Context-Aware Convolutional Neural Network for Grading of Colorectal Cancer Histology Images

Computational pathology: A survey review and the way forward

Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.

Artificial Intelligence in Oncology: Current Landscape, Challenges, and Future Directions

Artificial intelligence (AI) in oncology is advancing beyond algorithm development to integration into clinical practice. This review describes the current state of the field, with a specific focus on clinical integration. AI applications are structured according to cancer type and clinical domain, focusing on the four most common cancers and tasks of detection, diagnosis, and treatment. These applications encompass various data modalities, including imaging, genomics, and medical records. We conclude with a summary of existing challenges, evolving solutions, and potential future directions for the field.

SIGNIFICANCE

AI is increasingly being applied to all aspects of oncology, where several applications are maturing beyond research and development to direct clinical integration. This review summarizes the current state of the field through the lens of clinical translation along the clinical care continuum. Emerging areas are also highlighted, along with common challenges, evolving solutions, and potential future directions for the field.

Hepatic and portal vein segmentation with dual-stream deep neural network

BACKGROUND

Liver lesions mainly occur inside the liver parenchyma, which are difficult to locate and have complicated relationships with essential vessels. Thus, preoperative planning is crucial for the resection of liver lesions. Accurate segmentation of the hepatic and portal veins (PVs) on computed tomography (CT) images is of great importance for preoperative planning. However, manually labeling the mask of vessels is laborious and time-consuming, and the labeling results of different clinicians are prone to inconsistencies. Hence, developing an automatic segmentation algorithm for hepatic and PVs on CT images has attracted the attention of researchers. Unfortunately, existing deep learning based automatic segmentation methods are prone to misclassifying peripheral vessels into wrong categories.

PURPOSE

This study aims to provide a fully automatic and robust semantic segmentation algorithm for hepatic and PVs, guiding subsequent preoperative planning. In addition, to address the deficiency of the public dataset for hepatic and PV segmentation, we revise the annotations of the Medical Segmentation Decathlon (MSD) hepatic vessel segmentation dataset and add the masks of the hepatic veins (HVs) and PVs.

METHODS

We proposed a structure with a dual-stream encoder combining convolution and Transformer block, named Dual-stream Hepatic Portal Vein segmentation Network, to extract local features and long-distance spatial information, thereby extracting anatomical information of hepatic and portal vein, avoiding misdivisions of adjacent peripheral vessels. Besides, a multi-scale feature fusion block based on dilated convolution is proposed to extract multi-scale features on expanded perception fields for local features, and a multi-level fusing attention module is introduced for efficient context information extraction. Paired t-test is conducted to evaluate the significant difference in dice between the proposed methods and the comparing methods.

RESULTS

Two datasets are constructed from the original MSD dataset. For each dataset, 50 cases are randomly selected for model evaluation in the scheme of 5-fold cross-validation. The results show that our method outperforms the state-of-the-art Convolutional Neural Network-based and transformer-based methods. Specifically, for the first dataset, our model reaches 0.815, 0.830, and 0.807 at overall dice, precision, and sensitivity. The dice of the hepatic and PVs are 0.835 and 0.796, which also exceed the numeric result of the comparing methods. Almost all the p-values of paired t-tests on the proposed approach and comparing approaches are smaller than 0.05. On the second dataset, the proposed algorithm achieves 0.749, 0.762, 0.726, 0.835, and 0.796 for overall dice, precision, sensitivity, dice for HV, and dice for PV, among which the first four numeric results exceed comparing methods.

CONCLUSIONS

The proposed method is effective in solving the problem of misclassifying interlaced peripheral veins for the HV and PV segmentation task and outperforming the comparing methods on the relabeled dataset.

Social network analysis of cell networks improves deep learning for prediction of molecular pathways and key mutations in colorectal cancer

