DH, Gur RE, Gur RC, Morris JC, Albert MS, Grabe HJ, Resnick SM, Bryan NR, Wittfeld K, Bülow R, Wolk DA, Shou H, Nasrallah IM, Davatzikos C; iSTAGING and PHENOM consortia. Deep Generative Medical Image Harmonization for Improving Cross-Site Generalization in Deep Learning Predictors. J Magn Reson Imaging. 2021 Sep 25. doi: 10.1002/jmri.27908. Epub ahead of print. PMID: 34564904.
  • Panitch R, Hu J, Chung J, Zhu C, Meng G, Xia W, Bennett DA, Lunetta KL, Ikezu T, Au R, Stein TD, Farrer LA, Jun GR. Integrative brain transcriptome analysis links complement component 4 and HSPA2 to the APOE ε2 protective effect in Alzheimer disease. Mol Psychiatry. 2021 Oct;26(10):6054-6064. doi: 10.1038/s41380-021-01266-z. Epub 2021 Sep 3. PMID: 34480088; PMCID: PMC8758485. 
  • Tosun D, Veitch D, Aisen P, Jack CR, Jagust WJ, Petersen RC, Saykin AJ, Bollinger J, Ovod V, Mawuenyega KG, Bateman RJ, Shaw LM, Trojanowski JQ, Blennow K, Zetterberg H, Weiner MW. Detection of β-amyloid positivity in Alzheimer’s Disease Neuroimaging Initiative participants with demographics, cognition, MRI and plasma biomarkers. Brain Commun. 2021; 3(2):fcab008. PMID: 33842885. PMCID: PMC8023542
  • Rubinski A, Tosun D, Franzmeier N, Neitzel J, Frontzkowski L, Weiner M, Ewers M. Lower cerebral perfusion is associated with tau-PET in the entorhinal cortex across the Alzheimer’s continuum. Neurobiol Aging. 2021 06; 102:111-118. PMID: 33765424. PMCID: PMC8205941 
  • Ashford MT, Veitch DP, Neuhaus J, Nosheny RL, Tosun D, Weiner MW. The search for a convenient procedure to detect one of the earliest signs of Alzheimer’s disease: A systematic review of the prediction of brain amyloid status. Alzheimers Dement. 2021 05; 17(5):866-887. PMID: 33583100 
  • Branislav Kovacech , Stanislav Katina , Reinhold Schmidt , Philip Scheltens , Eva Kontsekova , Stefan Ropele , Lubica Fialova , Milica Kramberger , Natalia Paulenka-Ivanovova , Miroslav Smisek , Jozef Hanes , Eva Stevens , Andrej Kovac , Stanislav Sutovsky , Vojtech Parrak , Peter Koson , Michal Prcina , Jaroslav Galba , Martin Cente , Tomas Hromadka , Peter Filipcik , Juraj Piestansky , Maria Samcova , Carmen Prenn-Gologranc , Roman Sivak , Lutz Frölich , Michal Fresser , Martin Rakusa , John Harrison , Jakub Hort , Professor Markus Otto , Duygu Tosun , Matej Ondrus , Bengt Winblad , Michal Novak , Norbert Zilka. ADAMANT: a placebo-controlled randomised phase 2 study of AADvac1, an active immunotherapy against pathological tau protein in Alzheimer’s disease. Nat Aging 1, 521–534 (2021). 
  • Powell F, Tosun D, Raj A, Alzheimer’s Disease Neuroimaging Initiative. Network-constrained technique to characterize pathology progression rate in Alzheimer’s disease. Brain Commun. 2021; 3(3):fcab144. PMID: 34704025. PMCID: PMC8376686 
  • Veitch DP, Weiner MW, Aisen PS, Beckett LA, DeCarli C, Green RC, Harvey D, Jack CR, Jagust W, Landau SM, Morris JC, Okonkwo O, Perrin RJ, Petersen RC, Rivera-Mindt M, Saykin AJ, Shaw LM, Toga AW, Tosun D, Trojanowski JQ, Alzheimer’s Disease Neuroimaging Initiative. Using the Alzheimer’s Disease Neuroimaging Initiative to improve early detection, diagnosis, and treatment of Alzheimer’s disease. Alzheimers Dement. 2021 Sep 28. PMID: 34581485 
  • Tosun D, Demir Z, Veitch DP, Weintraub D, Aisen P, Jack CR, Jagust WJ, Petersen RC, Saykin AJ, Shaw LM, Trojanowski JQ, Weiner MW, Alzheimer’s Disease Neuroimaging Initiative. Contribution of Alzheimer’s biomarkers and risk factors to cognitive impairment and decline across the Alzheimer’s disease continuum. Alzheimers Dement. 2021 Oct 14. PMID: 34647694. PMCID: PMC9014819 
