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Hierarchical Compositionality in Hyperbolic Space for Robust Medical Image Segmentation

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Domain Adaptation and Representation Transfer (DART 2023)

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Abstract

Deep learning based medical image segmentation models need to be robust to domain shifts and image distortion for the safe translation of these models into clinical practice. The most popular methods for improving robustness are centred around data augmentation and adversarial training. Many image segmentation tasks exhibit regular structures with only limited variability. We aim to exploit this notion by learning a set of base components in the latent space whose composition can account for the entire structural variability of a specific segmentation task. We enforce a hierarchical prior in the composition of the base components and consider the natural geometry in which to build our hierarchy. Specifically, we embed the base components on a hyperbolic manifold which we claim leads to a more natural composition. We demonstrate that our method improves model robustness under various perturbations and in the task of single domain generalisation.

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References

  1. Atigh, M.G., Schoep, J., Acar, E., van Noord, N., Mettes, P.: Hyperbolic image segmentation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. pp. 4453–4462 (2022)

    Google Scholar 

  2. Bloch, N., Madabhushi, A., Huisman, H., Freymann, J., Kirby, J., Grauer, M., Enquobahrie, A., Jaffe, C., Clarke, L., Farahani, K.: Cancer imaging archive wiki. https://doi.org/10.7937/K9/TCIA.2015.zF0vlOPv (2015)

  3. Bloch, N., Madabhushi, A., Huisman, H., Freymann, J., Kirby, J., Grauer, M., Enquobahrie, A., Jaffe, C., Clarke, L., Farahani, K.: Nci-isbi 2013 challenge: automated segmentation of prostate structures. The Cancer Imaging Archive 370, 6 (2015)

    Google Scholar 

  4. Carlucci, F.M., D’Innocente, A., Bucci, S., Caputo, B., Tommasi, T.: Domain generalization by solving jigsaw puzzles. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. pp. 2229–2238 (2019)

    Google Scholar 

  5. Chami, I., Ying, Z., Ré, C., Leskovec, J.: Hyperbolic graph convolutional neural networks. Advances in neural information processing systems 32 (2019)

    Google Scholar 

  6. Chen, C., Qin, C., Qiu, H., Ouyang, C., Wang, S., Chen, L., Tarroni, G., Bai, W., Rueckert, D.: Realistic adversarial data augmentation for mr image segmentation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. pp. 667–677. Springer (2020)

    Google Scholar 

  7. Chen, J., Lu, Y., Yu, Q., Luo, X., Adeli, E., Wang, Y., Lu, L., Yuille, A.L., Zhou, Y.: Transunet: Transformers make strong encoders for medical image segmentation. arXiv preprint arXiv:2102.04306 (2021)

  8. Chen, Y.: Towards to robust and generalized medical image segmentation framework. arXiv preprint arXiv:2108.03823 (2021)

  9. Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., et al.: The cancer imaging archive (tcia): maintaining and operating a public information repository. J. Digit. Imaging 26, 1045–1057 (2013)

    Article  Google Scholar 

  10. DeVries, T., Taylor, G.W.: Improved regularization of convolutional neural networks with cutout. arxiv 2017. arXiv preprint arXiv:1708.04552 (2017)

  11. He, K., Zhang, X., Ren, S., Sun, J.: Identity mappings in deep residual networks. In: Computer Vision-ECCV 2016: 14th European Conference, Amsterdam, The Netherlands, October 11–14, 2016, Proceedings, Part IV 14. pp. 630–645. Springer (2016)

    Google Scholar 

  12. Jang, E., Gu, S., Poole, B.: Categorical reparameterization with gumbel-softmax. arXiv preprint arXiv:1611.01144 (2016)

  13. Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014)

  14. Kortylewski, A., He, J., Liu, Q., Yuille, A.L.: Compositional convolutional neural networks: A deep architecture with innate robustness to partial occlusion. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. pp. 8940–8949 (2020)

    Google Scholar 

  15. Landman, B., Xu, Z., Igelsias, J., Styner, M., Langerak, T., Klein, A.: Miccai multi-atlas labeling beyond the cranial vault-workshop and challenge. In: Proc. MICCAI Multi-Atlas Labeling Beyond Cranial Vault-Workshop Challenge. vol. 5, p. 12 (2015)

