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Deep pattern-based tumor segmentation in brain MRIs

  • S.I. : Emerging trends in AI & ML
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Abstract

It is still hard to deal with artifacts in magnetic resonance images (MRIs), particularly when the latter are to be segmented. This paper introduces a novel deep-based scheme for tumor segmentation in brain MRIs. According to the proposed scheme, a large set of partial sub-images are paved form sliced from an MRI volume then inputted to an ensemble of convolutional neural networks (CNNs) in order to label the voxels in the centers of the sub-images, according to the classes to which they should belong. Partial sub-images, that capture local patterns around central voxels, have allowed to speed-up both the training and the prediction steps, allowing efficient use of such a scheme for real MRI-based tumor diagnosis. Experiments were performed using the BraTS (brain tumor segmentation) database, where the obtained results show that the proposed scheme allows both fast and accurate brain tumor detection and segmentation in pathological MRIs.

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References

  1. Amin J, Sharif M, Yasmin M, Fernandes SL (2018) Big data analysis for brain tumor detection: deep convolutional neural networks. Fut Gener Comput Syst 87:290–297. https://doi.org/10.1016/j.future.2018.04.065

    Article  Google Scholar 

  2. Bennai MT, Guessoum Z, Mazouzi S, Cormier S, Mezghiche M (2020) A stochastic multi-agent approach for medical-image segmentation: application to tumor segmentation in brain MR images. Artif Intell Med 110:101980. https://doi.org/10.1016/j.artmed.2020.101980

    Article  Google Scholar 

  3. Bezdek J, Ehrlich R, Full WE (1984) FCM: the fuzzy C-means clustering algorithm. Comput Geosci 10:191–203

    Article  Google Scholar 

  4. Bringmann B, Nijssen S, Zimmermann A (2010) From local patterns to classification models. In: Dzeroski S, Goethals B, Panov P (eds) Inductive databases and constraint-based data mining. Springer, pp. 127–154. https://doi.org/10.1007/978-1-4419-7738-0_6

  5. Chen G, Li Q, Shi F, Rekik I, Pan Z (2020) RFDCR: automated brain lesion segmentation using cascaded random forests with dense conditional random fields. NeuroImage 211:116620. https://doi.org/10.1016/j.neuroimage.2020.116620

    Article  Google Scholar 

  6. Choudhury CL, Mahanty C, Kumar R, Mishra BK (2020) Brain tumor detection and classification using convolutional neural network and deep neural network. In: 2020 international conference on computer science, engineering and applications (ICCSEA), pp 1–4. https://doi.org/10.1109/ICCSEA49143.2020.9132874

  7. Coupé P, Mansencal B, Clément M, Giraud R, de Senneville BD, Ta VT, Lepetit V, Manjon JV (2020) AssemblyNet: a large ensemble of CNNs for 3D whole brain MRI segmentation. NeuroImage 219:117026. https://doi.org/10.1016/j.neuroimage.2020.117026

    Article  Google Scholar 

  8. de Brébisson A, Montana G (2015) Deep neural networks for anatomical brain segmentation. In: Proceedings of the IEEE conference on computer vision and pattern recognition workshops, pp 20–28

  9. Freund Y, Schapire R (1999) A short introduction to boosting. J Jpn Soc Artif Intell 14(771–780):1612

    Google Scholar 

  10. Fülöp T, Győrfi Á, Surányi B, Kovács L, Szilágyi L (2020) Brain tumor segmentation from MRI data using ensemble learning and multi-atlas. In: 2020 IEEE 18th world symposium on applied machine intelligence and informatics (SAMI), pp 111–116. https://doi.org/10.1109/SAMI48414.2020.9108752

  11. Gordillo N, Montseny E, Sobrevilla P (2013) State of the art survey on MRI brain tumor segmentation. Magn Resonance Imaging 31(8):1426–1438. https://doi.org/10.1016/j.mri.2013.05.002

    Article  Google Scholar 

  12. Hornik K (1991) Approximation capabilities of multilayer feedforward networks. Neural Netw 4(2):251–257. https://doi.org/10.1016/0893-6080(91)90009-T

