DuoFormer: Leveraging Hierarchical Visual Representations by Local and Global Attention

We here propose a novel hierarchical transformer model that adeptly integrates the feature extraction capabilities of Convolutional Neural Networks (CNNs) with the advanced representational potential of Vision Transformers (ViTs). Addressing the lack of inductive biases and dependence on extensive training datasets in ViTs, our model employs a CNN backbone to generate hierarchical visual representations. These representations are then adapted for transformer input through an innovative patch tokenization. We also introduce a 'scale attention' mechanism that captures cross-scale dependencies, complementing patch attention to enhance spatial understanding and preserve global perception. Our approach significantly outperforms baseline models on small and medium-sized medical datasets, demonstrating its efficiency and generalizability. The components are designed as plug-and-play for different CNN architectures and can be adapted for multiple applications. The code is available at https://github.com/xiaoyatang/DuoFormer.git.

CLASS-M: Adaptive stain separation-based contrastive learning with pseudo-labeling for histopathological image classification

Histopathological image classification is an important task in medical image analysis. Recent approaches generally rely on weakly supervised learning due to the ease of acquiring case-level labels from pathology reports. However, patch-level classification is preferable in applications where only a limited number of cases are available or when local prediction accuracy is critical. On the other hand, acquiring extensive datasets with localized labels for training is not feasible. In this paper, we propose a semi-supervised patch-level histopathological image classification model, named CLASS-M, that does not require extensively labeled datasets. CLASS-M is formed by two main parts: a contrastive learning module that uses separated Hematoxylin and Eosin images generated through an adaptive stain separation process, and a module with pseudo-labels using MixUp. We compare our model with other state-of-the-art models on two clear cell renal cell carcinoma datasets. We demonstrate that our CLASS-M model has the best performance on both datasets. Our code is available at github.com/BzhangURU/Paper_CLASS-M/tree/main

Stain based contrastive co-training for histopathological image analysis

We propose a novel semi-supervised learning approach for classification of histopathology images. We employ strong supervision with patch-level annotations combined with a novel co-training loss to create a semi-supervised learning framework. Co-training relies on multiple conditionally independent and sufficient views of the data. We separate the hematoxylin and eosin channels in pathology images using color deconvolution to create two views of each slide that can partially fulfill these requirements. Two separate CNNs are used to embed the two views into a joint feature space. We use a contrastive loss between the views in this feature space to implement co-training. We evaluate our approach in clear cell renal cell and prostate carcinomas, and demonstrate improvement over state-of-the-art semi-supervised learning methods.