  • Yang Z, Nasrallah IM, Shou H, Wen J, Doshi J, Habes M, Erus G, Abdulkadir A, Resnick SM, Albert MS, Maruff P, Fripp J, Morris JC, Wolk DA, Davatzikos C; iSTAGING Consortium; Baltimore Longitudinal Study of Aging (BLSA); Alzheimer’s Disease Neuroimaging Initiative (ADNI). A deep learning framework identifies dimensional representations of Alzheimer’s Disease from brain structure. Nat Commun. 2021 Dec 3;12(1):7065. doi: 10.1038/s41467-021-26703-z. PMID: 34862382; PMCID: PMC8642554.
  • Shishegar R, Cox T, Rolls D, Bourgeat P, Doré V, Lamb F, Robertson J, Laws SM, Porter T, Fripp J, Tosun D, Maruff P, Savage G, Rowe CC, Masters CL, Weiner MW, Villemagne VL, Burnham SC. Using imputation to provide harmonized longitudinal measures of cognition across AIBL and ADNI. Sci Rep. 2021 12 10; 11(1):23788. PMID: 34893624. PMCID: PMC8664816
  • Myoraku A, Klein G, Landau S, Tosun D, Alzheimer’s Disease Neuroimaging Initiative. Regional uptakes from early-frame amyloid PET and 18F-FDG PET scans are comparable independent of disease state. Eur J Hybrid Imaging. 2022 Jan 18; 6(1):2. PMID: 35039928. PMCID: PMC8763988 
  • Jun GR, You Y, Zhu C, Meng G, Chung J, Panitch R, Hu J, Xia W; Alzheimer’s Disease Genetics Consortium, Bennett DA, Foroud TM, Wang LS, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Au R, Lunetta KL, Ikezu T, Stein TD, Farrer LA. Protein phosphatase 2A and complement component 4 are linked to the protective effect of APOE ɛ2 for Alzheimer’s disease. Alzheimers Dement. 2022 Feb 9:10.1002/alz.12607. doi: 10.1002/alz.12607. Epub ahead of print. PMID: 35142023; PMCID: PMC9360190.
  • Ushizima D, Chen Y, Alegro M, Ovando D, Eser R, Lee W, Poon K, Shankar A, Kantamneni N, Satrawada S, Junior EA, Heinsen H, Tosun D, Grinberg LT. Deep learning for Alzheimer’s disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation. Neuroimage. 2022 03; 248:118790. PMID: 34933123. PMCID: PMC8983026 
  • ​​Bashyam VM, Doshi J, Erus G, Srinivasan D, Abdulkadir A, Singh A, Habes M, Fan Y, Masters CL, Maruff P, Zhuo C, Völzke H, Johnson SC, Fripp J, Koutsouleris N, Satterthwaite TD, Wolf DH, Gur RE, Gur RC, Morris JC, Albert MS, Grabe HJ, Resnick SM, Bryan NR, Wittfeld K, Bülow R, Wolk DA, Shou H, Nasrallah IM, Davatzikos C; iSTAGING and PHENOM consortia. Deep Generative Medical Image Harmonization for Improving Cross-Site Generalization in Deep Learning Predictors. J Magn Reson Imaging. 2022 Mar;55(3):908-916. doi: 10.1002/jmri.27908. Epub 2021 Sep 25. PMID: 34564904; PMCID: PMC8844038.
  • Jo T, Nho K, Bice P, Saykin AJ; Alzheimer’s Disease Neuroimaging Initiative. Deep learning-based identification of genetic variants: application to Alzheimer’s disease classification. Brief Bioinform. 2022 Mar 10;23(2):bbac022. doi: 10.1093/bib/bbac022. PMID: 35183061; PMCID: PMC8921609.
  • Vogel JW, Tosun D. Multiple Cortical to Striatal Accumulation Trajectories of ß-Amyloid: Do All Roads Lead to Rome? Neurology. 2022 Mar 25. PMID: 35338076
  •  Stocks J, Popuri K, Heywood A, Tosun D, Alpert K, Beg MF, Rosen H, Wang L; Alzheimer’s Disease Neuroimaging Initiative. Network-wise concordance of multimodal neuroimaging features across the Alzheimer’s disease continuum. Alzheimers Dement (Amst). 2022 Apr 26;14(1):e12304. doi: 10.1002/dad2.12304. PMID: 35496375; PMCID: PMC9043119.