    Article  MathSciNet  Google Scholar 

  13. Hu K, Gan Q, Zhang Y, Deng S, Xiao F, Huang W, Cao C, Gao X (2019) Brain tumor segmentation using multi-cascaded convolutional neural networks and conditional random field. IEEE Access 7:92615–92629. https://doi.org/10.1109/ACCESS.2019.2927433

    Article  Google Scholar 

  14. Kaleem M, Sanaullah M, Hussain MA, Jaffar MA, Choi TS (2012) Segmentation of brain tumor tissue using marker controlled watershed transform method. In: Chowdhry BS, Shaikh FK, Hussain DMA, Uqaili MA (eds) Emerging trends and applications in information communication technologies. Springer, Berlin, pp 222–227

    Chapter  Google Scholar 

  15. Knerr S, Personnaz L, Dreyfus G (1990) Single-layer learning revisited: a stepwise procedure for building and training a neural network. In: Fogelman Soulié F, Hérault J (eds) Neurocomputing: algorithms, architectures and applications, NATO ASI Series, vol F68. Springer, Berlin, pp 41–50

    Chapter  Google Scholar 

  16. Kumar N, Kaur N, Gupta D (2020) Major convolutional neural networks in image classification: a survey. In: Dutta M, Krishna CR, Kumar R, Kalra M (eds) Proceedings of international conference on iot inclusive life (ICIIL 2019), NITTTR Chandigarh, India. Springer Singapore, Singapore, pp 243–258

  17. Kwon D, Shinohara RT, Akbari H, Davatzikos C (2014) Combining generative models for multifocal glioma segmentation and registration. In: Golland P, Hata N, Barillot C, Hornegger J, Howe R (eds) Medical image computing and computer-assisted intervention—MICCAI 2014. Springer, Cham, pp 763–770

    Chapter  Google Scholar 

  18. Li SZ (2009) Markov random field modeling in image analysis. Springer, Berlin

    MATH  Google Scholar 

  19. Menze B, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, Kirby J, Burren Y, Porz N, Slotboom J, Wiest R, Lanczi L, Gerstner E, Weber MA, Arbel T, Avants B, Ayache N, Buendia P, Collins L, Cordier N, Corso J, Criminisi A, Das T, Delingette H, Demiralp C, Durst C, Dojat M, Doyle S, Festa J, Forbes F, Geremia E, Glocker B, Golland P, Guo X, Hamamci A, Iftekharuddin K, Jena R, John N, Konukoglu E, Lashkari D, Antonio Mariz J, Meier R, Pereira S, Precup D, Price SJ, Riklin-Raviv T, Reza S, Ryan M, Schwartz L, Shin HC, Shotton J, Silva C, Sousa N, Subbanna N, Szekely G, Taylor T, Thomas O, Tustison N, Unal G, Vasseur F, Wintermark M, Hye Ye D, Zhao L, Zhao B, Zikic D, Prastawa M, Reyes M, Van Leemput K (2014) The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans Med Imag. https://doi.org/10.1109/TMI.2014.2377694

  20. Oliveira GC, Varoto R, Cliquet Jr A (2018) Brain tumor segmentation in magnetic resonance images using genetic algorithm clustering and AdaBoost classifier. In: Proceedings of the 11th international joint conference on biomedical engineering systems and technologies—BioImaging, vol 2. INSTICC, SciTePress, pp 77–82. https://doi.org/10.5220/0006534900770082

  21. Pan Y, Huang W, Lin Z, Zhu W, Zhou J, Wong J, Ding Z (2015) Brain tumor grading based on neural networks and convolutional neural networks. In: 2015 37th annual international conference of the IEEE engineering in medicine and biology society (EMBC), pp 699–702. https://doi.org/10.1109/EMBC.2015.7318458

  22. Park J, Sandberg IW (1993) Approximation and radial-basis-function networks. Neural Comput 5(2):305–316. https://doi.org/10.1162/neco.1993.5.2.305

