AttResDU-Net: Medical Image Segmentation Using Attention-based Residual Double U-Net (2306.14255v1)
Abstract: Manually inspecting polyps from a colonoscopy for colorectal cancer or performing a biopsy on skin lesions for skin cancer are time-consuming, laborious, and complex procedures. Automatic medical image segmentation aims to expedite this diagnosis process. However, numerous challenges exist due to significant variations in the appearance and sizes of objects with no distinct boundaries. This paper proposes an attention-based residual Double U-Net architecture (AttResDU-Net) that improves on the existing medical image segmentation networks. Inspired by the Double U-Net, this architecture incorporates attention gates on the skip connections and residual connections in the convolutional blocks. The attention gates allow the model to retain more relevant spatial information by suppressing irrelevant feature representation from the down-sampling path for which the model learns to focus on target regions of varying shapes and sizes. Moreover, the residual connections help to train deeper models by ensuring better gradient flow. We conducted experiments on three datasets: CVC Clinic-DB, ISIC 2018, and the 2018 Data Science Bowl datasets and achieved Dice Coefficient scores of 94.35%, 91.68% and 92.45% respectively. Our results suggest that AttResDU-Net can be facilitated as a reliable method for automatic medical image segmentation in practice.
- R. Wang, T. Lei, R. Cui, B. Zhang, H. Meng, and A. K. Nandi, “Medical image segmentation using deep learning: A survey,” IET Image Processing, vol. 16, no. 5, pp. 1243–1267, 2022. [Online]. Available: https://ietresearch.onlinelibrary.wiley.com/doi/abs/10.1049/ipr2.12419
- Z. Wei, F. Shi, H. Song, W. Ji, and G. Han, “Attentive boundary aware network for multi-scale skin lesion segmentation with adversarial training,” Multimedia Tools and Applications, vol. 79, no. 37, pp. 27 115–27 136, 2020. [Online]. Available: https://link.springer.com/article/10.1007/s11042-020-09334-2
- D.-P. Fan, G.-P. Ji, T. Zhou, G. Chen, H. Fu, J. Shen, and L. Shao, “Pranet: Parallel reverse attention network for polyp segmentation,” in International conference on medical image computing and computer-assisted intervention. Springer, 2020, pp. 263–273. [Online]. Available: https://arxiv.org/abs/2006.11392
- O. Ronneberger, P. Fischer, and T. Brox, “U-net: Convolutional networks for biomedical image segmentation,” in International Conference on Medical image computing and computer-assisted intervention. Springer, 2015, pp. 234–241. [Online]. Available: https://link.springer.com/chapter/10.1007/978-3-319-24574-4_28
- O. Oktay, J. Schlemper, L. L. Folgoc, M. C. H. Lee, M. P. Heinrich, K. Misawa, K. Mori, S. G. McDonagh, N. Y. Hammerla, B. Kainz, B. Glocker, and D. Rueckert, “Attention U-Net: Learning Where to Look for the Pancreas,” CoRR, vol. abs/1804.03999, 2018. [Online]. Available: http://arxiv.org/abs/1804.03999
- D. Jha, M. A. Riegler, D. Johansen, P. Halvorsen, and H. D. Johansen, “DoubleU-Net: A Deep Convolutional Neural Network for Medical Image Segmentation,” in 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS). Los Alamitos, CA, USA: IEEE Computer Society, jul 2020, pp. 558–564. [Online]. Available: https://doi.ieeecomputersociety.org/10.1109/CBMS49503.2020.00111
- A. Lin, B. Chen, J. Xu, Z. Zhang, G. Lu, and D. Zhang, “DS-TransUNet: Dual Swin Transformer U-Net for Medical Image Segmentation,” IEEE Trans. Instrum. Meas., vol. 71, pp. 1–15, 2022. [Online]. Available: https://ieeexplore.ieee.org/document/9785614/
- K. He, X. Zhang, S. Ren, and J. Sun, “Deep Residual Learning for Image Recognition,” in 2016 IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2016, Las Vegas, NV, USA, June 27-30, 2016. IEEE Computer Society, 2016, pp. 770–778. [Online]. Available: https://ieeexplore.ieee.org/document/7780459/
- M. Bencevic, I. Galic, M. Habijan, and D. Babin, “Training on Polar Image Transformations Improves Biomedical Image Segmentation,” IEEE Access, vol. 9, pp. 133 365–133 375, 2021. [Online]. Available: https://doi.org/10.1109/ACCESS.2021.3116265
- S. Ahmed, M. B. Hasan, T. Ahmed, M. R. K. Sony, and M. H. Kabir, “Less is More: Lighter and Faster Deep Neural Architecture for Tomato Leaf Disease Classification,” IEEE Access, vol. 10, pp. 68 868–68 884, 2022.
