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Orthogonal Ensemble Networks for Biomedical Image Segmentation

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Medical Image Computing and Computer Assisted Intervention – MICCAI 2021 (MICCAI 2021)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 12903))

Abstract

Despite the astonishing performance of deep-learning based approaches for visual tasks such as semantic segmentation, they are known to produce miscalibrated predictions, which could be harmful for critical decision-making processes. Ensemble learning has shown to not only boost the performance of individual models but also reduce their miscalibration by averaging independent predictions. In this scenario, model diversity has become a key factor, which facilitates individual models converging to different functional solutions. In this work, we introduce Orthogonal Ensemble Networks (OEN), a novel framework to explicitly enforce model diversity by means of orthogonal constraints. The proposed method is based on the hypothesis that inducing orthogonality among the constituents of the ensemble will increase the overall model diversity. We resort to a new pairwise orthogonality constraint which can be used to regularize a sequential ensemble training process, resulting on improved predictive performance and better calibrated model outputs. We benchmark the proposed framework in two challenging brain lesion segmentation tasks –brain tumor and white matter hyper-intensity segmentation in MR images. The experimental results show that our approach produces more robust and well-calibrated ensemble models and can deal with challenging tasks in the context of biomedical image segmentation.

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Notes

  1. 1.

    Our code associated to the orthogonal ensemble networks training is publicly available at: https://github.com/agosl/Orthogonal_Ensemble_Networks.

References

  1. Guo, C., Pleiss, G., Sun, Y., Weinberger, K.Q.: On calibration of modern neural networks. In: ICML, pp. 1321–1330 (2017)

    Google Scholar 

  2. Lakshminarayanan, B., Pritzel, A., Blundell, C.: Simple and scalable predictive uncertainty estimation using deep ensembles. In: NeurIPS (2017)

    Google Scholar 

  3. Stickland, A.C., Murray, I.: Diverse ensembles improve calibration. In: ICML 2020 Workshop on Uncertainty and Robustness in Deep Learning (2020)

    Google Scholar 

  4. Ovadia, Y., et al.: Can you trust your model’s uncertainty? Evaluating predictive uncertainty under dataset shift. In: NeurIPS (2019)

    Google Scholar 

  5. Gal, Y., Ghahramani, Z.: Dropout as a Bayesian approximation: Representing model uncertainty in deep learning. In: International Conference on Machine Learning, pp. 1050–1059 (2016)

    Google Scholar 

  6. Wen, Y., Tran, D., Ba, J.: Batchensemble: an alternative approach to efficient ensemble and lifelong learning. In: ICLR (2020)

    Google Scholar 

  7. Wenzel, F., Snoek, J., Tran, D., Jenatton, R.: Hyperparameter ensembles for robustness and uncertainty quantification. In: NeurIPS (2020)

    Google Scholar 

  8. Sinha, S., Bharadhwaj, H., Goyal, A., Larochelle, H., Garg, A., Shkurti, F.: Dibs: diversity inducing information bottleneck in model ensembles. In: AAAI (2020)

    Google Scholar 

  9. Kim, W., Goyal, B., Chawla, K., Lee, J., Kwon, K.: Attention-based ensemble for deep metric learning. In: ECCV, pp. 736–751 (2018)

    Google Scholar 

  10. Yang, H., et al.: DVERGE: diversifying vulnerabilities for enhanced robust generation of ensembles. arXiv preprint arXiv:2009.14720 (2020)

  11. 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 

  12. Sander, J., de Vos, B.D., Wolterink, J.M., Išgum, I.: Towards increased trustworthiness of deep learning segmentation methods on cardiac MRI. In: Medical Imaging 2019: Image Processing, vol. 10949, p. 1094919. International Society for Optics and Photonics (2019)

    Google Scholar 

  13. Mehrtash, A., Wells, W.M., Tempany, C.M., Abolmaesumi, P., Kapur, T.: Confidence calibration and predictive uncertainty estimation for deep medical image segmentation. IEEE Trans. Med. Imaging 39(12), 3868–3878 (2020)

    Article  Google Scholar 

  14. Kamnitsas, K., et al.: Ensembles of multiple models and architectures for robust brain tumour segmentation. In: Crimi, A., Bakas, S., Kuijf, H., Menze, B., Reyes, M. (eds.) BrainLes 2017. LNCS, vol. 10670, pp. 450–462. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-75238-9_38

    Chapter  Google Scholar 

  15. Feng, X., Tustison, N.J., Patel, S.H., Meyer, C.H.: Brain tumor segmentation using an ensemble of 3D U-Nets and overall survival prediction using radiomic features. Front. Comput. Neurosci. 14, 25 (2020)

    Article  Google Scholar 

  16. Ma, T., et al.: Ensembling low precision models for binary biomedical image segmentation. In: Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, pp. 325–334 (2021)

    Google Scholar 

  17. Wang, J., Chen, Y., Chakraborty, R., Yu, S.X.: Orthogonal convolutional neural networks. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 11505–11515 (2020)

    Google Scholar 

  18. Ayinde, B.O., Inanc, T., Zurada, J.M.: Regularizing deep neural networks by enhancing diversity in feature extraction. IEEE Trans. Neural Networks Learning Syst. 30(9), 2650–2661 (2019)

    Article  Google Scholar 

  19. Bakas, S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4, 170117 (2017)

    Google Scholar 

  20. Bakas, S., et al.: Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the brats challenge. arXiv preprint arXiv:1811.02629 (2018)

  21. Menze, B.H., et al.: The multimodal brain tumor image segmentation benchmark (brats). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2014)

    Article  Google Scholar 

  22. Kuijf, H.J., et al.: Standardized assessment of automatic segmentation of white matter hyperintensities and results of the WMH segmentation challenge. IEEE Trans. Med. Imaging 38(11), 2556–2568 (2019)

    Article  Google Scholar 

  23. Zhang, Z., Liu, Q., Wang, Y.: Road extraction by deep residual U-Net. IEEE Geosci. Remote Sens. Lett. 15(5), 749–753 (2018)

    Article  Google Scholar 

  24. Brier, G.W.: Verification of forecasts expressed in terms of probability. Mon. Weather Rev. 78(1), 1–3 (1950)

    Article  Google Scholar 

  25. Wallace, B.C., Dahabreh, I.J.: Improving class probability estimates for imbalanced data. Knowl. Inf. Syst. 41(1), 33–52 (2013). https://doi.org/10.1007/s10115-013-0670-6

    Article  Google Scholar 

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Acknowledgments

The authors gratefully acknowledge NVIDIA Corporation with the donation of the GPUs used for this research, and the support of UNL (CAID-0620190100145LI, CAID-50220140100084LI) and ANPCyT (PICT 2018-03907). This research was enabled in part by support provided by Calcul Québec and Compute Canada.

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Correspondence to Agostina J. Larrazabal .

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Larrazabal, A.J., Martínez, C., Dolz, J., Ferrante, E. (2021). Orthogonal Ensemble Networks for Biomedical Image Segmentation. In: de Bruijne, M., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2021. MICCAI 2021. Lecture Notes in Computer Science(), vol 12903. Springer, Cham. https://doi.org/10.1007/978-3-030-87199-4_56

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  • DOI: https://doi.org/10.1007/978-3-030-87199-4_56

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  • Online ISBN: 978-3-030-87199-4

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