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Adaptive Weighted Loss Makes Brain Tumors Segmentation More Accurate in 3D MRI Volume

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Published:05 July 2020Publication History

ABSTRACT

Accurately segmenting brain tumors in Magnetic Resonance Imaging (MRI) volume can benefit the diagnosis, monitoring, and surgery planning of the disease. Manual delineation practices require anatomical knowledge, are expensive, time consuming and can be inaccurate due to human error. In the data era, machines with learning capabilities can achieve automatic brain tumor segmentation in MRI volume with promising performance on large region. However, it is not very effective for tumor segmentation on small region. Although more and more methods use pixel-level loss to guide algorithms to pay more attention to accurate segmentation of small regions, this problem still exists. In this paper, we propose an adaptive weighted loss, which can automatically adjust the proportion of loss generated by different region segmentation, thereby making small region segmentation more accurate. We added the adaptive weighted loss to a 3D MRI brain tumor segmentation network using auto-encoder regularization (3D-AE), and performed extensive validation on the MICCAI Brain Tumor Segmentation Challenge 2018 dataset (BRATS 2018). The achieved dice score is 0.769 for core tumor, 0.904 for the whole tumor and 0.887 for enhanced tumor. The overall results show better performance than the state-of-the-art in both dice score and precision on BRATS 2018.

