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Geometric Deep Learning for Multifocal Diseases

Type: MA thesis

Status: finished

Date: July 1, 2020 - January 7, 2021

Supervisors: Florian Thamm, Felix Denzinger

Diseases are classi ed as multifocal if they are relating to or arising from many foci. They are present in various
medical disciplines, e.g. multifocal atrial tachycardia [1], breast cancer [2] or multifocal motor neuropathy [3].
However, analyzing diseases with multiple centers brings several challenges for conventional deep learning ar-
chitectures. On a technical side, it is complex to handle a varying number of centers which have no unique
sequence. From a medical view, it is important to model structures and relationships between the foci. The grid
structure used in convolutional neural networks cannot handle non-regular neighborhoods. A suitable approach
for this task would be to convert the data into graph structures, where the nodes describe the properties of the
foci and the edges model their mutual relationships. With geometric deep learning, it is possible to learn from
graph structures. It is an emerging eld of research with many possible applications, e.g. classifying documents
in citation graphs or analyzing molecular structures [4]. There also exist several medical applications, e.g. for
analysis of parcinson’s disease [5] or artery segmentation [6]. This thesis aims to investigate the applicability of
this method for relatively small graphs coming from multifocal diseases. The networks are trained to predict
time to events of failure as a metric for the severeness of the disease. Di erent geometric layer architectures,
such as Graph-Attention-Networks [7] and Di erential Pooling [8], are investigated and compared to the per-
formance of a conventional neural network. As we aim to create explicable models, it is intended to provide
visualizations of salient sub-graphs and features of the results. In addition to that, methods to incorporate prior
knowledge from the medical domain into the training process are tested to improve the speed of convergence
and strengthen the medical validity of the predictions. In the end, the networks are tested on liver data.

Summary:

1. Transfer multifocal diseases to meaningful graph structures
2. Provide conventional neural network for time to event regression as baseline
3. Investigate and tune di erent geometric deep learning architectures
4. Visualize salient graph structures

References
[1] Jane F. Desforges and John A. Kastor. Multifocal Atrial Tachycardia. New England Journal of Medicine,
322(24):1713{1717, jun 1990.
[2] John Boyages and Nathan J Coombs. Multifocal and Multicentric Breast Cancer: Does Each Focus Matter?
Article in Journal of Clinical Oncology, 23:7497{7502, 2005.
[3] Eduardo Nobile-Orazio. Multifocal motor neuropathy. Journal of Neuroimmunology, 115(1-2):4{18, apr
2001.
[4] Michael Bronstein, Joan Bruna, Yann Lecun, Arthur Szlam, and Pierre Vandergheynst. Geometric Deep
Learning: Going beyond Euclidean data. IEEE Signal Processing Magazine, 34(4):18{42, 2017.
[5] Xi Zhang, Lifang He, Kun Chen, Yuan Luo, Jiayu Zhou, and Fei Wang. Multi-View Graph Convolutional
Network and Its Applications on Neuroimage Analysis for Parkinson’s Disease. AMIA … Annual Symposium
proceedings. AMIA Symposium, 2018:1147{1156, 2018.
[6] Jelmer M. Wolterink, Tim Leiner, and Ivana Isgum. Graph Convolutional Networks for Coronary Artery
Segmentation in Cardiac CT Angiography. In Lecture Notes in Computer Science (including subseries
Lecture Notes in Arti cial Intelligence and Lecture Notes in Bioinformatics), volume 11849 LNCS, pages
62{69. Springer, oct 2019.
[7] Petar Velickovic, Arantxa Casanova, Pietro Lio, Guillem Cucurull, Adriana Romero, and Yoshua Bengio.
Graph attention networks. 6th International Conference on Learning Representations, ICLR 2018 – Con-
ference Track Proceedings, pages 1{12, 2018.
[8] Rex Ying, Jiaxuan You, Christopher Morris, Xiang Ren, William L. Hamilton, and Jure Leskovec. Hierarchi-
cal Graph Representation Learning with Di erentiable Pooling. Advances in Neural Information Processing
Systems, 2018-Decem:4800{4810, jun 2018.