Kernel Attention Transformer (KAT) for Histopathology Whole Slide Image Classification

Transformer has been widely used in histopathology whole slide image (WSI) classification for the purpose of tumor grading, prognosis analysis, etc. However, the design of token-wise self-attention and positional embedding strategy in the common Transformer limits the effectiveness and efficiency in the application to gigapixel histopathology images. In this paper, we propose a kernel attention Transformer (KAT) for histopathology WSI classification. The information transmission of the tokens is achieved by cross-attention between the tokens and a set of kernels related to a set of positional anchors on the WSI. Compared to the common Transformer structure, the proposed KAT can better describe the hierarchical context information of the local regions of the WSI and meanwhile maintains a lower computational complexity. The proposed method was evaluated on a gastric dataset with 2040 WSIs and an endometrial dataset with 2560 WSIs, and was compared with 6 state-of-the-art methods. The experimental results have demonstrated the proposed KAT is effective and efficient in the task of histopathology WSI classification and is superior to the state-of-the-art methods. The code is available at https://github.com/zhengyushan/kat.

Lesion-Aware Contrastive Representation Learning for Histopathology Whole Slide Images Analysis

Local representation learning has been a key challenge to promote the performance of the histopathological whole slide images analysis. The previous representation learning methods followed the supervised learning paradigm. However, manual annotation for large-scale WSIs is time-consuming and labor-intensive. Hence, the self-supervised contrastive learning has recently attracted intensive attention. The present contrastive learning methods treat each sample as a single class, which suffers from class collision problems, especially in the domain of histopathology image analysis. In this paper, we proposed a novel contrastive representation learning framework named Lesion-Aware Contrastive Learning (LACL) for histopathology whole slide image analysis. We built a lesion queue based on the memory bank structure to store the representations of different classes of WSIs, which allowed the contrastive model to selectively define the negative pairs during the training. Moreover, We designed a queue refinement strategy to purify the representations stored in the lesion queue. The experimental results demonstrate that LACL achieves the best performance in histopathology image representation learning on different datasets, and outperforms state-of-the-art methods under different WSI classification benchmarks. The code is available at https://github.com/junl21/lacl.

Histopathology WSI Encoding based on GCNs for Scalable and Efficient Retrieval of Diagnostically Relevant Regions

Content-based histopathological image retrieval (CBHIR) has become popular in recent years in the domain of histopathological image analysis. CBHIR systems provide auxiliary diagnosis information for pathologists by searching for and returning regions that are contently similar to the region of interest (ROI) from a pre-established database. While, it is challenging and yet significant in clinical applications to retrieve diagnostically relevant regions from a database that consists of histopathological whole slide images (WSIs) for a query ROI. In this paper, we propose a novel framework for regions retrieval from WSI-database based on hierarchical graph convolutional networks (GCNs) and Hash technique. Compared to the present CBHIR framework, the structural information of WSI is preserved through graph embedding of GCNs, which makes the retrieval framework more sensitive to regions that are similar in tissue distribution. Moreover, benefited from the hierarchical GCN structures, the proposed framework has good scalability for both the size and shape variation of ROIs. It allows the pathologist defining query regions using free curves according to the appearance of tissue. Thirdly, the retrieval is achieved based on Hash technique, which ensures the framework is efficient and thereby adequate for practical large-scale WSI-database. The proposed method was validated on two public datasets for histopathological WSI analysis and compared to the state-of-the-art methods. The proposed method achieved mean average precision above 0.857 on the ACDC-LungHP dataset and above 0.864 on the Camelyon16 dataset in the irregular region retrieval tasks, which are superior to the state-of-the-art methods. The average retrieval time from a database within 120 WSIs is 0.802 ms.

Deep Attributes from Context-Aware Regional Neural Codes

Recently, many researches employ middle-layer output of convolutional neural network models (CNN) as features for different visual recognition tasks. Although promising results have been achieved in some empirical studies, such type of representations still suffer from the well-known issue of semantic gap. This paper proposes so-called deep attribute framework to alleviate this issue from three aspects. First, we introduce object region proposals as intermedia to represent target images, and extract features from region proposals. Second, we study aggregating features from different CNN layers for all region proposals. The aggregation yields a holistic yet compact representation of input images. Results show that cross-region max-pooling of soft-max layer output outperform all other layers. As soft-max layer directly corresponds to semantic concepts, this representation is named "deep attributes". Third, we observe that only a small portion of generated regions by object proposals algorithm are correlated to classification target. Therefore, we introduce context-aware region refining algorithm to pick out contextual regions and build context-aware classifiers. We apply the proposed deep attributes framework for various vision tasks. Extensive experiments are conducted on standard benchmarks for three visual recognition tasks, i.e., image classification, fine-grained recognition and visual instance retrieval. Results show that deep attribute approaches achieve state-of-the-art results, and outperforms existing peer methods with a significant margin, even though some benchmarks have little overlap of concepts with the pre-trained CNN models.

Factorization of View-Object Manifolds for Joint Object Recognition and Pose Estimation

Due to large variations in shape, appearance, and viewing conditions, object recognition is a key precursory challenge in the fields of object manipulation and robotic/AI visual reasoning in general. Recognizing object categories, particular instances of objects and viewpoints/poses of objects are three critical subproblems robots must solve in order to accurately grasp/manipulate objects and reason about their environments. Multi-view images of the same object lie on intrinsic low-dimensional manifolds in descriptor spaces (e.g. visual/depth descriptor spaces). These object manifolds share the same topology despite being geometrically different. Each object manifold can be represented as a deformed version of a unified manifold. The object manifolds can thus be parameterized by its homeomorphic mapping/reconstruction from the unified manifold. In this work, we develop a novel framework to jointly solve the three challenging recognition sub-problems, by explicitly modeling the deformations of object manifolds and factorizing it in a view-invariant space for recognition. We perform extensive experiments on several challenging datasets and achieve state-of-the-art results.