Colorectal cancer (CRC) is a primary global health concern, and identifying the molecular pathways, genetic subtypes, and mutations associated with CRC is crucial for precision medicine. However, traditional measurement techniques such as gene sequencing are costly and time-consuming, while most deep learning methods proposed for this task lack interpretability. This study offers a new approach to enhance the state-of-the-art deep learning methods for molecular pathways and key mutation prediction by incorporating cell network information. We build cell graphs with nuclei as nodes and nuclei connections as edges of the network and leverage Social Network Analysis (SNA) measures to extract abstract, perceivable, and interpretable features that explicitly describe the cell network characteristics in an image. Our approach does not rely on precise nuclei segmentation or feature extraction, is computationally efficient, and is easily scalable. In this study, we utilize the TCGA-CRC-DX dataset, comprising 499 patients and 502 diagnostic slides from primary colorectal tumours, sourced from 36 distinct medical centres in the United States. By incorporating the SNA features alongside deep features in two multiple instance learning frameworks, we demonstrate improved performance for chromosomal instability (CIN), hypermutated tumour (HM), TP53 gene, BRAF gene, and Microsatellite instability (MSI) status prediction tasks (2.4%-4% and 7-8.8% improvement in AUROC and AUPRC on average). Additionally, our method achieves outstanding performance on MSI prediction in an external PAIP dataset (99% AUROC and 98% AUPRC), demonstrating its generalizability. Our findings highlight the discrimination power of SNA features and how they can be beneficial to deep learning models' performance and provide insights into the correlation of cell network profiles with molecular pathways and key mutations.

From Pixels to Prognosis: A Survey on AI-Driven Cancer Patient Survival Prediction Using Digital Histology Images

Survival analysis is an integral part of medical statistics that is extensively utilized to establish prognostic indices for mortality or disease recurrence, assess treatment efficacy, and tailor effective treatment plans. The identification of prognostic biomarkers capable of predicting patient survival is a primary objective in the field of cancer research. With the recent integration of digital histology images into routine clinical practice, a plethora of Artificial Intelligence (AI)-based methods for digital pathology has emerged in scholarly literature, facilitating patient survival prediction. These methods have demonstrated remarkable proficiency in analyzing and interpreting whole slide images, yielding results comparable to those of expert pathologists. The complexity of AI-driven techniques is magnified by the distinctive characteristics of digital histology images, including their gigapixel size and diverse tissue appearances. Consequently, advanced patch-based methods are employed to effectively extract features that correlate with patient survival. These computational methods significantly enhance survival prediction accuracy and augment prognostic capabilities in cancer patients. The review discusses the methodologies employed in the literature, their performance metrics, ongoing challenges, and potential solutions for future advancements. This paper explains survival analysis and feature extraction methods for analyzing cancer patients. It also compiles essential acronyms related to cancer precision medicine. Furthermore, it is noteworthy that this is the inaugural review paper in the field. The target audience for this interdisciplinary review comprises AI practitioners, medical statisticians, and progressive oncologists who are enthusiastic about translating AI-driven solutions into clinical practice. We expect this comprehensive review article to guide future research directions in the field of cancer research.

Computational pathology-based weakly supervised prediction model for MGMT promoter methylation status in glioblastoma

Introduction

The methylation status of oxygen 6-methylguanine-DNA methyltransferase (MGMT) is closely related to the treatment and prognosis of glioblastoma. However, there are currently some challenges in detecting the methylation status of MGMT promoters. The hematoxylin and eosin (H&E)-stained histopathological slides have always been the gold standard for tumor diagnosis.

Methods

In this study, based on the TCGA database and H&E-stained Whole slide images (WSI) of Beijing Tiantan Hospital, we constructed a weakly supervised prediction model of MGMT promoter methylation status in glioblastoma by using two Transformer structure models.

Results

The accuracy scores of this model in the TCGA dataset and our independent dataset were 0.79 (AUC = 0.86) and 0.76 (AUC = 0.83), respectively.

Conclusion

The model demonstrates effective prediction of MGMT promoter methylation status in glioblastoma and exhibits some degree of generalization capability. At the same time, our study also shows that adding Patches automatic screening module to the computational pathology research framework of glioma can significantly improve the model effect.

CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

Reversed domain adaptation for nuclei segmentation-based pathological image classification

Despite the fact that digital pathology has provided a new paradigm for modern medicine, the insufficiency of annotations for training remains a significant challenge. Due to the weak generalization abilities of deep-learning models, their performance is notably constrained in domains without sufficient annotations. Our research aims to enhance the model's generalization ability through domain adaptation, increasing the prediction ability for the target domain data while only using the source domain labels for training. To further enhance classification performance, we introduce nuclei segmentation to provide the classifier with more diagnostically valuable nuclei information. In contrast to the general domain adaptation that generates source-like results in the target domain, we propose a reversed domain adaptation strategy that generates target-like results in the source domain, enabling the classification model to be more robust to inaccurate segmentation results. The proposed reversed unsupervised domain adaptation can effectively reduce the disparities in nuclei segmentation between the source and target domains without any target domain labels, leading to improved image classification performance in the target domain. The whole framework is designed in a unified manner so that the segmentation and classification modules can be trained jointly. Extensive experiments demonstrate that the proposed method significantly improves the classification performance in the target domain and outperforms existing general domain adaptation methods.

