Sampling Based Tumor Recognition in Whole-Slide Histology Image With Deep Learning Approaches

A comprehensive survey of intestine histopathological image analysis using machine vision approaches

Colorectal Cancer (CRC) is currently one of the most common and deadly cancers. CRC is the third most common malignancy and the fourth leading cause of cancer death worldwide. It ranks as the second most frequent cause of cancer-related deaths in the United States and other developed countries. Histopathological images contain sufficient phenotypic information, they play an indispensable role in the diagnosis and treatment of CRC. In order to improve the objectivity and diagnostic efficiency for image analysis of intestinal histopathology, Computer-aided Diagnosis (CAD) methods based on machine learning (ML) are widely applied in image analysis of intestinal histopathology. In this investigation, we conduct a comprehensive study on recent ML-based methods for image analysis of intestinal histopathology. First, we discuss commonly used datasets from basic research studies with knowledge of intestinal histopathology relevant to medicine. Second, we introduce traditional ML methods commonly used in intestinal histopathology, as well as deep learning (DL) methods. Then, we provide a comprehensive review of the recent developments in ML methods for segmentation, classification, detection, and recognition, among others, for histopathological images of the intestine. Finally, the existing methods have been studied, and the application prospects of these methods in this field are given.

A survey of Transformer applications for histopathological image analysis: New developments and future directions

Transformers have been widely used in many computer vision challenges and have shown the capability of producing better results than convolutional neural networks (CNNs). Taking advantage of capturing long-range contextual information and learning more complex relations in the image data, Transformers have been used and applied to histopathological image processing tasks. In this survey, we make an effort to present a thorough analysis of the uses of Transformers in histopathological image analysis, covering several topics, from the newly built Transformer models to unresolved challenges. To be more precise, we first begin by outlining the fundamental principles of the attention mechanism included in Transformer models and other key frameworks. Second, we analyze Transformer-based applications in the histopathological imaging domain and provide a thorough evaluation of more than 100 research publications across different downstream tasks to cover the most recent innovations, including survival analysis and prediction, segmentation, classification, detection, and representation. Within this survey work, we also compare the performance of CNN-based techniques to Transformers based on recently published papers, highlight major challenges, and provide interesting future research directions. Despite the outstanding performance of the Transformer-based architectures in a number of papers reviewed in this survey, we anticipate that further improvements and exploration of Transformers in the histopathological imaging domain are still required in the future. We hope that this survey paper will give readers in this field of study a thorough understanding of Transformer-based techniques in histopathological image analysis, and an up-to-date paper list summary will be provided at https://github.com/S-domain/Survey-Paper .

Deep learning for pancreatic diseases based on endoscopic ultrasound: A systematic review

BACKGROUND AND AIMS

Endoscopic ultrasonography (EUS) is one of the main examinations in pancreatic diseases. A series of the studies reported the application of deep learning (DL)-assisted EUS in the diagnosis of pancreatic diseases. This systematic review is to evaluate the role of DL algorithms in assisting EUS diagnosis of pancreatic diseases.

METHODS

Literature search were conducted in PubMed and Semantic Scholar databases. Studies that developed DL models for pancreatic diseases based on EUS were eligible for inclusion. This review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and quality assessment of the included studies was performed according to the IJMEDI checklist.

RESULTS

A total of 23 studies were enrolled into this systematic review, which could be categorized into three groups according to computer vision tasks: classification, detection and segmentation. Seventeen studies focused on the classification task, among which five studies developed simple neural network (NN) models while twelve studies constructed convolutional NN (CNN) models. Three studies were concerned the detection task and five studies were the segmentation task, all based on CNN architectures. All models presented in the studies performed well based on EUS images, videos or voice. According to the IJMEDI checklist, six studies were recognized as high-grade quality, with scores beyond 35 points.

CONCLUSIONS

DL algorithms show great potential in EUS images/videos/voice for pancreatic diseases. However, there is room for improvement such as sample sizes, multi-center cooperation, data preprocessing, model interpretability, and code sharing.

Risk-aware survival time prediction from whole slide pathological images

Deep-learning-based survival prediction can assist doctors by providing additional information for diagnosis by estimating the risk or time of death. The former focuses on ranking deaths among patients based on the Cox model, whereas the latter directly predicts the survival time of each patient. However, it is observed that survival time prediction for the patients, particularly with close observation times, possibly has incorrect orders, leading to low prediction accuracy. Therefore, in this paper, we present a whole slide image (WSI)-based survival time prediction method that takes advantage of both the risk as well as time prediction. Specifically, we propose to combine these two approaches by extracting the risk prediction features and using them as guides for the survival time prediction. Considering the high resolution of WSIs, we extract tumor patches from WSIs using a pre-trained tumor classifier and apply the graph convolutional network to aggregate information across these patches effectively. Extensive experiments demonstrate that the proposed method significantly improves the time prediction accuracy when compared with direct prediction of the survival times without guidance and outperforms existing methods.

Identify Representative Samples by Conditional Random Field of Cancer Histology Images

Pathology analysis is crucial to precise cancer diagnoses and the succeeding treatment plan as well. To detect abnormality in histopathology images with prevailing patch-based convolutional neural networks (CNNs), contextual information often serves as a powerful cue. However, as whole-slide images (WSIs) are characterized by intense morphological heterogeneity and extensive tissue scale, a straightforward visual span to a larger context may not well capture the information closely associated with the focal patch. In this paper, we propose a novel pixel-offset based patch-location method to identify high-representative tissues, with a CNN backbone. Pathology Deformable Conditional Random Field (PDCRF) is proposed to learn the offsets and weights of neighboring contexts in a spatial-adaptive manner, to search for high-representative patches. A CNN structure with the localized patches as training input is then capable of consistently reaching superior classification outcomes for histology images. Overall, the proposed method has achieved state-of-the-art performance, in terms of the test classification accuracy improvement to the baseline by 1.15-2.60%, 0.78-1.78%, and 1.47-2.18% on TCGA public datasets of TCGA-STAD, TCGA-COAD, and TCGA-READ respectively. It also achieves 88.95% test accuracy and 0.920 test AUC on Camelyon 16. To show the effectiveness of the proposed framework on downstream tasks, we take a further step by incorporating an active learning model, which noticeably reduces the number of manual annotations by PDCRF to reach a parallel patch-based histology classifier.

Deep Learning on Histopathological Images for Colorectal Cancer Diagnosis: A Systematic Review

Colorectal cancer (CRC) is the second most common cancer in women and the third most common in men, with an increasing incidence. Pathology diagnosis complemented with prognostic and predictive biomarker information is the first step for personalized treatment. The increased diagnostic load in the pathology laboratory, combined with the reported intra- and inter-variability in the assessment of biomarkers, has prompted the quest for reliable machine-based methods to be incorporated into the routine practice. Recently, Artificial Intelligence (AI) has made significant progress in the medical field, showing potential for clinical applications. Herein, we aim to systematically review the current research on AI in CRC image analysis. In histopathology, algorithms based on Deep Learning (DL) have the potential to assist in diagnosis, predict clinically relevant molecular phenotypes and microsatellite instability, identify histological features related to prognosis and correlated to metastasis, and assess the specific components of the tumor microenvironment.