Conference Papers

SPIE Medical Imaging 2024

  • Dhinagar NJ, Singh A, Ozarkar SS, Buwa KU, Thomopoulos S, Owens-Walton C, Laltoo E, Chen Y-L, Cook PA, McMillan C, Tsai C-C, Wang J-J, Wu Y-R, Thompson PM. Video and synthetic MRI pre-training of 3D vision architectures for neuroimage analysis. In: Astley SM, Chen W, editors. Medical Imaging 2024: Computer-Aided Diagnosis. SPIE; 2024. doi: 10.1117/12.3008837.

ISBI 2024

  • Zhang Y, Bao R, Liu G, Zhan L, Thompson PM, Huang H. Neurodegenerative Disease Prediction via Transferable Deep Networks. In 2024 IEEE International Symposium on Biomedical Imaging (ISBI), Athens, Greece, 2024, pp. 1-5, doi: 10.1109/ISBI56570.2024.10635409.
  • Zhang Y, Zhan L, Thompson PM, Huang. Brain Image Synthesis Using Incomplete Multimodal Data via Attention-Redistribution Network. In 2024 IEEE International Symposium on Biomedical Imaging (ISBI), Athens, Greece, 2024, pp. 1-5, doi: 10.1109/ISBI56570.2024.10635569.

AIME 2024

  • He B, Sangari N, Wu R, Varathan P, Patania A, Risacher S, Nho K, Apostolova L, Saykin A, Shen L, Yan J. (2024) Integrative analysis of amyloid imaging and genetics reveals subtypes of Alzheimer progression in early stage. AIME’24: 22nd International Conference of AI in Medicine, Salt Lake City, UT, USA, July 9-12, 2024.

EMBC 2024

  • Dhinagar NJ, Thomopoulos SI, Laltoo E, Thompson PM. Counterfactual MRI Generation with Denoising Diffusion Models for Interpretable Alzheimer’s Disease Effect Detection. 46th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC ), 2024.

SIPAIM 2024

  • Chattopadhyay T, Joshy NA, Jagad C, Gleave EJ, Thomopoulos SI, Feng Y, Villalón-Reina JE, Laltoo E, Joshi H, Venkatasubramanian G, John JP, Steeg GV, Ambite JL and Thompson PM. Comparison of Explainable AI Models for MRI-based Alzheimer’s Disease Classification. 2024. In the 20th International Symposium on Medical information Processing and Analysis (SIPAIM ) IEEE.

ISBI 2023

  • Gupta U, Chattopadhyay T, Dhinagar N, Thompson PM, Steeg GV, Initiative TADN. Transferring Models Trained on Natural Images to 3D MRI via Position Encoded Slice Models. 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) [Internet]. 2023.