- J. Ng, M. Goyal, B. Hewitt, and M. H. Yap, “The effect of color constancy algorithms on semantic segmentation of skin lesions,” in Medical Imaging 2019: Biomedical Applications in Molecular, Structural, and Functional Imaging, San Diego, California, United States, 16-21 February 2019, ser. SPIE Proceedings, B. Gimi and A. Król, Eds., vol. 10953. SPIE, 2019, p. 109530R. [Online]. Available: https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10953/2512702/The-effect-of-color-constancy-algorithms-on-semantic-segmentation-of/10.1117/12.2512702.full?SSO=1
- M. E. Celebi, W. Guo, Y. A. Aslandogan, and P. R. Bergstresser, “Skin Lesion Segmentation Using Clustering Techniques,” in Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference, Clearwater Beach, Florida, USA, I. Russell and Z. Markov, Eds. AAAI Press, 2005, pp. 364–369. [Online]. Available: http://www.aaai.org/Library/FLAIRS/2005/flairs05-060.php
- A. Wong, J. Scharcanski, and P. W. Fieguth, “Automatic Skin Lesion Segmentation via Iterative Stochastic Region Merging,” IEEE Trans. Inf. Technol. Biomed., vol. 15, no. 6, pp. 929–936, 2011. [Online]. Available: https://ieeexplore.ieee.org/document/5776681
- S. Gross, M. Kennel, T. Stehle, J. Wulff, J. J. W. Tischendorf, C. Trautwein, and T. Aach, “Polyp Segmentation in NBI Colonoscopy,” in Bildverarbeitung für die Medizin 2009: Algorithmen - Systeme - Anwendungen, Proceedings des Workshops vom 22. bis 25. März 2009 in Heidelberg, ser. Informatik Aktuell, H. Meinzer, T. M. Deserno, H. Handels, and T. Tolxdorff, Eds. Springer, 2009, pp. 252–256. [Online]. Available: https://link.springer.com/chapter/10.1007/978-3-540-93860-6_51
- G. Litjens, T. Kooi, B. E. Bejnordi, A. A. A. Setio, F. Ciompi, M. Ghafoorian, J. A. W. M. van der Laak, B. van Ginneken, and C. I. Sánchez, “A survey on deep learning in medical image analysis,” Medical Image Analysis, vol. 42, pp. 60–88, 2017. [Online]. Available: https://www.sciencedirect.com/science/article/abs/pii/S1361841517301135
- Z. Zhou, M. M. R. Siddiquee, N. Tajbakhsh, and J. Liang, “UNet++: A Nested U-Net Architecture for Medical Image Segmentation,” in Deep Learning in Medical Image Analysis - and - Multimodal Learning for Clinical Decision Support - 4th International Workshop, DLMIA 2018, and 8th International Workshop, ML-CDS 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 20, 2018, Proceedings, ser. Lecture Notes in Computer Science, D. Stoyanov, Z. Taylor, G. Carneiro, T. F. Syeda-Mahmood, A. L. Martel, L. Maier-Hein, J. M. R. S. Tavares, A. P. Bradley, J. P. Papa, V. Belagiannis, J. C. Nascimento, Z. Lu, S. Conjeti, M. Moradi, H. Greenspan, and A. Madabhushi, Eds., vol. 11045. Springer, 2018, pp. 3–11. [Online]. Available: https://link.springer.com/chapter/10.1007/978-3-030-00889-5_1
- L. Chen, G. Papandreou, F. Schroff, and H. Adam, “Rethinking Atrous Convolution for Semantic Image Segmentation,” CoRR, vol. abs/1706.05587, 2017. [Online]. Available: http://arxiv.org/abs/1706.05587
- J. Chen, Y. Lu, Q. Yu, X. Luo, E. Adeli, Y. Wang, L. Lu, A. L. Yuille, and Y. Zhou, “TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation,” CoRR, vol. abs/2102.04306, 2021. [Online]. Available: https://arxiv.org/abs/2102.04306
