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End-to-End Evidential-Efficient Net for Radiomics Analysis of Brain MRI to Predict Oncogene Expression and Overall Survival

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Medical Image Computing and Computer Assisted Intervention – MICCAI 2022 (MICCAI 2022)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 13433))

Abstract

We presented a novel radiomics approach using multimodality MRI to predict the expression of an oncogene (O6-Methylguanine-DNA methyltransferase, MGMT) and overall survival (OS) of glioblastoma (GBM) patients. Specifically, we employed an EffNetV2-T, which was down scaled and modified from EfficientNetV2, as the feature extractor. Besides, we used evidential layers based to control the distribution of prediction outputs. The evidential layers help to classify the high-dimensional radiomics features to predict the methylation status of MGMT and OS. Tests showed that our model achieved an accuracy of 0.844, making it possible to use as a clinic-enabling technique in the diagnosing and management of GBM. Comparison results indicated that our method performed better than existing work.

X. Gu and X. Xu were partially supported by NIH R01LM012434. X. Gu was partially supported by NSF 2115095, NSF 1762287, NIH 92025.

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References

  1. Agravat, R.R., Raval, M.S.: Brain tumor segmentation and survival prediction. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 338–348. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_32

    Chapter  Google Scholar 

  2. Amini, A., Schwarting, W., Soleimany, A., Rus, D.: Deep evidential regression. Adv. Neural. Inf. Process. Syst. 33, 14927–14937 (2020)

    Google Scholar 

  3. Baid, U., et al.: The RSNA-ASNR-MICCAI BraTS 2021 benchmark on brain tumor segmentation and radiogenomic classification. arXiv preprint arXiv:2107.02314 (2021)

  4. Baid, U., et al.: Deep learning radiomics algorithm for gliomas (DRAG) model: a novel approach using 3D UNET based deep convolutional neural network for predicting survival in gliomas. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 369–379. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_33

    Chapter  Google Scholar 

  5. Bakas, S., et al.: Advancing the cancer genome atlas glioma MRI collections with expert segmentation labels and radiomic features. Sci. Data 4(1), 1–13 (2017)

    Article  Google Scholar 

  6. 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)

  7. Carver, E., et al.: Automatic brain tumor segmentation and overall survival prediction using machine learning algorithms. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 406–418. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_36

    Chapter  Google Scholar 

  8. Chang, P., et al.: Deep-learning convolutional neural networks accurately classify genetic mutations in gliomas. Am. J. Neuroradiol. 39(7), 1201–1207 (2018)

    Article  Google Scholar 

  9. Feng, X., Dou, Q., Tustison, N., Meyer, C.: Brain tumor segmentation with uncertainty estimation and overall survival prediction. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 304–314. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_29

    Chapter  Google Scholar 

  10. 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 

  11. Han, L., Kamdar, M.R.: MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks. In: Pacific Symposium on Biocomputing 2018: Proceedings of the Pacific Symposium, pp. 331–342. World Scientific (2018)

    Google Scholar 

  12. He, K., Zhang, X., Ren, S., Sun, J.: Deep residual learning for image recognition. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 770–778 (2016)

    Google Scholar 

  13. Hermoza, R., Maicas, G., Nascimento, J.C., Carneiro, G.: Post-hoc overall survival time prediction from brain MRI. In: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), pp. 1476–1480. IEEE (2021)

    Google Scholar 

  14. Hu, L.S., et al.: Radiogenomics to characterize regional genetic heterogeneity in glioblastoma. Neuro-Oncol. 19(1), 128–137 (2016). https://doi.org/10.1093/neuonc/now135

    Article  Google Scholar 

  15. Kendall, A., Gal, Y.: What uncertainties do we need in Bayesian deep learning for computer vision? Adv. Neural Inf. Process. Syst. 30, 5580–5590 (2017)