Opportunities and challenges of computer aided diagnosis in new millennium: A bibliometric analysis from 2000 to 2023

BACKGROUND

After entering the new millennium, computer-aided diagnosis (CAD) is rapidly developing as an emerging technology worldwide. Expanding the spectrum of CAD-related diseases is a possible future research trend. Nevertheless, bibliometric studies in this area have not yet been reported. This study aimed to explore the hotspots and frontiers of research on CAD from 2000 to 2023, which may provide a reference for researchers in this field.

METHODS

In this paper, we use bibliometrics to analyze CAD-related literature in the Web of Science database between 2000 and 2023. The scientometric softwares VOSviewer and CiteSpace were used to visually analyze the countries, institutions, authors, journals, references and keywords involved in the literature. Keywords burst analysis were utilized to further explore the current state and development trends of research on CAD.

RESULTS

A total of 13,970 publications were included in this study, with a noticeably rising annual publication trend. China and the United States are major contributors to the publication, with the United States being the dominant position in CAD research. The American research institutions, lead by the University of Chicago, are pioneers of CAD. Acharya UR, Zheng B and Chan HP are the most prolific authors. Institute of Electrical and Electronics Engineers Transactions on Medical Imaging focuses on CAD and publishes the most articles. New computer technologies related to CAD are in the forefront of attention. Currently, CAD is used extensively in breast diseases, pulmonary diseases and brain diseases.

CONCLUSION

Expanding the spectrum of CAD-related diseases is a possible future research trend. How to overcome the lack of large sample datasets and establish a universally accepted standard for the evaluation of CAD system performance are urgent issues for CAD development and validation. In conclusion, this paper provides valuable information on the current state of CAD research and future developments.

A Novel and Efficient Digital Pathology Classifier for Predicting Cancer Biomarkers Using Sequencer Architecture

In digital pathology tasks, transformers have achieved state-of-the-art results, surpassing convolutional neural networks (CNNs). However, transformers are usually complex and resource intensive. This study developed a novel and efficient digital pathology classifier called DPSeq to predict cancer biomarkers through fine-tuning a sequencer architecture integrating horizontal and vertical bidirectional long short-term memory networks. Using hematoxylin and eosin-stained histopathologic images of colorectal cancer from two international data sets (The Cancer Genome Atlas and Molecular and Cellular Oncology), the predictive performance of DPSeq was evaluated in a series of experiments. DPSeq demonstrated exceptional performance for predicting key biomarkers in colorectal cancer (microsatellite instability status, hypermutation, CpG island methylator phenotype status, BRAF mutation, TP53 mutation, and chromosomal instability), outperforming most published state-of-the-art classifiers in a within-cohort internal validation and a cross-cohort external validation. In addition, under the same experimental conditions using the same set of training and testing data sets, DPSeq surpassed four CNNs (ResNet18, ResNet50, MobileNetV2, and EfficientNet) and two transformer (Vision Transformer and Swin Transformer) models, achieving the highest area under the receiver operating characteristic curve and area under the precision-recall curve values in predicting microsatellite instability status, BRAF mutation, and CpG island methylator phenotype status. Furthermore, DPSeq required less time for both training and prediction because of its simple architecture. Therefore, DPSeq appears to be the preferred choice over transformer and CNN models for predicting cancer biomarkers.

A Hierarchical Graph V-Net With Semi-Supervised Pre-Training for Histological Image Based Breast Cancer Classification