- A. Srivastava, D. Jha, S. Chanda, U. Pal, H. D. Johansen, D. Johansen, M. A. Riegler, S. Ali, and P. Halvorsen, “MSRF-Net: A Multi-Scale Residual Fusion Network for Biomedical Image Segmentation,” IEEE J. Biomed. Health Informatics, vol. 26, no. 5, pp. 2252–2263, 2022. [Online]. Available: https://ieeexplore.ieee.org/document/9662196/
- K. Simonyan and A. Zisserman, “Very Deep Convolutional Networks for Large-Scale Image Recognition,” in 3rd International Conference on Learning Representations, ICLR 2015, San Diego, CA, USA, May 7-9, 2015, Conference Track Proceedings, Y. Bengio and Y. LeCun, Eds., 2015. [Online]. Available: http://arxiv.org/abs/1409.1556
- J. Hu, L. Shen, and G. Sun, “Squeeze-and-Excitation Networks,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE, 2018, pp. 7132–7141. [Online]. Available: https://ieeexplore.ieee.org/document/8578843
- G. D. Finlayson and E. Trezzi, “Shades of Gray and Colour Constancy,” in The Twelfth Color Imaging Conference: Color Science and Engineering Systems, Technologies, Applications, CIC 2004, Scottsdale, Arizona, USA, November 9-12, 2004. IS&T - The Society for Imaging Science and Technology, 2004.
- N. C. F. Codella, V. Rotemberg, P. Tschandl, M. E. Celebi, S. W. Dusza, D. A. Gutman, B. Helba, A. Kalloo, K. Liopyris, M. A. Marchetti, H. Kittler, and A. Halpern, “Skin lesion analysis toward melanoma detection 2018: A challenge hosted by the international skin imaging collaboration (ISIC),” CoRR, vol. abs/1902.03368, 2019. [Online]. Available: http://arxiv.org/abs/1902.03368
- J. Bernal, F. J. Sánchez, G. Fernández-Esparrach, D. Gil, C. R. de Miguel, and F. Vilariño, “WM-DOVA maps for accurate polyp highlighting in colonoscopy: Validation vs. saliency maps from physicians,” Comput. Medical Imaging Graph., vol. 43, pp. 99–111, 2015. [Online]. Available: https://www.sciencedirect.com/science/article/abs/pii/S0895611115000567
- N. C. F. Codella, D. A. Gutman, M. E. Celebi, B. Helba, M. A. Marchetti, S. W. Dusza, A. Kalloo, K. Liopyris, N. K. Mishra, H. Kittler, and A. Halpern, “Skin Lesion Analysis Toward Melanoma Detection: A Challenge at the 2017 International Symposium on Biomedical Imaging (ISBI), Hosted by the International Skin Imaging Collaboration (ISIC),” vol. abs/1710.05006, 2017. [Online]. Available: http://arxiv.org/abs/1710.05006
- J. C. Caicedo, A. Goodman, K. W. Karhohs, B. A. Cimini, J. Ackerman, M. Haghighi, C. Heng, T. Becker, M. Doan, C. McQuin et al., “Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl,” Nature methods, vol. 16, no. 12, pp. 1247–1253, 2019. [Online]. Available: https://www.nature.com/articles/s41592-019-0612-7
- C. H. Sudre, W. Li, T. Vercauteren, S. Ourselin, and M. J. Cardoso, “Generalised dice overlap as a deep learning loss function for highly unbalanced segmentations,” in Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - Third International Workshop, DLMIA 2017, and 7th International Workshop, ML-CDS 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 14, 2017, Proceedings, ser. Lecture Notes in Computer Science, M. J. Cardoso, T. Arbel, G. Carneiro, T. F. Syeda-Mahmood, J. M. R. S. Tavares, M. Moradi, A. P. Bradley, H. Greenspan, J. P. Papa, A. Madabhushi, J. C. Nascimento, J. S. Cardoso, V. Belagiannis, and Z. Lu, Eds., vol. 10553. Springer, 2017, pp. 240–248. [Online]. Available: https://doi.org/10.1007/978-3-319-67558-9_28
- T. Dozat, “Incorporating Nesterov Momentum into Adam,” in International Conference on Learning Representations, Caribe Hilton, San Juan, Puerto Rico, May 2 - 4, 2016, 2016.