References

  1. Alqazzaz, S., Sun, X., Yang, X., & Nokes, L. (2019). Automated brain tumor segmentation on multi-modal MR image using SegNet. Computational Visual Media, 5(2), 209--219.Google ScholarGoogle ScholarCross RefCross Ref
  2. Arshad Javed, Wang Yin Chai, (2014). Abdulhameed Rakan Alenezi, and Narayan Kulathuramaiyer, "Enhancement of Magnetic Resonance Images Using Soft Computing Based Segmentation," International Journal of Machine Learning and Computing vol.4, no. 1, (pp. 73--78)Google ScholarGoogle ScholarCross RefCross Ref
  3. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J. S., ... & Davatzikos, C. (2017). Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Scientific data, 4, 170117.Google ScholarGoogle Scholar
  4. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., ... & Davatzikos, C. (2017). Segmentation labels and radiomic features for the pre-operative scans of the TCGA-GBM collection. The Cancer Imaging Archive.Google ScholarGoogle Scholar
  5. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., ... & Davatzikos, C. (2017). Segmentation labels and radiomic features for the pre-operative scans of the TCGA-LGG collection. The Cancer Imaging Archive, 286.Google ScholarGoogle Scholar
  6. Bakas, S., Reyes, M., Jakab, A., Bauer, S., Rempfler, M., Crimi, A., ... & Prastawa, M. (2018). Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge. arXiv preprint arXiv:1811.02629Google ScholarGoogle Scholar
  7. Banerjee, S., Mitra, S., Masulli, F., & Rovetta, S. (2019). Deep Radiomics for Brain Tumor Detection and Classification from Multi-Sequence MRI. arXiv preprint arXiv:1903.09240.Google ScholarGoogle Scholar
  8. Bian, C., Yang, X., Ma, J., Zheng, S., Liu, Y. A., Nezafat, R., ... & Zheng, Y. (2018, September). Pyramid network with online hard example mining for accurate left atrium segmentation. In International Workshop on Statistical Atlases and Computational Models of the Heart (pp. 237--245). Springer, Cham.Google ScholarGoogle Scholar
  9. Chen, L. C., Zhu, Y., Papandreou, G., Schroff, F., & Adam, H. (2018). Encoder-decoder with atrous separable convolution for semantic image segmentation. In Proceedings of the European conference on computer vision (ECCV) (pp. 801--818).Google ScholarGoogle ScholarDigital LibraryDigital Library
  10. Chollet, F. (2017). Xception: Deep learning with depthwise separable convolutions. In Proceedings of the IEEE conference on computer vision and pattern recognition (pp. 1251--1258).Google ScholarGoogle ScholarCross RefCross Ref
  11. Debapriya Hazra and Yungcheol Byun, (2020). "Brain Tumor Detection Using Skull Stripping and U-Net Architecture," International Journal of Machine Learning and Computing vol. 10, no. 2, (pp. 400--405)Google ScholarGoogle Scholar
  12. Dhiman, Adarsh & Satpute, Prof. (2019). Brain Tumor Segmentation in MRI Images. International Journal of Research in Advent Technology. 7. 10--14. 10.32622/ijrat.78201916.Google ScholarGoogle ScholarCross RefCross Ref
  13. Doersch, C. (2016). Tutorial on variational auto-encoders. arXiv preprint arXiv: 1606.05908.Google ScholarGoogle Scholar
  14. Goodfellow, I., Pouget-Abadie, J., Mirza, M., Xu, B., Warde-Farley, D., Ozair, S., ... & Bengio, Y. (2014). Generative adversarial nets. In Advances in neural information processing systems (pp. 2672--2680).Google ScholarGoogle ScholarDigital LibraryDigital Library
  15. He, K., Gkioxari, G., Dollár, P., & Girshick, R. (2017). Mask r-cnn. In Proceedings of the IEEE international conference on computer vision (pp. 2961--2969).Google ScholarGoogle ScholarCross RefCross Ref
  16. He, K., Zhang, X., Ren, S., & Sun, J. (2016, October). Identity mappings in deep residual networks. In European conference on computer vision (pp. 630--645). Springer, Cham.Google ScholarGoogle ScholarCross RefCross Ref
  17. Huang, G., Liu, Z., Van Der Maaten, L., & Weinberger, K. Q. (2017). Densely connected convolutional networks. In Proceedings of the IEEE conference on computer vision and pattern recognition (pp. 4700--4708).Google ScholarGoogle ScholarCross RefCross Ref
  18. Isensee, F., Kickingereder, P., Wick, W., Bendszus, M., & Maier-Hein, K. H. (2017, September). Brain tumor segmentation and radiomics survival prediction: Contribution to the brats 2017 challenge. In International MICCAI Brainlesion Workshop (pp. 287--297). Springer, Cham.Google ScholarGoogle Scholar
  19. Kamnitsas, K., Ledig, C., Newcombe, V. F., Simpson, J. P., Kane, A. D., Menon, D. K., ... & Glocker, B. (2017). Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation. Medical image analysis, 36, 61--78.Google ScholarGoogle Scholar
  20. Kao, P. Y., Ngo, T., Zhang, A., Chen, J. W., & Manjunath, B. S. (2018, September). Brain tumor segmentation and tractographic feature extraction from structural mr images for overall survival prediction. In International MICCAI Brainlesion Workshop (pp. 128--141). Springer, Cham.Google ScholarGoogle Scholar
  21. Ketkar, N. (2017). Introduction to pytorch. In Deep learning with python (pp. 195--208). Apress, Berkeley, CA.Google ScholarGoogle ScholarCross RefCross Ref
  22. Kingma, D. P., & Welling, M. (2013). Auto-encoding variational bayes. arXiv preprint arXiv: 1312.6114.Google ScholarGoogle Scholar
  23. McKinley, R., Meier, R., & Wiest, R. (2018, September). Ensembles of densely-connected CNNs with label-uncertainty for brain tumor segmentation. In International MICCAI Brainlesion Workshop (pp. 456--465). Springer, Cham.Google ScholarGoogle Scholar
  24. Menze, B. H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., ... & Lanczi, L. (2014). The multimodal brain tumor image segmentation benchmark (BRATS). IEEE transactions on medical imaging, 34(10), 1993--2024.Google ScholarGoogle Scholar
  25. Milletari, F., Navab, N., & Ahmadi, S. A. (2016, October). V-net: Fully convolutional neural networks for volumetric medical image segmentation. In 2016 Fourth International Conference on 3D Vision (3DV) (pp. 565--571). IEEE.Google ScholarGoogle ScholarCross RefCross Ref
  26. Myronenko, A. (2018, September). 3D MRI brain tumor segmentation using autoencoder regularization. In International MICCAI Brainlesion Workshop (pp. 311--320). Springer, Cham.Google ScholarGoogle Scholar
  27. Rajput, Anuj & Goodman, Michael & Bangiyev, Lev. (2018). High-Grade Glioma. 10.1007/978-3-319-65106-4_112.Google ScholarGoogle Scholar
  28. Ronneberger, O., Fischer, P., & Brox, T. (2015, October). U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention (pp. 234--241). Springer, Cham.Google ScholarGoogle ScholarCross RefCross Ref
  29. Simonyan, K., & Zisserman, A. (2014). Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv: 1409.1556.Google ScholarGoogle Scholar
  30. Sreedhar Kollem, Katta Rama Linga Reddy, and Duggirala Srinivasa Rao. (2019). A Review of Image Denoising and Segmentation Methods Based on Medical Images. International Journal of Machine Learning and Computing vol. 9, no. 3, (pp. 288--295)Google ScholarGoogle ScholarCross RefCross Ref
  31. Wu, Y., & He, K. (2018). Group normalization. In Proceedings of the European Conference on Computer Vision (ECCV) (pp. 3--19).Google ScholarGoogle ScholarDigital LibraryDigital Library
  32. Xue, Y., Xu, T., Zhang, H., Long, L. R., & Huang, X. (2018). Segan: Adversarial network with multi-scale 11 loss for medical image segmentation. Neuroinformatics, 16(3-4), 383--392.Google ScholarGoogle ScholarCross RefCross Ref
  33. Zhao, H., Shi, J., Qi, X., Wang, X., & Jia, J. (2017). Pyramid scene parsing network. In Proceedings of the IEEE conference on computer vision and pattern recognition (pp. 2881--2890).Google ScholarGoogle ScholarCross RefCross Ref

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      BDE '20: Proceedings of the 2020 2nd International Conference on Big Data Engineering
      May 2020
      146 pages
      ISBN:9781450377225
      DOI:10.1145/3404512

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      Publication History

      • Published: 5 July 2020

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