Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
skip to main content
10.1145/3404512.3404518acmotherconferencesArticle/Chapter ViewAbstractPublication PagesbdeConference Proceedingsconference-collections
research-article

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

Published: 05 July 2020 Publication 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.
[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)
[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.
[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.
[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.
[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:1811.02629
[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.
[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.
[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).
[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).
[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)
[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.
[13]
Doersch, C. (2016). Tutorial on variational auto-encoders. arXiv preprint arXiv: 1606.05908.
[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).
[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).
[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.
[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).
[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.
[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.
[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.
[21]
Ketkar, N. (2017). Introduction to pytorch. In Deep learning with python (pp. 195--208). Apress, Berkeley, CA.
[22]
Kingma, D. P., & Welling, M. (2013). Auto-encoding variational bayes. arXiv preprint arXiv: 1312.6114.
[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.
[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.
[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.
[26]
Myronenko, A. (2018, September). 3D MRI brain tumor segmentation using autoencoder regularization. In International MICCAI Brainlesion Workshop (pp. 311--320). Springer, Cham.
[27]
Rajput, Anuj & Goodman, Michael & Bangiyev, Lev. (2018). High-Grade Glioma. 10.1007/978-3-319-65106-4_112.
[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.
[29]
Simonyan, K., & Zisserman, A. (2014). Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv: 1409.1556.
[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)
[31]
Wu, Y., & He, K. (2018). Group normalization. In Proceedings of the European Conference on Computer Vision (ECCV) (pp. 3--19).
[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.
[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).

Cited By

View all
  • (2022)Innovative Detection of Brain Tumor using Conventional Neural Networks Classifier and comparison with Support Vector Machine Classifier2022 14th International Conference on Mathematics, Actuarial Science, Computer Science and Statistics (MACS)10.1109/MACS56771.2022.10022328(1-5)Online publication date: 12-Nov-2022

Index Terms

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

    Recommendations

    Comments

    Information & Contributors

    Information

    Published In

    cover image ACM Other conferences
    BDE '20: Proceedings of the 2020 2nd International Conference on Big Data Engineering
    May 2020
    146 pages
    ISBN:9781450377225
    DOI:10.1145/3404512
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

    Publisher

    Association for Computing Machinery

    New York, NY, United States

    Publication History

    Published: 05 July 2020

    Permissions

    Request permissions for this article.

    Check for updates

    Author Tags

    1. 3D MRI volume
    2. Adaptive Weighted Loss
    3. Auto-encoder
    4. BRATS 2018
    5. Medical image segmentation

    Qualifiers

    • Research-article
    • Research
    • Refereed limited

    Conference

    BDE 2020

    Contributors

    Other Metrics

    Bibliometrics & Citations

    Bibliometrics

    Article Metrics

    • Downloads (Last 12 months)7
    • Downloads (Last 6 weeks)0
    Reflects downloads up to 30 Dec 2024

    Other Metrics

    Citations

    Cited By

    View all
    • (2022)Innovative Detection of Brain Tumor using Conventional Neural Networks Classifier and comparison with Support Vector Machine Classifier2022 14th International Conference on Mathematics, Actuarial Science, Computer Science and Statistics (MACS)10.1109/MACS56771.2022.10022328(1-5)Online publication date: 12-Nov-2022

    View Options

    Login options

    View options

    PDF

    View or Download as a PDF file.

    PDF

    eReader

    View online with eReader.

    eReader

    Media

    Figures

    Other

    Tables

    Share

    Share

    Share this Publication link

    Share on social media