- A. Buslaev, V. I. Iglovikov, E. Khvedchenya, A. Parinov, M. Druzhinin, and A. A. Kalinin, “Albumentations: Fast and Flexible Image Augmentations,” Inf., vol. 11, no. 2, p. 125, 2020. [Online]. Available: https://www.mdpi.com/2078-2489/11/2/125
- K. H. Zou, S. K. Warfield, A. Bharatha, C. M. Tempany, M. R. Kaus, S. J. Haker, W. M. Wells III, F. A. Jolesz, and R. Kikinis, “Statistical validation of image segmentation quality based on a spatial overlap index1: scientific reports,” Academic Radiology, vol. 11, no. 2, pp. 178–189, 2004. [Online]. Available: https://www.sciencedirect.com/science/article/pii/S1076633203006718
- L. Chen, Y. Zhu, G. Papandreou, F. Schroff, and H. Adam, “Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation,” in Computer Vision - ECCV 2018 - 15th European Conference, Munich, Germany, September 8-14, 2018, Proceedings, Part VII, ser. Lecture Notes in Computer Science, V. Ferrari, M. Hebert, C. Sminchisescu, and Y. Weiss, Eds., vol. 11211. Springer, 2018, pp. 833–851. [Online]. Available: https://link.springer.com/chapter/10.1007/978-3-030-01234-2_49
- D. Jha, P. H. Smedsrud, M. A. Riegler, D. Johansen, T. de Lange, P. Halvorsen, and H. D. Johansen, “ResUNet++: An Advanced Architecture for Medical Image Segmentation,” in IEEE International Symposium on Multimedia, ISM 2019, San Diego, CA, USA, December 9-11, 2019. IEEE, 2019, pp. 225–230. [Online]. Available: https://ieeexplore.ieee.org/document/8959021/
- T. Kim, H. Lee, and D. Kim, “UACANet: Uncertainty Augmented Context Attention for Polyp Segmentation,” in MM ’21: ACM Multimedia Conference, Virtual Event, China, October 20 - 24, 2021, H. T. Shen, Y. Zhuang, J. R. Smith, Y. Yang, P. César, F. Metze, and B. Prabhakaran, Eds. ACM, 2021, pp. 2167–2175. [Online]. Available: https://dl.acm.org/doi/10.1145/3474085.3475375
- Z. Liu, Y. Lin, Y. Cao, H. Hu, Y. Wei, Z. Zhang, S. Lin, and B. Guo, “Swin Transformer: Hierarchical Vision Transformer using Shifted Windows,” in 2021 IEEE/CVF International Conference on Computer Vision, ICCV 2021, Montreal, QC, Canada, October 10-17, 2021. IEEE, 2021, pp. 9992–10 002. [Online]. Available: https://ieeexplore.ieee.org/document/9710580/