    Article  Google Scholar 

  23. Pereia S, Pinto A, Alves V, Silva CA (2016) Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans Med Imaging 35(5):1240–1251. https://doi.org/10.1109/TMI.2016.2538465

    Article  Google Scholar 

  24. Rabeh AB, Benzarti F, Amiri H (2017) Segmentation of brain MRI using active contour model. Int J Imaging Syst Technol 27(1):3–11. https://doi.org/10.1002/IMA.22205

    Article  Google Scholar 

  25. Rajasree R, Columbus CC (2015) Brain tumour image segmentation and classification system based on the modified AdaBoost classifier. Int J Appl Eng Res 10(14):11911–11916

    Google Scholar 

  26. Roma AA, Diaz De Vivar A, Park KJ, Alvarado-Cabrero I, Rasty G, Chanona-Vilchis JG, Mikami Y, Hong SR, Teramoto N, Ali-Fehmi R, Rutgers JKL, Barbuto D, Silva EG (2015) Invasive endocervical adenocarcinoma: a new pattern-based classification system with important clinical significance. Am J Surg Pathol 39(5):667–672. https://doi.org/10.1097/pas.0000000000000402

    Article  Google Scholar 

  27. Schölkopf B, Burges C, Vapnik V (1995) Extracting support data for a given task. In: Proceedings of the 1st international conference on knowledge discovery & data mining, pp 252–257

  28. Subbanna NK, Precup D, Collins DL, Arbel T (2013) Hierarchical probabilistic gabor and MRF segmentation of brain tumours in MRI volumes. In: Mori K, Sakuma I, Sato Y, Barillot C, Navab N (eds) Medical image computing and computer-assisted intervention—MICCAI 2013. Springer, Berlin, pp 751–758

    Google Scholar 

  29. Yamanakkanavar N, Choi JY, Lee B (2020) MRI segmentation and classification of human brain using deep learning for diagnosis of alzheimer’s disease: a survey. Sensors 20(11):3243. https://doi.org/10.3390/s20113243

    Article  Google Scholar 

  30. Yousaf S, RaviPrakash H, Anwar SM, Sohail N, Bagci U (2020) State-of-the-art in brain tumor segmentation and current challenges. In: Kia SM, Mohy-ud-Din H, Abdulkadir A, Bass C, Habes M, Rondina JM, Tax CMW, Wang H, Wolfers T, Rathore S, Ingalhalikar M (eds) Machine learning in clinical neuroimaging and radiogenomics in neuro-oncology—third international workshop, MLCN 2020, and second international workshop, RNO-AI 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 4-8, 2020, Proceedings, Lecture notes in computer science, vol 12449. Springer, Berlin, pp 189–198. https://doi.org/10.1007/978-3-030-66843-3_19

  31. Zhang D, Huang G, Zhang Q, Han J, Han J, Wang Y, Yu Y (2020) Exploring task structure for brain tumor segmentation from multi-modality MR images. IEEE Trans Image Process 29:9032–9043. https://doi.org/10.1109/TIP.2020.3023609

    Article  Google Scholar 

  32. Zhang D, Huang G, Zhang Q, Han J, Han J, Yu Y (2021) Cross-modality deep feature learning for brain tumor segmentation. Pattern Recognit 110:107562. https://doi.org/10.1016/j.patcog.2020.107562

    Article  Google Scholar 

  33. Zhang W, Li R, Deng H, Wang L, Lin W, Ji S, Shen D (2015) Deep convolutional neural networks for multi-modality isointense infant brain image segmentation. Neuroimage 108:214–224

    Article  Google Scholar 

  34. Zhou C, Cule B, Goethals B (2016) Pattern based sequence classification. IEEE Trans Knowl Data Eng 28:1285–1298

    Article  Google Scholar 

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Correspondence to Nadjet Bouchaour.

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Bouchaour, N., Mazouzi, S. Deep pattern-based tumor segmentation in brain MRIs. Neural Comput & Applic 34, 14317–14326 (2022). https://doi.org/10.1007/s00521-022-07422-y

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