EMBC 2023

  • Cali R, Bhatt R, Thomopoulos SI, Gadewar SP, Gari IB, Chattopadhyay T, Jahanshad N, Thompson PM. The Influence of Brain MRI Defacing Algorithms on Brain-Age Predictions via 3D Convolutional Neural Networks. 2023. In 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, 2023, pp. 1-6, doi: 10.1109/EMBC40787.2023.10340740.
  • Dhinagar N, Thomopoulos SI, Thompson PM.Efficiently Training Vision Transformers on Structural MRI Scans for Alzheimer’s Disease Detection. 2023. In 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, 2023, pp. 1-6, doi: 10.1109/EMBC40787.2023.10341190.
  • Gadewar SP, Nourollahimoghadam E, Bhatt R, Ramesh A, Javid S, Gari IB, Zhu A, Thomopoulos SI, Thompson PM, Jahanshad N. A Comprehensive Corpus Callosum Segmentation Tool for Detecting Callosal Abnormalities and Genetic Associations from Multi Contrast MRIs. 2023. In 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, 2023, pp. 1-4, doi: 10.1109/EMBC40787.2023.10340442.
  • Goel N, Chattopadhyay T, Thompson PM, Thomopoulos SI. Predictive Modeling of Alzheimer’s Disease Prognosis using Anatomical & Diffusion MRI. 2023. In 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, 2023, pp. 1-5, doi: 10.1109/EMBC40787.2023.10341001.

SIPAIM 2023

  • Ba Gari I, Javid S, Zhu AH, Gadewar SP, Narula S, Ramesh A, Thomopoulos SI, Strike L, de Zubicaray GI, McMahon KL, Wright MJ, Thompson PM, Nir TM, Jahanshad N. Along-Tract Parameterization of White Matter Microstructure using Medial Tractography Analysis (MeTA). 2023 19th International Symposium on Medical Information Processing and Analysis (SIPAIM). IEEE; 2023. p. 1–5. doi: 10.1109/SIPAIM56729.2023.10373540.
  • Chattopadhyay T, Komandur D, Naik J, Buwa K, Ozarkar SS, Thomopoulos SI, Thompson PM. Can Structural MRIs be used to Detect Amyloid Positivity using Deep Learning? 2023 19th International Symposium on Medical Information Processing and Analysis (SIPAIM). IEEE; 2023. p. 1–4. doi: 10.1109/SIPAIM56729.2023.10373510.
  • Goel N, Thomopoulos SI, Thompson PM. Predicting Decline in Clinical Assessments of Alzheimer’s Disease With Machine Learning and 3D Brain MRI. 2023 19th International Symposium on Medical Information Processing and Analysis (SIPAIM). IEEE; 2023. p. 1–4. doi: 10.1109/SIPAIM56729.2023.10373444.
  • Komandur D, Gupta U, Chattopadhyay T, Dhinagar NJ, Thomopoulos SI, Chen J-C, Beavers D, Ver Steeg G, Thompson PM. Unsupervised harmonization of brain MRI using 3D CycleGANs and its effect on brain age prediction. 2023 19th International Symposium on Medical Information Processing and Analysis (SIPAIM). IEEE; 2023. p. 1–5. doi: 10.1109/SIPAIM56729.2023.10373501.

MICCAI 2023

  • Zhou R, Zhou H, Chen BY, Shen L, Zhang Y, He L. Attentive deep canonical correlation analysis for diagnosing Alzheimer’s disease using multimodal imaging genetics. Medical Image Computing and Computer Assisted Intervention – MICCAI 2023. MICCAI 2023. Lecture Notes in Computer Science, vol 14221, p. 681–691. Cham: Springer Nature Switzerland; 2023. doi: 10.1007/978-3-031-43895-0_64.
  • Ye K, Tang H, Dai S, Guo L, Liu JY, Wang Y, Leow A, Thompson PM, Huang H, Zhan L. Bidirectional Mapping with Contrastive Learning on Multimodal Neuroimaging Data. Med Image Comput Comput Assist Interv. 2023 Oct;14222:138-148. doi: 10.1007/978-3-031-43898-1_14. Epub 2023 Oct 1. PMID: 39005889; PMCID: PMC11245326.

PSB 2023

  • Eissman JM, Wells G, Khan OA, Liu D, Petyuk VA, Gifford KA, Dumitrescu L, Jefferson AL, Hohman TJ. Polygenic resilience score may be sensitive to preclinical Alzheimer’s disease changes. Pac Symp Biocomput. 2023;28:449-460. PMID: 36540999; PMCID: PMC9888419.

