Machine learning in neuroimaging

Instructors

Prof. Dr. Christian Wachinger, Tom Nuno Wolf, Fabian Bongratz, Bailiang Jian, Morteza Ghahremani

Contact

If you have any questions regarding this seminar contact seminars@ai-med.de.

Announcements

Pre-Course meeting is on July 3, 2023 at 1pm via Zoom. Zoom link: https://tum-conf.zoom.us/j/69713668455?pwd=VWtSdXJUWGJXczJOZVVNWE5UN2tKUT09 Meeting ID: 697 1366 8455 Passcode: 716773
Slides from the pre-course meeting are here: ML-Neuro pre-course SoSe2023-2.pdf
Available topics are released now in the table below. This semester, we selected papers with a particular focus on Transformers.
Slides from the kickoff are here: ML-Neuro Seminar Winter 2023_24 Kickoff.pdf

Registration

Registration to the seminar is done via the TUM Matching Platform. Pay attention to the deadlines!!

Timeline

July 3, 2023, 1pm: pre-course meeting
October 4, 2023, 23:59: Deadline for deregistration
October 23, 2023, 2pm: Kickoff (online, attendance mandatory), assignment of papers
During the semester: meet your supervisor (optional but recommended)
January 11, 13-17 & January 12, 9-14, Seminarraum Holbeinstrasse 11: Block seminar (attendance is mandatory)

Topics

Paper ID	Title	Published in	Link	Group/Supervisor	Student	Additional Material
1	UNesT: Local Spatial Representation Learning with Hierarchical Transformer for Efficient Medical Segmentation	Medical Image Analysis	https://arxiv.org/abs/2209.14378	Fabian Bongratz	Mehmet Celimli
2	Unsupervised brain imaging 3D anomaly detection and segmentation with transformers	Medical Image Analysis	https://www.sciencedirect.com/science/article/pii/S1361841522001220	Fabian Bongratz	Melisa Ankut
3	Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis	CVPR	https://arxiv.org/abs/2111.14791	Fabian Bongratz	Petru-Georgian Sicoe
4	One Model to Synthesize Them All: Multi-contrast Multi-scale Transformer for Missing Data Imputation	IEEE TMI	https://arxiv.org/abs/2204.13738	Christian Wachinger	Thomas Sedlmeyr
5	PTNet3D: A 3D High-Resolution Longitudinal Infant Brain MRI Synthesizer Based on Transformers	IEEE TMI	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9529847/	Christian Wachinger	Azza Jenane
6	Towards Generalist Biomedical AI		https://arxiv.org/abs/2307.14334	Christian Wachinger	Hui Cheng	Related to Palm-E https://arxiv.org/abs/2303.03378
7	TransMorph: Transformer for unsupervised medical image registration	Medical Image Analysis	https://arxiv.org/abs/2111.10480	Bailiang Jian	Hakan Buğra Erentuğ
8	Affine Medical Image Registration with Coarse-to-Fine Vision Transformer	CVPR	https://arxiv.org/abs/2203.15216	Bailiang Jian	Luis David Reyes Vargas
9	Preserving Tumor Volumes for Unsupervised Medical Image Registration	ICCV	https://openaccess.thecvf.com/content/ICCV2023/papers/Dong_Preserving_Tumor_Volumes_for_Unsupervised_Medical_Image_Registration_ICCV_2023_paper.pdf	Bailiang Jian	Furkan Yakal
10	Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data	IEEE TMI	https://ieeexplore.ieee.org/abstract/document/10242080	Yitong Li / Nuno Wolf	Yuliia Zinkeieva
11	MetaViT: Metabolism-Aware Vision Transformer for Differential Diagnosis of Parkinsonism with 18F-FDG PET	IPMI	https://link.springer.com/chapter/10.1007/978-3-031-34048-2_11	Yitong Li / Nuno Wolf	Ivan Stoyanov
12	A Hybrid Multi-Scale Attention Convolution and Aging Transformer Network for Alzheimer's Disease Diagnosis	IEEE Journal of Biomedical and Health Informatics	https://ieeexplore.ieee.org/abstract/document/10109788	Yitong Li / Nuno Wolf	Arda Hüseyinoglu