Semi-Supervised Classification of Noisy, Gigapixel Histology Images

Multi-scale representation attention based deep multiple instance learning for gigapixel whole slide image analysis

Recently, convolutional neural networks (CNNs) directly using whole slide images (WSIs) for tumor diagnosis and analysis have attracted considerable attention, because they only utilize the slide-level label for model training without any additional annotations. However, it is still a challenging task to directly handle gigapixel WSIs, due to the billions of pixels and intra-variations in each WSI. To overcome this problem, in this paper, we propose a novel end-to-end interpretable deep MIL framework for WSI analysis, by using a two-branch deep neural network and a multi-scale representation attention mechanism to directly extract features from all patches of each WSI. Specifically, we first divide each WSI into bag-, patch- and cell-level images, and then assign the slide-level label to its corresponding bag-level images, so that WSI classification becomes a MIL problem. Additionally, we design a novel multi-scale representation attention mechanism, and embed it into a two-branch deep network to simultaneously mine the bag with a correct label, the significant patches and their cell-level information. Extensive experiments demonstrate the superior performance of the proposed framework over recent state-of-the-art methods, in term of classification accuracy and model interpretability. All source codes are released at: https://github.com/xhangchen/MRAN/.

A Semi-supervised Learning for Segmentation of Gigapixel Histopathology Images from Brain Tissues

Automated segmentation of grey matter (GM) and white matter (WM) in gigapixel histopathology images is advantageous to analyzing distributions of disease pathologies, further aiding in neuropathologic deep phenotyping. Although supervised deep learning methods have shown good performance, its requirement of a large amount of labeled data may not be cost-effective for large scale projects. In the case of GM/WM segmentation, trained experts need to carefully trace the delineation in gigapixel images. To minimize manual labeling, we consider semi-surprised learning (SSL) and deploy one state-of-the-art SSL method (FixMatch) on WSIs. Then we propose a two-stage scheme to further improve the performance of SSL: the first stage is a self-supervised module to train an encoder to learn the visual representations of unlabeled data, subsequently, this well-trained encoder will be an initialization of consistency loss-based SSL in the second stage. We test our method on Amyloid-β stained histopathology images and the results outperform FixMatch with the mean IoU score at around 2% by using 6,000 labeled tiles while over 10% by using only 600 labeled tiles from 2 WSIs.Clinical relevance- this work minimizes the required labeling efforts by trained personnel. An improved GM/WM segmentation method could further aid in the study of brain diseases, such as Alzheimer's disease.

Joint Semi-supervised and Active Learning for Segmentation of Gigapixel Pathology Images with Cost-Effective Labeling

The need for manual and detailed annotations limits the applicability of supervised deep learning algorithms in medical image analyses, specifically in the field of pathology. Semi-supervised learning (SSL) provides an effective way for leveraging unlabeled data to relieve the heavy reliance on the amount of labeled samples when training a model. Although SSL has shown good performance, the performance of recent state-of-the-art SSL methods on pathology images is still under study. The problem for selecting the most optimal data to label for SSL is not fully explored. To tackle this challenge, we propose a semi-supervised active learning framework with a region-based selection criterion. This framework iteratively selects regions for annotation query to quickly expand the diversity and volume of the labeled set. We evaluate our framework on a grey-matter/white-matter segmentation problem using gigapixel pathology images from autopsied human brain tissues. With only 0.1% regions labeled, our proposed algorithm can reach a competitive IoU score compared to fully-supervised learning and outperform the current state-of-the-art SSL by more than 10% of IoU score and DICE coefficient.