AMIA 2023

  • Tong B, Risacher SL, Bao J, Feng Y, Wang X, Ritchie MD, Moore JH, Urbanowicz R, Saykin AJ, Shen L. Comparing Amyloid Imaging Normalization Strategies for Alzheimer’s Disease Classification using an Automated Machine Learning Pipeline. AMIA Jt Summits Transl Sci Proc. 2023 Jun 16;2023:525-533. PMID: 37350880; PMCID: PMC10283108.
  • Wang X, Feng Y, Tong B, Bao J, Ritchie MD, Saykin AJ, Moore JH, Urbanowicz R, Shen L. Exploring Automated Machine Learning for Cognitive Outcome Prediction from Multimodal Brain Imaging using STREAMLINE. AMIA Jt Summits Transl Sci Proc. 2023 Jun 16;2023:544-553. PMID: 37350896; PMCID: PMC10283099.

ACM BCB 2023

  • Wang Z, Tong B, Zhu Q, Huang H, Saykin A, Thompson PM, Davatzikos C, Shen L. Distance-Weighted Sinkhorn Loss: A Novel Approach for Alzheimer’s Disease Classification. In the 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Houston, TX, September 3-6, 2023.

SIPAIM 2022

  • Chattopadhyay T, Singh A, Joshy NA, Thomopoulos SI, Nir TM, Zheng H, Nourollahimoghadam E, Gupta U, Ver Steeg G, Jahanshad N, Thompson PM. Predicting Dementia Severity by Merging Anatomical and Diffusion MRI with Deep 3D Convolutional Neural Networks, SIPAIM 2022. Proceedings Volume 12567, 18th International Symposium on Medical Information Processing and Analysis; 125670C (2023). doi: 10.1117/12.2669725.
  • Dhinagar N, Thomopoulos SI, Rajagopalan P, Stripelis D, Ambite JL, Ver Steeg G, Thompson PM. Evaluation of Transfer Learning Methods for Detecting Alzheimer’s Disease with Brain MRI, SIPAIM 2022. Proceedings Volume 12567, 18th International Symposium on Medical Information Processing and Analysis; 125671L (2023) doi: 10.1117/12.2670457
  • Gadewar SP, Ramesh A, Liu M, Ba Gari I, Nir TM, Thompson P, Jahanshad N. Predicting individual brain MRIs at any age using style encoding generative adversarial networks. In: Linguraru MG, Rittner L, Lepore N, Romero Castro E, Brieva J, Guevara P, editors. 18th International Symposium on Medical Information Processing and Analysis. SPIE; 2023. p. 12. doi: 10.1117/12.2669741.

BIBM 2022

  • Pala D, Lee B, Ning X, Kim D, Shen L; ADNI. Mediation Analysis and Mixed-Effects Models for the Identification of Stage-specific Imaging Genetics Patterns in Alzheimer’s Disease. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2022 Dec;2022:2667-2673. doi: 10.1109/bibm55620.2022.9995405. PMID: 36824222; PMCID: PMC9942815.
  • Xu F, Garai S, Duong-Tran D, Saykin AJ, Zhao Y, Shen L; ADNI. Consistency of Graph Theoretical Measurements of Alzheimer’s Disease Fiber Density Connectomes Across Multiple Parcellation Scales. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2022 Dec;2022:1323-1328. doi: 10.1109/bibm55620.2022.9995657. Epub 2023 Jan 2. PMID: 37041884; PMCID: PMC10082965

PSB 2022

  • Bao J, Wen Z, Kim M, Zhao X, Lee BN, Jung SH, Davatzikos C, Saykin AJ, Thompson PM, Kim D, Zhao Y, Shen L; Alzheimer’s Disease Neuroimaging Initiative. Identifying highly heritable brain amyloid phenotypes through mining Alzheimer’s imaging and sequencing biobank data. Pac Symp Biocomput. 2022;27:109-120. PMID: 34890141; PMCID: PMC8730532.

ICLR 2022

  • Yang Z, Wen J and Davatzikos C, 2022. Surreal-GAN: Semi-Supervised Representation Learning via GAN for uncovering heterogeneous disease-related imaging patterns. The 10th International Conference on Learning Representation – ICLR 2022. Preprint also available at doi: arXiv:2205.04523.

Int Soc Opt Eng 2022

  • Zhou Z, Srinivasan D, Li H, Abdulkadir A, Shou H, Davatzikos C, Fan Y. Harmonization of multi-site functional connectivity measures in tangent space improves brain age prediction. Proc SPIE Int Soc Opt Eng. 2022 Feb-Mar;12036. doi: 10.1117/12.2611557. Epub 2022 Apr 4. PubMed PMID: 36845412; PubMed Central PMCID: PMC9951555.

SIPAIM 2022

  • Gadewar S, Ramesh A, Liu M, Ba Gari I, Nir TM, Thompson PT, Jahanshad N. Predicting individual brain MRIs at any age using style encoding generative adversarial networks. Accepted to SIPAIM 2022.

MICCAI 2022 + Workshops

  • Haddad E, Javid S, Dhinagar N, Zhu AH, Lam P, Ba Gari I, Gupta A, Thompson PM, Nir TM, Jahanshad, N. Lifestyle factors that promote brain structural resilience in individuals with genetic risk factors for dementia. Presented at MLCN – MICCAI Workshop 2022.

PMLR 2021

  • Gupta U, Stripelis D, Lam PK, Thompson P, Ambite JL, Steeg GV. Membership Inference Attacks on Deep Regression Models for Neuroimaging. In: Heinrich M, Dou Q, de Bruijne M, Lellmann J, Schläfer A, Ernst F, editors. Proceedings of the Fourth Conference on Medical Imaging with Deep Learning [Internet]. PMLR; 07–09 Jul 2021. p. 228–251.

MICCAI 2021

  • ZhangY , Zhan L, Wu S, Thompson PM, Huang H. Disentangled and Proportional Representation Learning for Multi-View Brain Connectomes (2021). Medical Image Computing and Computer Assisted Interventions (MICCAI), pp. 508-518. PMID: 35449787 PMCID: PMC9020272 DOI: 10.1007/978-3-030-87234-2_48
  • Liu M, Maiti P, Thomopoulos SI, Zhu A, Chai Y, Kim H, Jahanshad N (2021). Style Transfer Using Generative Adversarial Networks for Multi-Site MRI Harmonization. MICCAI 2021. Preprint available on bioRxiv 2021.03.17.435892; doi: https://doi.org/10.1101/2021.03.17.435892

ISBI 2021

  • Ficiarà E, Crespi V, Gadewar SP, Thomopoulos SI, Boyd J, Thompson PM, Jahanshad N, Pizzagalli F, and the Alzheimer’s Disease Neuroimaging Initiative (2021). Predicting Progression from Mild Cognitive Impairment to Alzheimer’s Disease using MRI-based Cortical Features and a Two-State Markov Model, ISBI 2021. https://ieeexplore.ieee.org/document/9434143/. 
  • Gupta U, Pradeep K. Lam, Greg Ver Steeg, Paul M. Thompson (2021). Improved Brain Age Estimation With Slice-based Set Networks, ISBI 2021. https://ieeexplore.ieee.org/document/9434081/. 
  • Stripelis D, José Luis Ambite, Pradeep Lam, Paul Thompson (2021). Scaling Neuroscience Research Using Federated Learning, ISBI 2021. https://ieeexplore.ieee.org/document/9433925/. 

MIDL 2021

  • Gupta U, Stripelis D, Lam PK, Thompson PM, Ambite JL, ver Steeg G. Membership Inference Attacks on Deep Regression Models for Neuroimaging, submitted to MIDL 2021. Preprint available at: arXiv. doi: arXiv:2105.02866

