Adversary-Robust Graph-Based Learning of WSIs
Abstract: Enhancing the robustness of deep learning models against adversarial attacks is crucial, especially in critical domains like healthcare where significant financial interests heighten the risk of such attacks. Whole slide images (WSIs) are high-resolution, digitized versions of tissue samples mounted on glass slides, scanned using sophisticated imaging equipment. The digital analysis of WSIs presents unique challenges due to their gigapixel size and multi-resolution storage format. In this work, we aim at improving the robustness of cancer Gleason grading classification systems against adversarial attacks, addressing challenges at both the image and graph levels. As regards the proposed algorithm, we develop a novel and innovative graph-based model which utilizes GNN to extract features from the graph representation of WSIs. A denoising module, along with a pooling layer is incorporated to manage the impact of adversarial attacks on the WSIs. The process concludes with a transformer module that classifies various grades of prostate cancer based on the processed data. To assess the effectiveness of the proposed method, we conducted a comparative analysis using two scenarios. Initially, we trained and tested the model without the denoiser using WSIs that had not been exposed to any attack. We then introduced a range of attacks at either the image or graph level and processed them through the proposed network. The performance of the model was evaluated in terms of accuracy and kappa scores. The results from this comparison showed a significant improvement in cancer diagnosis accuracy, highlighting the robustness and efficiency of the proposed method in handling adversarial challenges in the context of medical imaging.
- J. Levy, C. Haudenschild, C. Barwick, B. Christensen, and L. Vaickus, “Topological feature extraction and visualization of whole slide images using graph neural networks,” in BIOCOMPUTING 2021: Proceedings of the Pacific Symposium. World Scientific, 2020, pp. 285–296.
- I. J. Goodfellow, J. Shlens, and C. Szegedy, “Explaining and harnessing adversarial examples,” arXiv preprint arXiv:1412.6572, 2014.
- K. Xu, H. Chen, S. Liu, P.-Y. Chen, T.-W. Weng, M. Hong, and X. Lin, “Topology attack and defense for graph neural networks: An optimization perspective,” arXiv preprint arXiv:1906.04214, 2019.
- X. Zang, Y. Xie, J. Chen, and B. Yuan, “Graph universal adversarial attacks: A few bad actors ruin graph learning models,” arXiv preprint arXiv:2002.04784, 2020.
- S. Tao, H. Shen, Q. Cao, L. Hou, and X. Cheng, “Adversarial immunization for improving certifiable robustness on graphs,” arXiv preprint arXiv:2007.09647, 2020.
- Y. Ma, S. Wang, T. Derr, L. Wu, and J. Tang, “Attacking graph convolutional networks via rewiring,” arXiv preprint arXiv:1906.03750, 2019.
- N. Papernot, P. McDaniel, and I. Goodfellow, “Transferability in machine learning: from phenomena to black-box attacks using adversarial samples,” arXiv preprint arXiv:1605.07277, 2016.
- K. D. Apostolidis and G. A. Papakostas, “A survey on adversarial deep learning robustness in medical image analysis,” Electronics, vol. 10, no. 17, p. 2132, 2021.
- S. Finlayson, H. Chung, I. Kohane, and A. Beam, “Adversarial attacks against medical deep learning systems,” arXiv preprint arXiv:1804.05296, 2018.
- K. Apostolidis and G. Papakostas, “A survey on adversarial deep learning robustness in medical image analysis,” Electronics, vol. 10, no. 17, p. 2132, 2021.
- F. Aeffner, M. D. Zarella, N. Buchbinder, M. M. Bui, M. R. Goodman, D. J. Hartman, G. M. Lujan, M. A. Molani, A. V. Parwani, K. Lillard et al., “Introduction to digital image analysis in whole-slide imaging: a white paper from the digital pathology association,” Journal of pathology informatics, vol. 10, no. 1, p. 9, 2019.
- N. Ghaffari Laleh, D. Truhn, G. P. Veldhuizen, T. Han, M. van Treeck, R. D. Buelow, R. Langer, B. Dislich, P. Boor, V. Schulz et al., “Adversarial attacks and adversarial robustness in computational pathology,” Nature communications, vol. 13, no. 1, p. 5711, 2022.
- R. Feng, X. Liu, J. Chen, D. Z. Chen, H. Gao, and J. Wu, “A deep learning approach for colonoscopy pathology wsi analysis: accurate segmentation and classification,” IEEE Journal of Biomedical and Health Informatics, vol. 25, no. 10, pp. 3700–3708, 2020.
