Skip to main content

Federated Whole Prostate Segmentation in MRI with Personalized Neural Architectures

  • Conference paper
  • First Online:
Medical Image Computing and Computer Assisted Intervention – MICCAI 2021 (MICCAI 2021)

Abstract

Building robust deep learning-based models requires diverse training data, ideally from several sources. However, these datasets cannot be combined easily because of patient privacy concerns or regulatory hurdles, especially if medical data is involved. Federated learning (FL) is a way to train machine learning models without the need for centralized datasets. Each FL client trains on their local data while only sharing model parameters with a global server that aggregates the parameters from all clients. At the same time, each client’s data can exhibit differences and inconsistencies due to the local variation in the patient population, imaging equipment, and acquisition protocols. Hence, the federated learned models should be able to adapt to the local particularities of a client’s data. In this work, we combine FL with an AutoML technique based on local neural architecture search by training a “supernet”. Furthermore, we propose an adaptation scheme to allow for personalized model architectures at each FL client’s site. The proposed method is evaluated on four different datasets from 3D prostate MRI and shown to improve the local models’ performance after adaptation through selecting an optimal path through the AutoML supernet.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    http://medicaldecathlon.com.

  2. 2.

    https://promise12.grand-challenge.org.

  3. 3.

    http://doi.org/10.7937/K9/TCIA.2015.zF0vlOPv.

  4. 4.

    https://prostatex.grand-challenge.org.

  5. 5.

    https://pytorch.org.

  6. 6.

    https://monai.io.

  7. 7.

    https://pypi.org/project/nvflare.

References

  1. Cai, H., Zhu, L., Han, S.: Proxylessnas: direct neural architecture search on target task and hardware. arXiv preprint arXiv:1812.00332 (2018)

  2. Çiçek, Ö., Abdulkadir, A., Lienkamp, S.S., Brox, T., Ronneberger, O.: 3D U-net: learning dense volumetric segmentation from sparse annotation. In: Ourselin, S., Joskowicz, L., Sabuncu, M.R., Unal, G., Wells, W. (eds.) MICCAI 2016. LNCS, vol. 9901, pp. 424–432. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46723-8_49

    Chapter  Google Scholar 

  3. Elsken, T., Metzen, J.H., Hutter, F.: Neural architecture search: a survey. arXiv preprint arXiv:1808.05377 (2018)

  4. Ganin, Y., Lempitsky, V.: Unsupervised domain adaptation by backpropagation. In: Proceedings of the 32nd International Conference on International Conference on Machine Learning, vol. 37. pp. 1180–1189. JMLR. org (2015)

    Google Scholar 

  5. Ganin, Y., et al.: Domain-adversarial training of neural networks. J. Mach. Learn. Res. 17(1), 1–35 (2016). 2096-2030

    MathSciNet  MATH  Google Scholar 

  6. Ginsburg, B., et al.: Stochastic gradient methods with layer-wise adaptive moments for training of deep networks. arXiv preprint arXiv:1905.11286 (2019)

  7. He, C., Annavaram, M., Avestimehr, S.: Towards Non-IID and invisible data with fednas: federated deep learning via neural architecture search. arXiv preprint arXiv:2004.08546 (2020)

  8. Isensee, F., Jaeger, P.F., Kohl, S.A., Petersen, J., Maier-Hein, K.H.: NNU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat. Methods 18(2), 203–211 (2021)

    Article  Google Scholar 

  9. Isola, P., Zhu, J.Y., Zhou, T., Efros, A.A.: Image-to-image translation with conditional adversarial networks. In: CVPR, pp. 1125–1134 (2017)

    Google Scholar 

  10. Kairouz, P., et al.: Advances and open problems in federated learning. arXiv preprint arXiv:1912.04977 (2019)

  11. Kamnitsas, K., et al.: Unsupervised domain adaptation in brain lesion segmentation with adversarial networks. In: Niethammer, M., et al. (eds.) IPMI 2017. LNCS, vol. 10265, pp. 597–609. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59050-9_47

    Chapter  Google Scholar 

  12. Kamnitsas, K., et al.: Deepmedic for brain tumor segmentation. In: Crimi, A., Menze, B., Maier, O., Reyes, M., Winzeck, S., Handels, H. (eds.) Brainlesion: Glioma, multiple sclerosis, stroke and traumatic brain injuries, pp. 138–149. Springer, Heidelberg (2016). https://doi.org/10.1007/978-3-319-55524-9_14

