2022-05-19 更新
Global Contrast Masked Autoencoders Are Powerful Pathological Representation Learners
Authors:Hao Quan, Xingyu Li, Weixing Chen, Mingchen Zou, Ruijie Yang, Tingting Zheng, Ruiqun Qi, Xinghua Gao, Xiaoyu Cui
Based on digital whole slide scanning technique, artificial intelligence algorithms represented by deep learning have achieved remarkable results in the field of computational pathology. Compared with other medical images such as Computed Tomography (CT) or Magnetic Resonance Imaging (MRI), pathological images are more difficult to annotate, thus there is an extreme lack of data sets that can be used for supervised learning. In this study, a self-supervised learning (SSL) model, Global Contrast Masked Autoencoders (GCMAE), is proposed, which has the ability to represent both global and local domain-specific features of whole slide image (WSI), as well as excellent cross-data transfer ability. The Camelyon16 and NCTCRC datasets are used to evaluate the performance of our model. When dealing with transfer learning tasks with different data sets, the experimental results show that GCMAE has better linear classification accuracy than MAE, which can reach 81.10% and 89.22% respectively. Our method outperforms the previous state-of-the-art algorithm and even surpass supervised learning (improved by 3.86% on NCTCRC data sets). The source code of this paper is publicly available at https://github.com/StarUniversus/gcmae
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Contrastive Transformer-based Multiple Instance Learning for Weakly Supervised Polyp Frame Detection
Authors:Yu Tian, Guansong Pang, Fengbei Liu, Yuyuan Liu, Chong Wang, Yuanhong Chen, Johan W Verjans, Gustavo Carneiro
Current polyp detection methods from colonoscopy videos use exclusively normal (i.e., healthy) training images, which i) ignore the importance of temporal information in consecutive video frames, and ii) lack knowledge about the polyps. Consequently, they often have high detection errors, especially on challenging polyp cases (e.g., small, flat, or partially visible polyps). In this work, we formulate polyp detection as a weakly-supervised anomaly detection task that uses video-level labelled training data to detect frame-level polyps. In particular, we propose a novel convolutional transformer-based multiple instance learning method designed to identify abnormal frames (i.e., frames with polyps) from anomalous videos (i.e., videos containing at least one frame with polyp). In our method, local and global temporal dependencies are seamlessly captured while we simultaneously optimise video and snippet-level anomaly scores. A contrastive snippet mining method is also proposed to enable an effective modelling of the challenging polyp cases. The resulting method achieves a detection accuracy that is substantially better than current state-of-the-art approaches on a new large-scale colonoscopy video dataset introduced in this work.
PDF MICCAI 2022 Early Accept
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Breaking with Fixed Set Pathology Recognition through Report-Guided Contrastive Training
Authors:Constantin Seibold, Simon Reiß, M. Saquib Sarfraz, Rainer Stiefelhagen, Jens Kleesiek
When reading images, radiologists generate text reports describing the findings therein. Current state-of-the-art computer-aided diagnosis tools utilize a fixed set of predefined categories automatically extracted from these medical reports for training. This form of supervision limits the potential usage of models as they are unable to pick up on anomalies outside of their predefined set, thus, making it a necessity to retrain the classifier with additional data when faced with novel classes. In contrast, we investigate direct text supervision to break away from this closed set assumption. By doing so, we avoid noisy label extraction via text classifiers and incorporate more contextual information. We employ a contrastive global-local dual-encoder architecture to learn concepts directly from unstructured medical reports while maintaining its ability to perform free form classification. We investigate relevant properties of open set recognition for radiological data and propose a method to employ currently weakly annotated data into training. We evaluate our approach on the large-scale chest X-Ray datasets MIMIC-CXR, CheXpert, and ChestX-Ray14 for disease classification. We show that despite using unstructured medical report supervision, we perform on par with direct label supervision through a sophisticated inference setting.
PDF Provisionally Accepted at MICCAI2022
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