SIPAIM 2021

  • Sinha S, Thomopoulos SI, Lam P, Muir A, Thompson PM (2021). Alzheimer’s Disease Classification Accuracy is Improved by MRI Harmonization based on Attention-Guided Generative Adversarial Networks Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606155. 
  • Stripelis D*, Saleem H*, Ghai* T, Dhinagar N* , Gupta U, Anastasiou C, Ver Steeg G, Ravi S, Naveed N, Thompson PM, Ambite JL (2021). Secure Neuroimaging Analysis using Federated Learning with Homomorphic Encryption. Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606256.   
  • Dhinagar NJ, Thomopoulos SI, Owens-Walton C, Stripelis D, Ambite JL, Ver Steeg G, Weintraub D, Cook P, McMillan C, Thompson PM (2021). 3D convolutional neural networks for classification of Alzheimer’s and Parkinson’s disease with T1-weighted brain MRI. Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606297.  
  • Thomopoulos SI, Nir TM, Villalon-Reina JE, Zavaliangos-Petropulu A, Maiti P, Zheng H, Nourollahimoghadam E, Jahanshad N, Thompson PM, for the Alzheimer’s Disease Neuroimaging Initiative (2021). Diffusion MRI Metrics and their Relation to Dementia Severity: Effects of Harmonization Approaches. Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606337. 

BIBM 2021

  • Kim M, Kim J, Qu J, Huang H, Sohn KA, Long Q, Kim D, Shen L. (2021) Interpretable temporal graph neural network for prognostic prediction of Alzheimer’s disease using longitudinal neuroimaging data. BIBM’21: IEEE Int. Conf. on Bioinformatics and Biomedicine, pp. 1381-1384, Virtual Conference, Dec 9-12, 2021. https://ieeexplore.ieee.org/document/9669504

PSB 2022

  • Bao J, Wen Z, Kim M, Zhao X, Lee BN, Jung SH, Davatzikos C, Saykin AJ, Thompson PM, Kim D, Zhao Y, Shen L, for the ADNI. (2022) Identifying highly heritable brain amyloid phenotypes through mining Alzheimer’s imaging and sequencing biobank data. Pac Symp Biocomput. 2022;27:109-20. https://pubmed.ncbi.nlm.nih.gov/34890141/

EMBC 2022

  • Chandio BQ, Chattopadhyay T, Owens-Walton C, Reina JEV, Nabulsi L, Thomopoulos SI, Garyfallidis E, Thompson PM. FiberNeat: Unsupervised White Matter Tract Filtering. 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2022, pp. 5055-5061. doi: 10.1109/EMBC48229.2022.9870877. PMID: 36085780.  https://ieeexplore.ieee.org/document/9870877.

ISBI 2022

  • Chandio BQ, Chattopadhyay T, Owens-Walton C, Villalon Reina JE, Nabulsi L, Thomopoulos SI, Garyfallidis E, Thompson PM (2022). FIBERNEAT: Unsupervised Streamline Clustering and White Matter Tract Filtering in Latent Space. ISBI 2022.
  • Sinha S, Thomopoulos SI, Lam P, Muir A, Thompson PM (2022). Improving Alzheimer’s Disease Classification using Attention-Guided Neural Networks and MRI Domain Adaptation. ISBI 2022.
  • Tang HT, Guo L, Fu XY, Qu B, Thompson PM, Huang H, Zhan L. Hierarchical Brain Embedding Using Explainable Graph Learning. ISBI 2022. https://ieeexplore.ieee.org/document/9761543  

MICCAI 2022

Preprints (Manuscripts In Submission)