Numerous patch-based methods have recently been proposed for histological image based breast cancer classification. However, their performance could be highly affected by ignoring spatial contextual information in the whole slide image (WSI). To address this issue, we propose a novel hierarchical Graph V-Net by integrating 1) patch-level pre-training and 2) context-based fine-tuning, with a hierarchical graph network. Specifically, a semi-supervised framework based on knowledge distillation is first developed to pre-train a patch encoder for extracting disease-relevant features. Then, a hierarchical Graph V-Net is designed to construct a hierarchical graph representation from neighboring/similar individual patches for coarse-to-fine classification, where each graph node (corresponding to one patch) is attached with extracted disease-relevant features and its target label during training is the average label of all pixels in the corresponding patch. To evaluate the performance of our proposed hierarchical Graph V-Net, we collect a large WSI dataset of 560 WSIs, with 30 labeled WSIs from the BACH dataset (through our further refinement), 30 labeled WSIs and 500 unlabeled WSIs from Yunnan Cancer Hospital. Those 500 unlabeled WSIs are employed for patch-level pre-training to improve feature representation, while 60 labeled WSIs are used to train and test our proposed hierarchical Graph V-Net. Both comparative assessment and ablation studies demonstrate the superiority of our proposed hierarchical Graph V-Net over state-of-the-art methods in classifying breast cancer from WSIs. The source code and our annotations for the BACH dataset have been released at https://github.com/lyhkevin/Graph-V-Net.

CaMeL-Net: Centroid-aware metric learning for efficient multi-class cancer classification in pathology images

BACKGROUND AND OBJECTIVE

Cancer grading in pathology image analysis is a major task due to its importance in patient care, treatment, and management. The recent developments in artificial neural networks for computational pathology have demonstrated great potential to improve the accuracy and quality of cancer diagnosis. These improvements are generally ascribable to the advance in the architecture of the networks, often leading to increase in the computation and resources. In this work, we propose an efficient convolutional neural network that is designed to conduct multi-class cancer classification in an accurate and robust manner via metric learning.

METHODS

We propose a centroid-aware metric learning network for an improved cancer grading in pathology images. The proposed network utilizes centroids of different classes within the feature embedding space to optimize the relative distances between pathology images, which manifest the innate similarities/dissimilarities between them. For improved optimization, we introduce a new loss function and a training strategy that are tailored to the proposed network and metric learning.

RESULTS

We evaluated the proposed approach on multiple datasets of colorectal and gastric cancers. For the colorectal cancer, two different datasets were employed that were collected from different acquisition settings. the proposed method achieved an accuracy, F1-score, quadratic weighted kappa of 88.7%, 0.849, and 0.946 for the first dataset and 83.3%, 0.764, and 0.907 for the second dataset, respectively. For the gastric cancer, the proposed method obtained an accuracy of 85.9%, F1-score of 0.793, and quadratic weighted kappa of 0.939. We also found that the proposed method outperforms other competing models and is computationally efficient.

CONCLUSIONS

The experimental results demonstrate that the prediction results by the proposed network are both accurate and reliable. The proposed network not only outperformed other related methods in cancer classification but also achieved superior computational efficiency during training and inference. The future study will entail further development of the proposed method and the application of the method to other problems and domains.

CCF-GNN: A Unified Model Aggregating Appearance, Microenvironment, and Topology for Pathology Image Classification

Pathology images contain rich information of cell appearance, microenvironment, and topology features for cancer analysis and diagnosis. Among such features, topology becomes increasingly important in analysis for cancer immunotherapy. By analyzing geometric and hierarchically structured cell distribution topology, oncologists can identify densely-packed and cancer-relevant cell communities (CCs) for making decisions. Compared to commonly-used pixel-level Convolution Neural Network (CNN) features and cell-instance-level Graph Neural Network (GNN) features, CC topology features are at a higher level of granularity and geometry. However, topological features have not been well exploited by recent deep learning (DL) methods for pathology image classification due to lack of effective topological descriptors for cell distribution and gathering patterns. In this paper, inspired by clinical practice, we analyze and classify pathology images by comprehensively learning cell appearance, microenvironment, and topology in a fine-to-coarse manner. To describe and exploit topology, we design Cell Community Forest (CCF), a novel graph that represents the hierarchical formulation process of big-sparse CCs from small-dense CCs. Using CCF as a new geometric topological descriptor of tumor cells in pathology images, we propose CCF-GNN, a GNN model that successively aggregates heterogeneous features (e.g., appearance, microenvironment) from cell-instance-level, cell-community-level, into image-level for pathology image classification. Extensive cross-validation experiments show that our method significantly outperforms alternative methods on H&E-stained and immunofluorescence images for disease grading tasks with multiple cancer types. Our proposed CCF-GNN establishes a new topological data analysis (TDA) based method, which facilitates integrating multi-level heterogeneous features of point clouds (e.g., for cells) into a unified DL framework.