    Google Scholar 

  16. Korfiatis, P., Kline, T.L., Lachance, D.H., Parney, I.F., Buckner, J.C., Erickson, B.J.: Residual deep convolutional neural network predicts MGMT methylation status. J. Digit. Imaging 30(5), 622–628 (2017)

    Article  Google Scholar 

  17. Levner, I., Drabycz, S., Roldan, G., De Robles, P., Cairncross, J.G., Mitchell, R.: Predicting MGMT methylation status of glioblastomas from MRI texture. In: Yang, G.-Z., Hawkes, D., Rueckert, D., Noble, A., Taylor, C. (eds.) MICCAI 2009. LNCS, vol. 5762, pp. 522–530. Springer, Heidelberg (2009). https://doi.org/10.1007/978-3-642-04271-3_64

    Chapter  Google Scholar 

  18. 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 

  19. Saeed, N., Hardan, S., Abutalip, K., Yaqub, M.: Is it possible to predict MGMT promoter methylation from brain tumor MRI scans using deep learning models? Proc. Mach. Learn. Res. 1, 16 (2022)

    Google Scholar 

  20. Sensoy, M., Kaplan, L., Kandemir, M.: Evidential deep learning to quantify classification uncertainty. Adv. Neural Inf. Process. Syst. 31, 3183–3193 (2018)

    Google Scholar 

  21. Stupp, R., et al.: Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N. Engl. J. Med. 352(10), 987–996 (2005)

    Article  Google Scholar 

  22. Suter, Y., et al.: Deep learning versus classical regression for brain tumor patient survival prediction. In: Crimi, A., Bakas, S., Kuijf, H., Keyvan, F., Reyes, M., van Walsum, T. (eds.) BrainLes 2018. LNCS, vol. 11384, pp. 429–440. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-11726-9_38

    Chapter  Google Scholar 

  23. Tan, M., Le, Q.: EfficientNetV2: smaller models and faster training. In: International Conference on Machine Learning, pp. 10096–10106. PMLR (2021)

    Google Scholar 

  24. Taylor, O.G., Brzozowski, J.S., Skelding, K.A.: Glioblastoma multiforme: an overview of emerging therapeutic targets. Front. Oncol. 9, 963 (2019)

    Article  Google Scholar 

  25. Wang, F., Jiang, R., Zheng, L., Meng, C., Biswal, B.: 3D U-net based brain tumor segmentation and survival days prediction. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11992, pp. 131–141. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46640-4_13

    Chapter  Google Scholar 

  26. Wang, S., Dai, C., Mo, Y., Angelini, E., Guo, Y., Bai, W.: Automatic brain tumour segmentation and biophysics-guided survival prediction. In: Crimi, A., Bakas, S. (eds.) BrainLes 2019. LNCS, vol. 11993, pp. 61–72. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-46643-5_6

    Chapter  Google Scholar 

  27. Yogananda, C.G.B., et al.: MRI-based deep learning method for determining methylation status of the o6-methylguanine-DNA methyltransferase promoter outperforms tissue based methods in brain gliomas. bioRxiv (2020)

    Google Scholar 

  28. Zhou, T., et al.: \(\text{ M}^2\text{ Net }\): multi-modal multi-channel network for overall survival time prediction of brain tumor patients. In: Martel, A.L., et al. (eds.) MICCAI 2020. LNCS, vol. 12262, pp. 221–231. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-59713-9_22

    Chapter  Google Scholar 

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Feng, Y., Wang, J., An, D., Gu, X., Xu, X., Zhang, M. (2022). End-to-End Evidential-Efficient Net for Radiomics Analysis of Brain MRI to Predict Oncogene Expression and Overall Survival. In: Wang, L., Dou, Q., Fletcher, P.T., Speidel, S., Li, S. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2022. MICCAI 2022. Lecture Notes in Computer Science, vol 13433. Springer, Cham. https://doi.org/10.1007/978-3-031-16437-8_27

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