  • Jo T, Bice P, Nho K, Andrew SJ, Alzheimer’s Disease Sequencing Project. Linkage Disequilibrium-Informed Deep Learning Framework to Identify Genetic Loci for Alzheimer’s Disease Using Whole Genome Sequencing Data. medRxiv. 2024:2024.09.19.24313993 doi: 10.1101/2024.09.19.24313993
  • Lam P, Alyssa H. Zhu, Iyad Ba Gari, Neda Jahanshad, Paul M. Thompson (2021). 3D Grid-attention Networks For Interpretable Age And Alzheimer’s Disease Prediction From Structural MRI. Preprint available at: arXiv 2020: 2011.09115.
  • Rajabli F, Benchek P, Tosto G, Kushch N, Sha J, Bazemore K, Zhu C, Lee WP, Haut J, Hamilton-Nelson KL, Wheeler NR, Zhao Y, Farrell JJ, Grunin MA, Leung YY, Kuksa PP, Li D, Lucio da Fonseca E, Mez JB, Palmer EL, Pillai J, Sherva RM, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Abner E, Adams PM, Aguirre A, Albert MS, Albin RL, Allen M, Alvarez L, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Ayres G, Baldwin CT, Barber RC, Barnes LL, Barral S, Beach TG, Becker JT, Beecham GW, Beekly D, Benitez BA, Bennett D, Bertelson J, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Brewer J, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Chasse S, Chesselet MF, Chin NA, Chui HC, Chung J, Craft S, Crane PK, Cribbs DH, Crocco EA, Cruchaga C, Cuccaro ML, Cullum M, Darby E, Davis B, De Jager PL, DeCarli C, DeToledo J, Dick M, Dickson DW, Dombroski BA, Doody RS, Duara R, Ertekin-Taner N, Evans DA, Faber KM, Fairchild TJ, Fallon KB, Fardo DW, Farlow MR, Fernandez-Hernandez V, Ferris S, Foroud TM, Frosch MP, Fulton-Howard B, Galasko DR, Gamboa A, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Goate AM, Grabowski TJ, Graff-Radford NR, Green RC, Growdon JH, Hakonarson H, Hall J, Hamilton RL, Harari O, Hardy J, Harrell LE, Head E, Henderson VW, Hernandez M, Hohman T, Honig LS, Huebinger RM, Huentelman MJ, Hulette CM, Hyman BT, Hynan LS, Ibanez L, Jarvik GP, Jayadev S, Jin LW, Johnson K, Johnson L, Kamboh MI, Karydas AM, Katz MJ, Kauwe JS, Kaye JA, Keene CD, Khaleeq A, Kim R, Knebl J, Kowall NW, Kramer JH, Kukull WA, LaFerla FM, Lah JJ, Larson EB, Lerner A, Leverenz JB, Levey AI, Lieberman AP, Lipton RB, Logue M, Lopez OL, Lunetta KL, Lyketsos CG, Mains D, Margaret FE, Marson DC, Martin ERR, Martiniuk F, Mash DC, Masliah E, Massman P, Masurkar A, McCormick WC, McCurry SM, McDavid AN, McDonough S, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Monuki ES, Morris JC, Mukherjee S, Myers AJ, Nguyen T, O’Bryant S, Olichney JM, Ory M, Palmer R, Parisi JE, Paulson HL, Pavlik V, Paydarfar D, Perez V, Peskind E, Petersen RC, Pierce A, Polk M, Poon WW, Potter H, Qu L, Quiceno M, Quinn JF, Raj A, Raskind M, Reiman EM, Reisberg B, Reisch JS, Ringman JM, Roberson ED, Rodriguear M, Rogaeva E, Rosen HJ, Rosenberg RN, Royall DR, Sager MA, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Slifer SH, Small S, Smith AG, Smith JP, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Stevens AB, Strittmatter SM, Sultzer D, Swerdlow RH, Tanzi RE, Tilson JL, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, van Eldik LJ, Vance JM, Vardarajan BN, Vassar R, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Whitehead PL, Wijsman EM, Wilhelmsen KC, Williams B, Williamson J, Wilms H, Wingo TS, Wisniewski T, Woltjer RL, Woon M, Wright CB, Wu CK, Younkin SG, Yu CE, Yu L, Zhu X, Kunkle BW, Bush WS, Wang LS, Farrer LA, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Jun GR, Reitz C, Naj AC. Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK , GRB14 , and KIAA0825 as novel risk loci for Alzheimer’s disease: the Alzheimer’s Disease Genetics Consortium. medRxiv [Preprint]. 2023 Jul 8:2023.07.06.23292311. doi: 10.1101/2023.07.06.23292311. PMID: 37461624; PMCID: PMC10350126.
  • Sahelijo N, Rajagopalan P, Qian L, Rahman R, Priyadarshi D, Goldstein D, Thomopoulos SI, Bennett DA, Farrer LA, Stein TD, Shen L, Huang H, Nho K, Andrew SJ, Davatzikos C, Thompson PM, TCW J, Jun GR. Brain Cell-based Genetic Subtyping and Drug Repositioning for Alzheimer’s Disease. medRxiv. 2024:2024.06.21.24309255. doi: 10.1101/2024.06.21.24309255.