A Federated Learning Approach to Tumor Detection in Colon Histology Images

Federated learning (FL), a relatively new area of research in medical image analysis, enables collaborative learning of a federated deep learning model without sharing the data of participating clients. In this paper, we propose FedDropoutAvg, a new federated learning approach for detection of tumor in images of colon tissue slides. The proposed method leverages the power of dropout, a commonly employed scheme to avoid overfitting in neural networks, in both client selection and federated averaging processes. We examine FedDropoutAvg against other FL benchmark algorithms for two different image classification tasks using a publicly available multi-site histopathology image dataset. We train and test the proposed model on a large dataset consisting of 1.2 million image tiles from 21 different sites. For testing the generalization of all models, we select held-out test sets from sites that were not used during training. We show that the proposed approach outperforms other FL methods and reduces the performance gap (to less than 3% in terms of AUC on independent test sites) between FL and a central deep learning model that requires all data to be shared for centralized training, demonstrating the potential of the proposed FedDropoutAvg model to be more generalizable than other state-of-the-art federated models. To the best of our knowledge, ours is the first study to effectively utilize the dropout strategy in a federated setting for tumor detection in histology images.

Automated Diagnosis for Colon Cancer Diseases Using Stacking Transformer Models and Explainable Artificial Intelligence

Colon cancer is the third most common cancer type worldwide in 2020, almost two million cases were diagnosed. As a result, providing new, highly accurate techniques in detecting colon cancer leads to early and successful treatment of this disease. This paper aims to propose a heterogenic stacking deep learning model to predict colon cancer. Stacking deep learning is integrated with pretrained convolutional neural network (CNN) models with a metalearner to enhance colon cancer prediction performance. The proposed model is compared with VGG16, InceptionV3, Resnet50, and DenseNet121 using different evaluation metrics. Furthermore, the proposed models are evaluated using the LC25000 and WCE binary and muticlassified colon cancer image datasets. The results show that the stacking models recorded the highest performance for the two datasets. For the LC25000 dataset, the stacked model recorded the highest performance accuracy, recall, precision, and F1 score (100). For the WCE colon image dataset, the stacked model recorded the highest performance accuracy, recall, precision, and F1 score (98). Stacking-SVM achieved the highest performed compared to existing models (VGG16, InceptionV3, Resnet50, and DenseNet121) because it combines the output of multiple single models and trains and evaluates a metalearner using the output to produce better predictive results than any single model. Black-box deep learning models are represented using explainable AI (XAI).

Generalizability of Self-Supervised Training Models for Digital Pathology: A Multicountry Comparison in Colorectal Cancer

PURPOSE

In this multicountry study, we aim to explore the effectiveness of self-supervised learning (SSL) in colorectal cancer (CRC)-related predictive tasks using large amount of unlabeled digital pathology imaging data.

METHODS

We adopted SimSiam to conduct self-supervised pretraining on two large whole-slide image CRC data sets from the United States and Australia. The SSL pretrained encoder is then used in several predictive tasks, including supervised predictive tasks (tissue classification, microsatellite instability v microsatellite stability classification), and weakly supervised predictive tasks (polyp type classification and adenoma grading, and 5-year survival prediction). Performance on the tasks was compared between models using SSL pretraining and those using ImageNet pretraining, and performance for one-country pretraining was compared with two-country pretraining.

RESULTS

We demonstrate that SSL pretraining outperforms ImageNet pretraining in predictive tasks, that is, SSL pretraining outperforms the ImageNet pretraining by 3.01% of F 1 score on average over supervised predictive tasks and 1.53% of AUC on average over weakly supervised predictive tasks. Furthermore, two-country SSL pretraining has shown more stable performance than single-country pretraining, that is, two-country pretraining outperforms at least one of the single-country pretrainings by 1.93% of F 1 on average over supervised predictive tasks and 1.36% of AUC on average over weakly-supervised predictive tasks.

CONCLUSION

We find that using unlabeled image data for SSL pretraining in CRC related tasks is more effective than using ImageNet pretraining. Furthermore, SSL pretraining using data from multiple countries achieve more stable performance and better generalization than single-country pretraining.