- N. Bussola, J. Xu, L. Wu, L. Gorini, Y. Zhang, C. Furlanello, and W. Tong, “A weakly supervised deep learning framework for whole slide classification to facilitate digital pathology in animal study,” Chemical Research in Toxicology, vol. 36, no. 8, pp. 1321–1331, 2023.
- G. Campanella, M. G. Hanna, L. Geneslaw, A. Miraflor, V. Werneck Krauss Silva, K. J. Busam, E. Brogi, V. E. Reuter, D. S. Klimstra, and T. J. Fuchs, “Clinical-grade computational pathology using weakly supervised deep learning on whole slide images,” Nature medicine, vol. 25, no. 8, pp. 1301–1309, 2019.
- J. Li, W. Li, A. Sisk, H. Ye, W. D. Wallace, W. Speier, and C. W. Arnold, “A multi-resolution model for histopathology image classification and localization with multiple instance learning,” Computers in biology and medicine, vol. 131, p. 104253, 2021.
- M. Aryal and N. Yahyasoltani, “Context-aware self-supervised learning of whole slide images,” arXiv preprint arXiv:2306.04763, 2023.
- Y. Guan, J. Zhang, K. Tian, S. Yang, P. Dong, J. Xiang, W. Yang, J. Huang, Y. Zhang, and X. Han, “Node-aligned graph convolutional network for whole-slide image representation and classification,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2022, pp. 18 813–18 823.
- M. Aryal and N. Yahyasoltani, “Context-aware graph-based self-supervised learning of whole slide images,” in ICASSP 2022-2022 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE, 2022, pp. 3553–3557.
- C. Szegedy, W. Zaremba, I. Sutskever, J. Bruna, D. Erhan, I. Goodfellow, and R. Fergus, “Intriguing properties of neural networks,” arXiv preprint arXiv:1312.6199, 2013.
- D. Zügner, A. Akbarnejad, and S. Günnemann, “Adversarial attacks on neural networks for graph data,” in Proceedings of the 24th ACM SIGKDD international conference on knowledge discovery & data mining, 2018, pp. 2847–2856.
- N. Entezari, S. A. Al-Sayouri, A. Darvishzadeh, and E. E. Papalexakis, “All you need is low (rank) defending against adversarial attacks on graphs,” in Proceedings of the 13th International Conference on Web Search and Data Mining, 2020, pp. 169–177.
- J. Chen, Y. Wu, X. Xu, Y. Chen, H. Zheng, and Q. Xuan, “Fast gradient attack on network embedding,” arXiv preprint arXiv:1809.02797, 2018.
- Y. Sun, S. Wang, X. Tang, T.-Y. Hsieh, and V. Honavar, “Adversarial attacks on graph neural networks via node injections: A hierarchical reinforcement learning approach,” in Proceedings of the Web Conference 2020, 2020, pp. 673–683.
- H. Dai, H. Li, T. Tian, X. Huang, L. Wang, J. Zhu, and L. Song, “Adversarial attack on graph structured data,” in International conference on machine learning. PMLR, 2018, pp. 1115–1124.
- F. Tramèr, A. Kurakin, N. Papernot, I. Goodfellow, D. Boneh, and P. McDaniel, “Ensemble adversarial training: Attacks and defenses,” arXiv preprint arXiv:1705.07204, 2017.
- D. Loveland, S. Liu, B. Kailkhura, A. Hiszpanski, and Y. Han, “Reliable graph neural network explanations through adversarial training,” arXiv preprint arXiv:2106.13427, 2021.
- A. Qayyum, I. Ilahi, F. Shamshad, F. Boussaid, M. Bennamoun, and J. Qadir, “Untrained neural network priors for inverse imaging problems: A survey,” IEEE Transactions on Pattern Analysis and Machine Intelligence, 2022.
- A. Bora, A. Jalal, E. Price, and A. G. Dimakis, “Compressed sensing using generative models,” in International conference on machine learning. PMLR, 2017, pp. 537–546.
- D. Luo, W. Cheng, W. Yu, B. Zong, J. Ni, H. Chen, and X. Zhang, “Learning to drop: Robust graph neural network via topological denoising,” in Proceedings of the 14th ACM international conference on web search and data mining, 2021, pp. 779–787.
- P. Velickovic, G. Cucurull, A. Casanova, A. Romero, P. Lio, Y. Bengio et al., “Graph attention networks,” stat, vol. 1050, no. 20, pp. 10–48 550, 2017.
- A. Foote, A. Asif, A. Azam, T. Marshall-Cox, N. Rajpoot, and F. Minhas, “Now you see it, now you dont: adversarial vulnerabilities in computational pathology,” arXiv preprint arXiv:2106.08153, 2021.
