Self-supervised driven consistency training for annotation efficient histopathology image analysis [article]

Chetan L. Srinidhi, Seung Wook Kim, Fu-Der Chen, Anne L. Martel
2021 arXiv   pre-print
Training a neural network with a large labeled dataset is still a dominant paradigm in computational histopathology. However, obtaining such exhaustive manual annotations is often expensive, laborious, and prone to inter and Intra-observer variability. While recent self-supervised and semi-supervised methods can alleviate this need by learn-ing unsupervised feature representations, they still struggle to generalize well to downstream tasks when the number of labeled instances is small. In this
more » ... ork, we overcome this challenge by leveraging both task-agnostic and task-specific unlabeled data based on two novel strategies: i) a self-supervised pretext task that harnesses the underlying multi-resolution contextual cues in histology whole-slide images to learn a powerful supervisory signal for unsupervised representation learning; ii) a new teacher-student semi-supervised consistency paradigm that learns to effectively transfer the pretrained representations to downstream tasks based on prediction consistency with the task-specific un-labeled data. We carry out extensive validation experiments on three histopathology benchmark datasets across two classification and one regression-based tasks, i.e., tumor metastasis detection, tissue type classification, and tumor cellularity quantification. Under limited-label data, the proposed method yields tangible improvements, which is close or even outperforming other state-of-the-art self-supervised and supervised baselines. Furthermore, we empirically show that the idea of bootstrapping the self-supervised pretrained features is an effective way to improve the task-specific semi-supervised learning on standard benchmarks. Code and pretrained models will be made available at: https://github.com/srinidhiPY/SSL_CR_Histo
arXiv:2102.03897v3 fatcat:gydyinplx5gttgziblpdmi6vnm