Clinical applications of graph neural networks in computational histopathology: A review

Pathological examination is the optimal approach for diagnosing cancer, and with the advancement of digital imaging technologies, it has spurred the emergence of computational histopathology. The objective of computational histopathology is to assist in clinical tasks through image processing and analysis techniques. In the early stages, the technique involved analyzing histopathology images by extracting mathematical features, but the performance of these models was unsatisfactory. With the development of artificial intelligence (AI) technologies, traditional machine learning methods were applied in this field. Although the performance of the models improved, there were issues such as poor model generalization and tedious manual feature extraction. Subsequently, the introduction of deep learning techniques effectively addressed these problems. However, models based on traditional convolutional architectures could not adequately capture the contextual information and deep biological features in histopathology images. Due to the special structure of graphs, they are highly suitable for feature extraction in tissue histopathology images and have achieved promising performance in numerous studies. In this article, we review existing graph-based methods in computational histopathology and propose a novel and more comprehensive graph construction approach. Additionally, we categorize the methods and techniques in computational histopathology according to different learning paradigms. We summarize the common clinical applications of graph-based methods in computational histopathology. Furthermore, we discuss the core concepts in this field and highlight the current challenges and future research directions.

A digital score of peri-epithelial lymphocytic activity predicts malignant transformation in oral epithelial dysplasia

Oral squamous cell carcinoma (OSCC) is amongst the most common cancers, with more than 377,000 new cases worldwide each year. OSCC prognosis remains poor, related to cancer presentation at a late stage, indicating the need for early detection to improve patient prognosis. OSCC is often preceded by a premalignant state known as oral epithelial dysplasia (OED), which is diagnosed and graded using subjective histological criteria leading to variability and prognostic unreliability. In this work, we propose a deep learning approach for the development of prognostic models for malignant transformation and their association with clinical outcomes in histology whole slide images (WSIs) of OED tissue sections. We train a weakly supervised method on OED cases (n = 137) with malignant transformation (n = 50) and mean malignant transformation time of 6.51 years (±5.35 SD). Stratified five-fold cross-validation achieved an average area under the receiver-operator characteristic curve (AUROC) of 0.78 for predicting malignant transformation in OED. Hotspot analysis revealed various features of nuclei in the epithelium and peri-epithelial tissue to be significant prognostic factors for malignant transformation, including the count of peri-epithelial lymphocytes (PELs) (p < 0.05), epithelial layer nuclei count (NC) (p < 0.05), and basal layer NC (p < 0.05). Progression-free survival (PFS) using the epithelial layer NC (p < 0.05, C-index = 0.73), basal layer NC (p < 0.05, C-index = 0.70), and PELs count (p < 0.05, C-index = 0.73) all showed association of these features with a high risk of malignant transformation in our univariate analysis. Our work shows the application of deep learning for the prognostication and prediction of PFS of OED for the first time and offers potential to aid patient management. Further evaluation and testing on multi-centre data is required for validation and translation to clinical practice. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Integrative deep learning analysis improves colon adenocarcinoma patient stratification at risk for mortality

BACKGROUND

Colorectal cancers are the fourth most diagnosed cancer and the second leading cancer in number of deaths. Many clinical variables, pathological features, and genomic signatures are associated with patient risk, but reliable patient stratification in the clinic remains a challenging task. Here we assess how image, clinical, and genomic features can be combined to predict risk.

METHODS

We developed and evaluated integrative deep learning models combining formalin-fixed, paraffin-embedded (FFPE) whole slide images (WSIs), clinical variables, and mutation signatures to stratify colon adenocarcinoma (COAD) patients based on their risk of mortality. Our models were trained using a dataset of 108 patients from The Cancer Genome Atlas (TCGA), and were externally validated on newly generated dataset from Wayne State University (WSU) of 123 COAD patients and rectal adenocarcinoma (READ) patients in TCGA (N = 52).

