Abstract
Although Magnetic Resonance Imaging (MRI) is crucial for segmenting brain tumors, it frequently lacks specific modalities in clinical practice, which limits prediction performance. In current methods, training involves multiple stages, and encoders are different for each modality, which means hybrid modules must be manually designed to incorporate multiple modalities’ features, lacking interaction across modalities. To ameliorate this problem, we propose a transformer-based end-to-end model with just one auto-encoder to provide interactive computations in any modality missing condition. Considering that it is challenging for a single model to perceive several missing states, we introduce learnable modality combination queries to assist the transformer decoder in adjusting to the incomplete multi-modal segmentation. Furthermore, to address the suboptimization issue of the Transformer under small datasets, we adopt a re-training mechanism to facilitate convergence to a better local minimum. The extensive experiments on the BraTS2018 and BraTS2020 datasets demonstrate that our method outperforms the current state-of-the-art methods for incomplete multi-modal brain tumor segmentation on average.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Cao, H., et al.: Swin-Unet: Unet-like pure transformer for medical image segmentation. In: Karlinsky, L., Michaeli, T., Nishino, K. (eds.) ECCV 2022. LNCS, vol. 13803, pp. 205–218. Springer, Cham (2023). https://doi.org/10.1007/978-3-031-25066-8_9
Carion, N., Massa, F., Synnaeve, G., Usunier, N., Kirillov, A., Zagoruyko, S.: End-to-end object detection with transformers. In: Vedaldi, A., Bischof, H., Brox, T., Frahm, J.-M. (eds.) ECCV 2020. LNCS, vol. 12346, pp. 213–229. Springer, End-to-end object detection with transformers (2020). https://doi.org/10.1007/978-3-030-58452-8_13
Chen, C., Dou, Q., Jin, Y., Chen, H., Qin, J., Heng, P.-A.: Robust multimodal brain tumor segmentation via feature disentanglement and gated fusion. In: Shen, D., et al. (eds.) MICCAI 2019. LNCS, vol. 11766, pp. 447–456. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32248-9_50
Dice, L.R.: Measures of the amount of ecologic association between species. Ecology 26(3), 297–302 (1945)
Ding, Y., Yu, X., Yang, Y.: RFNet: region-aware fusion network for incomplete multi-modal brain tumor segmentation. In: Proceedings of the IEEE/CVF International Conference on Computer Vision, pp. 3975–3984 (2021)
Dorent, R., Joutard, S., Modat, M., Ourselin, S., Vercauteren, T.: Hetero-modal variational encoder-decoder for joint modality completion and segmentation. In: Shen, D., et al. (eds.) MICCAI 2019. LNCS, vol. 11765, pp. 74–82. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32245-8_9
Dosovitskiy, A., et al.: An image is worth 16x16 words: transformers for image recognition at scale (2020). https://doi.org/10.48550/ARXIV.2010.11929. https://arxiv.org/abs/2010.11929
Isensee, F., Jaeger, P.F., Kohl, S.A., Petersen, J., Maier-Hein, K.H.: NNU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat. Methods 18(2), 203–211 (2021)
Kingma, D.P., Ba, J.: Adam: a method for stochastic optimization. In: Proceedings of the International Conference on Learning Representations (2015)
Liu, H., et al.: ModDrop++: a dynamic filter network with intra-subject co-training for multiple sclerosis lesion segmentation with missing modalities (2022). https://doi.org/10.48550/ARXIV.2203.04959. https://arxiv.org/abs/2203.04959
Liu, Y., Fan, L., et al.: Incomplete multi-modal representation learning for Alzheimer’s disease diagnosis. Med. Image Anal. 69, 101953 (2021)
Liu, Z., Lin, Y., et al.: Swin transformer: hierarchical vision transformer using shifted windows. In: IEEE International Conference on Computer Vision, pp. 10012–10022 (2021)
Peiris, H., Hayat, M., Chen, Z., Egan, G., Harandi, M.: A robust volumetric transformer for accurate 3D tumor segmentation. In: Wang, L., Dou, Q., Fletcher, P.T., Speidel, S., Li, S. (eds.) ECCV 2022, Part V. LNCS, vol. 13435, pp. 162–172. Springer, Cham (2022)
Qiu, Y., Chen, D., Yao, H., Xu, Y., Wang, Z.: Scratch each other’s back: Incomplete multi-modal brain tumor segmentation via category aware group self-support learning. In: Proceedings of the IEEE/CVF International Conference on Computer Vision (2023)
Qiu, Y., Zhao, Z., Yao, H., Chen, D., Wang, Z.: Modal-aware visual prompting for incomplete multi-modal brain tumor segmentation. In: Proceedings of the 31th ACM International Conference on Multimedia (2023)
Qu, M., et al.: SiRi: a simple selective retraining mechanism for transformer-based visual grounding. In: Avidan, S., Brostow, G., Cissé, M., Farinella, G.M., Hassner, T. (eds.) ECCV 2022, Part XXXV. LNCS, vol. 13695, pp. 546–562. Springer, Cham (2022). https://doi.org/10.1007/978-3-031-19833-5_32
Tang, Y., et al.: Self-supervised pre-training of swin transformers for 3d medical image analysis (2021). https://doi.org/10.48550/ARXIV.2111.14791. https://arxiv.org/abs/2111.14791
Valanarasu, J.M.J., Yasarla, R., et al.: TransWeather: transformer-based restoration of images degraded by adverse weather conditions. In: IEEE Conference on Computer Vision and Pattern Recognition, pp. 2353–2363 (2022)
Vaswani, A., Shazeer, N., et al.: Attention is all you need. In: Proceedings Advances in Neural Information Processing Systems, vol. 30 (2017)
Wang, L., Lee, C.Y., et al.: Training deeper convolutional networks with deep supervision. arXiv preprint arXiv:1505.02496 (2015)
Wang, S., et al.: LT-Net: label transfer by learning reversible voxel-wise correspondence for one-shot medical image segmentation. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 9162–9171 (2020)
Zhang, Y., He, N., et al.: mmFormer: multimodal medical transformer for incomplete multimodal learning of brain tumor segmentation. In: Proceedings of the International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 107–117 (2022)
Zhang, Y., et al.: Modality-aware mutual learning for multi-modal medical image segmentation. In: de Bruijne, M., et al. (eds.) MICCAI 2021, Part I. LNCS, vol. 12901, pp. 589–599. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-87193-2_56
Zhao, Z., Yang, H., et al.: Modality-adaptive feature interaction for brain tumor segmentation with missing modalities. In: Proceedings of the International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 183–192 (2022)
Zhou, C., Ding, C., Lu, Z., Wang, X., Tao, D.: One-pass multi-task convolutional neural networks for efficient brain tumor segmentation. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) MICCAI 2018, Part III. LNCS, vol. 11072, pp. 637–645. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00931-1_73
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Chen, D., Qiu, Y., Wang, Z. (2023). Query Re-Training for Modality-Gnostic Incomplete Multi-modal Brain Tumor Segmentation. In: Woo, J., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2023 Workshops. MICCAI 2023. Lecture Notes in Computer Science, vol 14394. Springer, Cham. https://doi.org/10.1007/978-3-031-47425-5_13
Download citation
DOI: https://doi.org/10.1007/978-3-031-47425-5_13
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-47424-8
Online ISBN: 978-3-031-47425-5
eBook Packages: Computer ScienceComputer Science (R0)