    Google Scholar 

  16. Liu, Q., Nickel, M., Kiela, D.: Hyperbolic graph neural networks. Advances in Neural Information Processing Systems 32 (2019)

    Google Scholar 

  17. Liu, X., Thermos, S., Sanchez, P., O’Neil, A.Q., Tsaftaris, S.A.: vmfnet: Compositionality meets domain-generalised segmentation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. pp. 704–714. Springer (2022)

    Google Scholar 

  18. Madry, A., Makelov, A., Schmidt, L., Tsipras, D., Vladu, A.: Towards deep learning models resistant to adversarial attacks. arXiv preprint arXiv:1706.06083 (2017)

  19. Milletari, F., Navab, N., Ahmadi, S.A.: V-net: Fully convolutional neural networks for volumetric medical image segmentation. In: 2016 fourth international conference on 3D vision (3DV). pp. 565–571. IEEE (2016)

    Google Scholar 

  20. Nickel, M., Kiela, D.: Poincaré embeddings for learning hierarchical representations. Advances in neural information processing systems 30 (2017)

    Google Scholar 

  21. Pérez-García, F., Sparks, R., Ourselin, S.: Torchio: a python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning. Comput. Methods Programs Biomed. 208, 106236 (2021)

    Article  Google Scholar 

  22. Ronneberger, O., Fischer, P., Brox, T.: U-net: Convolutional networks for biomedical image segmentation. In: International Conference on Medical image computing and computer-assisted intervention. pp. 234–241. Springer (2015)

    Google Scholar 

  23. Santhirasekaram, A., Kori, A., Winkler, M., Rockall, A., Glocker, B.: Vector quantisation for robust segmentation. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. pp. 663–672. Springer (2022)

    Google Scholar 

  24. Tramer, F., Boneh, D.: Adversarial training and robustness for multiple perturbations. Advances in Neural Information Processing Systems 32 (2019)

    Google Scholar 

  25. Van Den Oord, A., Vinyals, O., et al.: Neural discrete representation learning. Advances in neural information processing systems 30 (2017)

    Google Scholar 

  26. Wang, Z., Luo, Y., Qiu, R., Huang, Z., Baktashmotlagh, M.: Learning to diversify for single domain generalization. In: Proceedings of the IEEE/CVF International Conference on Computer Vision. pp. 834–843 (2021)

    Google Scholar 

  27. Xu, Z., Liu, D., Yang, J., Raffel, C., Niethammer, M.: Robust and generalizable visual representation learning via random convolutions. arXiv preprint arXiv:2007.13003 (2020)

  28. Zhang, H., Cisse, M., Dauphin, Y.N., Lopez-Paz, D.: mixup: Beyond empirical risk minimization. arXiv preprint arXiv:1710.09412 (2017)

  29. Zhang, H., Rich, P.D., Lee, A.K., Sharpee, T.O.: Hippocampal spatial representations exhibit a hyperbolic geometry that expands with experience. Nature Neuroscience pp. 1–9 (2022)

    Google Scholar 

  30. Zhang, L., Wang, X., Yang, D., Sanford, T., Harmon, S., Turkbey, B., Wood, B.J., Roth, H., Myronenko, A., Xu, D., et al.: Generalizing deep learning for medical image segmentation to unseen domains via deep stacked transformation. IEEE Trans. Med. Imaging 39(7), 2531–2540 (2020)

    Article  Google Scholar 

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Acknowledgements

This work was supported and funded by Cancer Research UK (CRUK) (C309/A28804).

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Correspondence to Ainkaran Santhirasekaram .

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Santhirasekaram, A., Winkler, M., Rockall, A., Glocker, B. (2024). Hierarchical Compositionality in Hyperbolic Space for Robust Medical Image Segmentation. In: Koch, L., et al. Domain Adaptation and Representation Transfer. DART 2023. Lecture Notes in Computer Science, vol 14293. Springer, Cham. https://doi.org/10.1007/978-3-031-45857-6_6

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  • DOI: https://doi.org/10.1007/978-3-031-45857-6_6

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