    Chapter  Google Scholar 

  13. Li, W., et al.: Privacy-preserving federated brain tumour segmentation. In: Suk, H.-I., Liu, M., Yan, P., Lian, C. (eds.) MLMI 2019. LNCS, vol. 11861, pp. 133–141. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32692-0_16

    Chapter  Google Scholar 

  14. Li, W., Wang, G., Fidon, L., Ourselin, S., Cardoso, M.J., Vercauteren, T.: On the compactness, efficiency, and representation of 3d convolutional networks: brain parcellation as a pretext task. In: Niethammer, M., et al. (eds.) IPMI 2017. LNCS, vol. 10265, pp. 348–360. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59050-9_28

    Chapter  Google Scholar 

  15. Li, Z., Hoiem, D.: Learning without forgetting. IEEE Trans. Pattern Anal. Mach. Intell. 40(12), 2935–2947 (2017)

    Article  Google Scholar 

  16. Litjens, G., Debats, O., Barentsz, J., Karssemeijer, N., Huisman, H.: Computer-aided detection of prostate cancer in MRI. TMI 33(5), 1083–1092 (2014)

    Google Scholar 

  17. Litjens, G., et al.: Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge. Med. Image Anal. 18(2), 359–373 (2014)

    Article  Google Scholar 

  18. Liu, H., Simonyan, K., Yang, Y.: Darts: differentiable architecture search. arXiv preprint arXiv:1806.09055 (2018)

  19. McMahan, H.B., Moore, E., Ramage, D., Hampson, S., et al.: Communication-efficient learning of deep networks from decentralized data. arXiv preprint arXiv:1602.05629 (2016)

  20. 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 

  21. Ronneberger, O., Fischer, P., Brox, T.: U-Net: convolutional networks for biomedical image segmentation. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9351, pp. 234–241. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-24574-4_28

    Chapter  Google Scholar 

  22. Sheller, M.J., Reina, G.A., Edwards, B., Martin, J., Bakas, S.: Multi-institutional deep learning modeling without sharing patient data: a feasibility study on brain tumor segmentation. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11383, pp. 92–104. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11723-8_9

    Chapter  Google Scholar 

  23. Shin, H.C., Roth, H.R., Gao, M., Lu, L., Xu, Z., Nogues, I., Yao, J., Mollura, D., Summers, R.M.: Deep convolutional neural networks for computer-aided detection: CNN architectures, dataset characteristics and transfer learning. TMI 35(5), 1285–1298 (2016)

    Google Scholar 

  24. Simpson, A.L., et al.: A large annotated medical image dataset for the development and evaluation of segmentation algorithms. arXiv preprint arXiv:1902.09063 (2019)

  25. Tan, M., Le, Q.: EfficientNet: rethinking model scaling for convolutional neural networks. In: International Conference on Machine Learning, pp. 6105–6114 (2019)

    Google Scholar 

  26. Yang, D., et al.: Federated semi-supervised learning for COVID region segmentation in chest CT using multi-national data from China, Italy, Japan. Med. Image Anal. 70, 101992 (2021)

    Article  Google Scholar 

  27. You, S., Huang, T., Yang, M., Wang, F., Qian, C., Zhang, C.: GreedyNAS: towards fast one-shot NAS with greedy supernet. In: CVPR, pp. 1999–2008 (2020)

    Google Scholar 

  28. Yu, Q., et al.: C2fnas: coarse-to-fine neural architecture search for 3D medical image segmentation. In: CVPR, pp. 4126–4135 (2020)

    Google Scholar 

  29. Zhang, L., et al.: Generalizing deep learning for medical image segmentation to unseen domains via deep stacked transformation. TMI (2020)

    Google Scholar 

  30. Zhang, Y., Miao, S., Mansi, T., Liao, R.: Task driven generative modeling for unsupervised domain adaptation: application to x-ray image segmentation. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) MICCAI 2018. LNCS, vol. 11071, pp. 599–607. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00934-2_67

    Chapter  Google Scholar 

  31. Zhu, H., Jin, Y.: Real-time federated evolutionary neural architecture search. arXiv preprint arXiv:2003.02793 (2020)

  32. Zhu, J.Y., Park, T., Isola, P., Efros, A.A.: Unpaired image-to-image translation using cycle-consistent adversarial networks. In: Proceedings of the IEEE International Conference on Computer Vision, pp. 2223–2232 (2017)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Holger R. Roth or Daguang Xu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Roth, H.R. et al. (2021). Federated Whole Prostate Segmentation in MRI with Personalized Neural Architectures. 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_34

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-87199-4_34

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-87198-7

  • Online ISBN: 978-3-030-87199-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics