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SimCLR-based Self-Supervised Learning Approach for Limited Brain MRI and Unlabeled Images

Year 2024, , 1304 - 1313, 31.12.2024
https://doi.org/10.17798/bitlisfen.1558069

Abstract

In this study, a SimCLR-based model is proposed for the classification of unlabeled brain tumor images in medical imaging using a self-supervised learning (SSL) technique. Additionally, the performances of different SSL techniques (Barlow Twins, NnCLR, and SimCLR) are analyzed to evaluate the performance of the proposed model. Three different datasets, consisting of pituitary, meningioma, and glioma brain tumors as well as non-tumor images, were used as the dataset. Out of a total of 7,671 images, 6,128 were used as unlabeled data, and the model was trained with both labeled and unlabeled data. The proposed model achieved high performance with unlabeled data, reducing the need for manual labeling. As a result, the model demonstrated superior performance compared to other models, with high performance values such as 99.35% c_acc and 96.31% p_acc.

Ethical Statement

The study is complied with research and publication ethics.

References

  • [1] M. Toğaçar, N. Muzoğlu, B. Ergen, B. S. B. Yarman, and A. M. Halefoğlu, “Detection of COVID-19 findings by the local interpretable model-agnostic explanations method of types-based activations extracted from CNNs,” Biomed. Signal Process. Control, vol. 71, p. 103128, Jan. 2022, doi: 10.1016/j.bspc.2021.103128.
  • [2] G. Celik, “Detection of Covid-19 and other pneumonia cases from CT and X-ray chest images using deep learning based on feature reuse residual block and depthwise dilated convolutions neural network,” Appl. Soft Comput., vol. 133, p. 109906, Jan. 2023, doi: 10.1016/j.asoc.2022.109906.
  • [3] E. Başaran, “A new brain tumor diagnostic model: Selection of textural feature extraction algorithms and convolution neural network features with optimization algorithms,” Comput. Biol. Med., vol. 148, p. 105857, Sep. 2022, doi: 10.1016/j.compbiomed.2022.105857.
  • [4] G. Çelik and M. F. Talu, “A new 3D MRI segmentation method based on Generative Adversarial Network and Atrous Convolution,” Biomed. Signal Process. Control, vol. 71, p. 103155, Jan. 2022, doi: 10.1016/j.bspc.2021.103155.
  • [5] S. Altun Güven and M. F. Talu, “Brain MRI high resolution image creation and segmentation with the new GAN method,” Biomed. Signal Process. Control, vol. 80, p. 104246, Feb. 2023, doi: 10.1016/j.bspc.2022.104246.
  • [6] Z. Bozdag and M. F. Talu, “Pyramidal position attention model for histopathological image segmentation,” Biomed. Signal Process. Control, vol. 80, p. 104374, Feb. 2023, doi: 10.1016/j.bspc.2022.104374.
  • [7] G. Celik and E. Başaran, “Proposing a new approach based on convolutional neural networks and random forest for the diagnosis of Parkinson’s disease from speech signals,” Appl. Acoust., vol. 211, p. 109476, Aug. 2023, doi: 10.1016/j.apacoust.2023.109476.
  • [8] S. Mavaddati, “Voice-based age, gender, and language recognition based on ResNet deep model and transfer learning in spectro-temporal domain,” Neurocomputing, vol. 580, p. 127429, May 2024, doi: 10.1016/j.neucom.2024.127429.
  • [9] M. A. Islam, M. Z. Hasan Majumder, M. A. Hussein, K. M. Hossain, and M. S. Miah, “A review of machine learning and deep learning algorithms for Parkinson’s disease detection using handwriting and voice datasets,” Heliyon, vol. 10, no. 3, p. e25469, Feb. 2024, doi: 10.1016/j.heliyon.2024.e25469.
  • [10] R. B. Rahman, S. A. Tanim, N. Alfaz, T. E. Shrestha, M. S. U. Miah, and M. F. Mridha, “A comprehensive dental dataset of six classes for deep learning based object detection study,” Data Br., vol. 57, p. 110970, Dec. 2024, doi: 10.1016/j.dib.2024.110970.
  • [11] B. Ganga, L. B.T., and V. K.R., “Object detection and crowd analysis using deep learning techniques: Comprehensive review and future directions,” Neurocomputing, vol. 597, p. 127932, Sep. 2024, doi: 10.1016/j.neucom.2024.127932.
  • [12] K. Kantor and M. Morzy, “Machine learning and natural language processing in clinical trial eligibility criteria parsing: a scoping review,” Drug Discov. Today, vol. 29, no. 10, p. 104139, Oct. 2024, doi: 10.1016/j.drudis.2024.104139.
  • [13] A. Montejo-Ráez, M. D. Molina-González, S. M. Jiménez-Zafra, M. Á. García-Cumbreras, and L. J. García-López, “A survey on detecting mental disorders with natural language processing: Literature review, trends and challenges,” Comput. Sci. Rev., vol. 53, p. 100654, Aug. 2024, doi: 10.1016/j.cosrev.2024.100654.
  • [14] L. Chen, P. Bentley, K. Mori, K. Misawa, M. Fujiwara, and D. Rueckert, “Self-supervised learning for medical image analysis using image context restoration,” Med. Image Anal., vol. 58, p. 101539, Dec. 2019, doi: 10.1016/j.media.2019.101539.
  • [15] A. Jaiswal, A. R. Babu, M. Z. Zadeh, D. Banerjee, and F. Makedon, “A Survey on Contrastive Self-Supervised Learning,” Technologies, vol. 9, no. 1, p. 2, Dec. 2020, doi: 10.3390/technologies9010002.
  • [16] X. Liu et al., “Self-supervised Learning: Generative or Contrastive,” IEEE Trans. Knowl. Data Eng., pp. 1–1, 2021, doi: 10.1109/TKDE.2021.3090866.
  • [17] I. Misra and L. van der Maaten, “Self-Supervised Learning of Pretext-Invariant Representations,” in 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), IEEE, Jun. 2020, pp. 6706–6716. doi: 10.1109/CVPR42600.2020.00674.
  • [18] Y. Wang, C. M. Albrecht, N. A. A. Braham, L. Mou, and X. X. Zhu, “Self-Supervised Learning in Remote Sensing: A review,” IEEE Geosci. Remote Sens. Mag., vol. 10, no. 4, pp. 213–247, Dec. 2022, doi: 10.1109/MGRS.2022.3198244.
  • [19] S. Shurrab and R. Duwairi, “Self-supervised learning methods and applications in medical imaging analysis: a survey,” PeerJ Comput. Sci., vol. 8, p. e1045, Jul. 2022, doi: 10.7717/peerj-cs.1045.
  • [20] V. R. de Sa, “Learning Classification with Unlabeled Data,” Adv. Neural Inf. Process. Syst., pp. 112–119, 1994, [Online]. Available: https://dl.acm.org/doi/10.5555/2987189.2987204
  • [21] S. Gupta, “Brain MRI Scans for brain tumor classification.” Accessed: Jan. 25, 2024. [Online]. Available: https://www.kaggle.com/datasets/shreyag1103/brain-mri-scans-for-brain-tumor-classification
  • [22] S. Bhuvaji, A. Kadam, P. Bhumkar, S. Dedge, and S. Kanchan, “Brain Tumor Classification (MRI).” Accessed: Jan. 12, 2024. [Online]. Available: https://www.kaggle.com/datasets/sartajbhuvaji/brain-tumor-classification-mri/data
  • [23] Thomas, “Brain tumors.” Accessed: Jan. 18, 2024. [Online]. Available: https://www.kaggle.com/datasets/thomasdubail/brain-tumors-256x256?select=Data
  • [24] T. Chen, S. Kornblith, M. Norouzi, and G. Hinton, “A Simple Framework for Contrastive Learning of Visual Representations,” Feb. 2020, [Online]. Available: http://arxiv.org/abs/2002.05709
  • [25] J. Zbontar, L. Jing, I. Misra, Y. LeCun, and S. Deny, “Barlow Twins: Self-Supervised Learning via Redundancy Reduction,” Mar. 2021, [Online]. Available: http://arxiv.org/abs/2103.03230
  • [26] D. Dwibedi, Y. Aytar, J. Tompson, P. Sermanet, and A. Zisserman, “With a Little Help from My Friends: Nearest-Neighbor Contrastive Learning of Visual Representations,” Apr. 2021, [Online]. Available: http://arxiv.org/abs/2104.14548
  • [27] A. van den Oord, Y. Li, and O. Vinyals, “Representation Learning with Contrastive Predictive Coding,” Jul. 2018.
  • [28] J. C. Triana-Martinez, J. Gil-González, J. A. Fernandez-Gallego, A. M. Álvarez-Meza, and C. G. Castellanos-Dominguez, “Chained Deep Learning Using Generalized Cross-Entropy for Multiple Annotators Classification,” Sensors, vol. 23, no. 7, p. 3518, Mar. 2023, doi: 10.3390/s23073518.
Year 2024, , 1304 - 1313, 31.12.2024
https://doi.org/10.17798/bitlisfen.1558069

Abstract

References

  • [1] M. Toğaçar, N. Muzoğlu, B. Ergen, B. S. B. Yarman, and A. M. Halefoğlu, “Detection of COVID-19 findings by the local interpretable model-agnostic explanations method of types-based activations extracted from CNNs,” Biomed. Signal Process. Control, vol. 71, p. 103128, Jan. 2022, doi: 10.1016/j.bspc.2021.103128.
  • [2] G. Celik, “Detection of Covid-19 and other pneumonia cases from CT and X-ray chest images using deep learning based on feature reuse residual block and depthwise dilated convolutions neural network,” Appl. Soft Comput., vol. 133, p. 109906, Jan. 2023, doi: 10.1016/j.asoc.2022.109906.
  • [3] E. Başaran, “A new brain tumor diagnostic model: Selection of textural feature extraction algorithms and convolution neural network features with optimization algorithms,” Comput. Biol. Med., vol. 148, p. 105857, Sep. 2022, doi: 10.1016/j.compbiomed.2022.105857.
  • [4] G. Çelik and M. F. Talu, “A new 3D MRI segmentation method based on Generative Adversarial Network and Atrous Convolution,” Biomed. Signal Process. Control, vol. 71, p. 103155, Jan. 2022, doi: 10.1016/j.bspc.2021.103155.
  • [5] S. Altun Güven and M. F. Talu, “Brain MRI high resolution image creation and segmentation with the new GAN method,” Biomed. Signal Process. Control, vol. 80, p. 104246, Feb. 2023, doi: 10.1016/j.bspc.2022.104246.
  • [6] Z. Bozdag and M. F. Talu, “Pyramidal position attention model for histopathological image segmentation,” Biomed. Signal Process. Control, vol. 80, p. 104374, Feb. 2023, doi: 10.1016/j.bspc.2022.104374.
  • [7] G. Celik and E. Başaran, “Proposing a new approach based on convolutional neural networks and random forest for the diagnosis of Parkinson’s disease from speech signals,” Appl. Acoust., vol. 211, p. 109476, Aug. 2023, doi: 10.1016/j.apacoust.2023.109476.
  • [8] S. Mavaddati, “Voice-based age, gender, and language recognition based on ResNet deep model and transfer learning in spectro-temporal domain,” Neurocomputing, vol. 580, p. 127429, May 2024, doi: 10.1016/j.neucom.2024.127429.
  • [9] M. A. Islam, M. Z. Hasan Majumder, M. A. Hussein, K. M. Hossain, and M. S. Miah, “A review of machine learning and deep learning algorithms for Parkinson’s disease detection using handwriting and voice datasets,” Heliyon, vol. 10, no. 3, p. e25469, Feb. 2024, doi: 10.1016/j.heliyon.2024.e25469.
  • [10] R. B. Rahman, S. A. Tanim, N. Alfaz, T. E. Shrestha, M. S. U. Miah, and M. F. Mridha, “A comprehensive dental dataset of six classes for deep learning based object detection study,” Data Br., vol. 57, p. 110970, Dec. 2024, doi: 10.1016/j.dib.2024.110970.
  • [11] B. Ganga, L. B.T., and V. K.R., “Object detection and crowd analysis using deep learning techniques: Comprehensive review and future directions,” Neurocomputing, vol. 597, p. 127932, Sep. 2024, doi: 10.1016/j.neucom.2024.127932.
  • [12] K. Kantor and M. Morzy, “Machine learning and natural language processing in clinical trial eligibility criteria parsing: a scoping review,” Drug Discov. Today, vol. 29, no. 10, p. 104139, Oct. 2024, doi: 10.1016/j.drudis.2024.104139.
  • [13] A. Montejo-Ráez, M. D. Molina-González, S. M. Jiménez-Zafra, M. Á. García-Cumbreras, and L. J. García-López, “A survey on detecting mental disorders with natural language processing: Literature review, trends and challenges,” Comput. Sci. Rev., vol. 53, p. 100654, Aug. 2024, doi: 10.1016/j.cosrev.2024.100654.
  • [14] L. Chen, P. Bentley, K. Mori, K. Misawa, M. Fujiwara, and D. Rueckert, “Self-supervised learning for medical image analysis using image context restoration,” Med. Image Anal., vol. 58, p. 101539, Dec. 2019, doi: 10.1016/j.media.2019.101539.
  • [15] A. Jaiswal, A. R. Babu, M. Z. Zadeh, D. Banerjee, and F. Makedon, “A Survey on Contrastive Self-Supervised Learning,” Technologies, vol. 9, no. 1, p. 2, Dec. 2020, doi: 10.3390/technologies9010002.
  • [16] X. Liu et al., “Self-supervised Learning: Generative or Contrastive,” IEEE Trans. Knowl. Data Eng., pp. 1–1, 2021, doi: 10.1109/TKDE.2021.3090866.
  • [17] I. Misra and L. van der Maaten, “Self-Supervised Learning of Pretext-Invariant Representations,” in 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), IEEE, Jun. 2020, pp. 6706–6716. doi: 10.1109/CVPR42600.2020.00674.
  • [18] Y. Wang, C. M. Albrecht, N. A. A. Braham, L. Mou, and X. X. Zhu, “Self-Supervised Learning in Remote Sensing: A review,” IEEE Geosci. Remote Sens. Mag., vol. 10, no. 4, pp. 213–247, Dec. 2022, doi: 10.1109/MGRS.2022.3198244.
  • [19] S. Shurrab and R. Duwairi, “Self-supervised learning methods and applications in medical imaging analysis: a survey,” PeerJ Comput. Sci., vol. 8, p. e1045, Jul. 2022, doi: 10.7717/peerj-cs.1045.
  • [20] V. R. de Sa, “Learning Classification with Unlabeled Data,” Adv. Neural Inf. Process. Syst., pp. 112–119, 1994, [Online]. Available: https://dl.acm.org/doi/10.5555/2987189.2987204
  • [21] S. Gupta, “Brain MRI Scans for brain tumor classification.” Accessed: Jan. 25, 2024. [Online]. Available: https://www.kaggle.com/datasets/shreyag1103/brain-mri-scans-for-brain-tumor-classification
  • [22] S. Bhuvaji, A. Kadam, P. Bhumkar, S. Dedge, and S. Kanchan, “Brain Tumor Classification (MRI).” Accessed: Jan. 12, 2024. [Online]. Available: https://www.kaggle.com/datasets/sartajbhuvaji/brain-tumor-classification-mri/data
  • [23] Thomas, “Brain tumors.” Accessed: Jan. 18, 2024. [Online]. Available: https://www.kaggle.com/datasets/thomasdubail/brain-tumors-256x256?select=Data
  • [24] T. Chen, S. Kornblith, M. Norouzi, and G. Hinton, “A Simple Framework for Contrastive Learning of Visual Representations,” Feb. 2020, [Online]. Available: http://arxiv.org/abs/2002.05709
  • [25] J. Zbontar, L. Jing, I. Misra, Y. LeCun, and S. Deny, “Barlow Twins: Self-Supervised Learning via Redundancy Reduction,” Mar. 2021, [Online]. Available: http://arxiv.org/abs/2103.03230
  • [26] D. Dwibedi, Y. Aytar, J. Tompson, P. Sermanet, and A. Zisserman, “With a Little Help from My Friends: Nearest-Neighbor Contrastive Learning of Visual Representations,” Apr. 2021, [Online]. Available: http://arxiv.org/abs/2104.14548
  • [27] A. van den Oord, Y. Li, and O. Vinyals, “Representation Learning with Contrastive Predictive Coding,” Jul. 2018.
  • [28] J. C. Triana-Martinez, J. Gil-González, J. A. Fernandez-Gallego, A. M. Álvarez-Meza, and C. G. Castellanos-Dominguez, “Chained Deep Learning Using Generalized Cross-Entropy for Multiple Annotators Classification,” Sensors, vol. 23, no. 7, p. 3518, Mar. 2023, doi: 10.3390/s23073518.
There are 28 citations in total.

Details

Primary Language English
Subjects Artificial Intelligence (Other)
Journal Section Araştırma Makalesi
Authors

Kazım Fırıldak 0000-0002-1958-3627

Gaffari Çelik 0000-0001-5658-9529

Muhammed Fatih Talu 0000-0003-1166-8404

Early Pub Date December 30, 2024
Publication Date December 31, 2024
Submission Date September 29, 2024
Acceptance Date October 28, 2024
Published in Issue Year 2024

Cite

IEEE K. Fırıldak, G. Çelik, and M. F. Talu, “SimCLR-based Self-Supervised Learning Approach for Limited Brain MRI and Unlabeled Images”, Bitlis Eren Üniversitesi Fen Bilimleri Dergisi, vol. 13, no. 4, pp. 1304–1313, 2024, doi: 10.17798/bitlisfen.1558069.

Bitlis Eren University
Journal of Science Editor
Bitlis Eren University Graduate Institute
Bes Minare Mah. Ahmet Eren Bulvari, Merkez Kampus, 13000 BITLIS