- S. Bhojanapalli, A. Chakrabarti, D. Glasner, D. Li, T. Unterthiner, and A. Veit, “Understanding robustness of transformers for image classification,” in Proceedings of the IEEE/CVF international conference on computer vision, 2021, pp. 10 231–10 241.
- Y. Zhang, Y. Sun, H. Li, S. Zheng, C. Zhu, and L. Yang, “Benchmarking the robustness of deep neural networks to common corruptions in digital pathology,” in International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, 2022, pp. 242–252.
- M. Adnan, S. Kalra, and H. R. Tizhoosh, “Representation learning of histopathology images using graph neural networks,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops, 2020, pp. 988–989.
- D. Anand, S. Gadiya, and A. Sethi, “Histographs: graphs in histopathology,” in Medical Imaging 2020: Digital Pathology, vol. 11320. SPIE, 2020, pp. 150–155.
- R. Reddy, R. Reddy, C. Sharma, C. Jackson, S. Palisoul, R. Barney, F. Kolling, L. Salas, B. Christensen, G. Brooks et al., “Graph neural networks ameliorate potential impacts of imprecise large-scale autonomous immunofluorescence labeling of immune cells on whole slide images,” in Geometric Deep Learning in Medical Image Analysis. PMLR, 2022, pp. 15–33.
- X. Wang, S. Yang, J. Zhang, M. Wang, J. Zhang, W. Yang, J. Huang, and X. Han, “Transformer-based unsupervised contrastive learning for histopathological image classification.” Elsevier, 2022.
- T. N. Kipf and M. Welling, “Semi-supervised classification with graph convolutional networks,” 2017.
- X. Tang, Y. Li, Y. Sun, H. Yao, P. Mitra, and S. Wang, “Transferring robustness for graph neural network against poisoning attacks,” in Proceedings of the 13th international conference on web search and data mining, 2020, pp. 600–608.
- X. Liu, S. Si, X. Zhu, Y. Li, and C.-J. Hsieh, “A unified framework for data poisoning attack to graph-based semi-supervised learning,” arXiv preprint arXiv:1910.14147, 2019.
- Q. Zhou, Y. Ren, T. Xia, L. Yuan, and L. Chen, “Data poisoning attacks on graph convolutional matrix completion,” in International Conference on Algorithms and Architectures for Parallel Processing. Springer, 2019, pp. 427–439.
- H. Zhang, T. Zheng, J. Gao, C. Miao, L. Su, Y. Li, and K. Ren, “Towards data poisoning attack against knowledge graph embedding,” arXiv preprint arXiv:1904.12052, 2019.
- H. Wu, C. Wang, Y. Tyshetskiy, A. Docherty, K. Lu, and L. Zhu, “Adversarial examples on graph data: Deep insights into attack and defense,” arXiv preprint arXiv:1903.01610, 2019.
- D. Zügner and S. Günnemann, “Adversarial attacks on graph neural networks via meta learning,” 2019.
- M. Andrychowicz, M. Denil, S. Gomez, M. W. Hoffman, D. Pfau, T. Schaul, B. Shillingford, and N. De Freitas, “Learning to learn by gradient descent by gradient descent,” Advances in neural information processing systems, vol. 29, 2016.
- C. Finn, P. Abbeel, and S. Levine, “Model-agnostic meta-learning for fast adaptation of deep networks,” in International conference on machine learning. PMLR, 2017, pp. 1126–1135.
- S. Yun, M. Jeong, R. Kim, J. Kang, and H. J. Kim, “Graph transformer networks,” Advances in neural information processing systems, vol. 32, 2019.
- A. Vaswani, N. Shazeer, N. Parmar, J. Uszkoreit, L. Jones, A. N. Gomez, L. Kaiser, and I. Polosukhin, “Attention is all you need,” 2023.
- Y. Zheng, R. H. Gindra, E. J. Green, E. J. Burks, M. Betke, J. E. Beane, and V. B. Kolachalama, “A graph-transformer for whole slide image classification,” 2022.
- S. Rey, S. Segarra, R. Heckel, and A. G. Marques, “Untrained graph neural networks for denoising,” IEEE Transactions on Signal Processing, vol. 70, pp. 5708–5723, 2022.
- W. Bulten, K. Kartasalo, P.-H. C. Chen, P. Ström, H. Pinckaers, K. Nagpal, Y. Cai, D. F. Steiner, H. van Boven, R. Vink et al., “Artificial intelligence for diagnosis and gleason grading of prostate cancer: the panda challenge,” Nature medicine, vol. 28, no. 1, pp. 154–163, 2022.
Paper Prompts
Sign up for free to create and run prompts on this paper using GPT-5.
Top Community Prompts
Collections
Sign up for free to add this paper to one or more collections.