FINDINGS

We first observe that deep learning models trained on FFPE WSIs of TCGA-COAD separate high-risk (OS < 3 years, N = 38) and low-risk (OS > 5 years, N = 25) patients (AUC = 0.81 ± 0.08, 5 year survival p < 0.0001, 5 year relative risk = 1.83 ± 0.04) though such models are less effective at predicting overall survival (OS) for moderate-risk (3 years < OS < 5 years, N = 45) patients (5 year survival p-value = 0.5, 5 year relative risk = 1.05 ± 0.09). We find that our integrative models combining WSIs, clinical variables, and mutation signatures can improve patient stratification for moderate-risk patients (5 year survival p < 0.0001, 5 year relative risk = 1.87 ± 0.07). Our integrative model combining image and clinical variables is also effective on an independent pathology dataset (WSU-COAD, N = 123) generated by our team (5 year survival p < 0.0001, 5 year relative risk = 1.52 ± 0.08), and the TCGA-READ data (5 year survival p < 0.0001, 5 year relative risk = 1.18 ± 0.17). Our multicenter integrative image and clinical model trained on combined TCGA-COAD and WSU-COAD is effective in predicting risk on TCGA-READ (5 year survival p < 0.0001, 5 year relative risk = 1.82 ± 0.13) data. Pathologist review of image-based heatmaps suggests that nuclear size pleomorphism, intense cellularity, and abnormal structures are associated with high-risk, while low-risk regions have more regular and small cells. Quantitative analysis shows high cellularity, high ratios of tumor cells, large tumor nuclei, and low immune infiltration are indicators of high-risk tiles.

INTERPRETATION

The improved stratification of colorectal cancer patients from our computational methods can be beneficial for treatment plans and enrollment of patients in clinical trials.

FUNDING

This study was supported by the National Cancer Institutes (Grant No. R01CA230031 and P30CA034196). The funders had no roles in study design, data collection and analysis or preparation of the manuscript.

Unleashing the potential of AI for pathology: challenges and recommendations

Computational pathology is currently witnessing a surge in the development of AI techniques, offering promise for achieving breakthroughs and significantly impacting the practices of pathology and oncology. These AI methods bring with them the potential to revolutionize diagnostic pipelines as well as treatment planning and overall patient care. Numerous peer-reviewed studies reporting remarkable performance across diverse tasks serve as a testimony to the potential of AI in the field. However, widespread adoption of these methods in clinical and pre-clinical settings still remains a challenge. In this review article, we present a detailed analysis of the major obstacles encountered during the development of effective models and their deployment in practice. We aim to provide readers with an overview of the latest developments, assist them with insights into identifying some specific challenges that may require resolution, and suggest recommendations and potential future research directions. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Lymphoma Recognition in Histology Image of Gastric Mucosal Biopsy with Prototype Learning

Lymphomas are a group of malignant tumors developed from lymphocytes, which may occur in many organs. Therefore, accurately distinguishing lymphoma from solid tumors is of great clinical significance. Due to the strong ability of graph structure to capture the topology of the micro-environment of cells, graph convolutional networks (GCNs) have been widely used in pathological image processing. Nevertheless, the softmax classification layer of the graph convolutional models cannot drive learned representations compact enough to distinguish some types of lymphomas and solid tumors with strong morphological analogies on H&E-stained images. To alleviate this problem, a prototype learning based model is proposed, namely graph convolutional prototype network (GCPNet). Specifically, the method follows the patch-to-slide architecture first to perform patch-level classification and obtain image-level results by fusing patch-level predictions. The classification model is assembled with a graph convolutional feature extractor and prototype-based classification layer to build more robust feature representations for classification. For model training, a dynamic prototype loss is proposed to give the model different optimization priorities at different stages of training. Besides, a prototype reassignment operation is designed to prevent the model from getting stuck in local minima during optimization. Experiments are conducted on a dataset of 183 Whole slide images (WSI) of gastric mucosa biopsy. The proposed method achieved superior performance than existing methods.Clinical relevance- The work proposed a new deep learning framework tailored to lymphoma recognition on pathological image of gastric mucosal biopsy to differentiate lymphoma, adenocarcinoma and inflammation.

An aggregation of aggregation methods in computational pathology

Image analysis and machine learning algorithms operating on multi-gigapixel whole-slide images (WSIs) often process a large number of tiles (sub-images) and require aggregating predictions from the tiles in order to predict WSI-level labels. In this paper, we present a review of existing literature on various types of aggregation methods with a view to help guide future research in the area of computational pathology (CPath). We propose a general CPath workflow with three pathways that consider multiple levels and types of data and the nature of computation to analyse WSIs for predictive modelling. We categorize aggregation methods according to the context and representation of the data, features of computational modules and CPath use cases. We compare and contrast different methods based on the principle of multiple instance learning, perhaps the most commonly used aggregation method, covering a wide range of CPath literature. To provide a fair comparison, we consider a specific WSI-level prediction task and compare various aggregation methods for that task. Finally, we conclude with a list of objectives and desirable attributes of aggregation methods in general, pros and cons of the various approaches, some recommendations and possible future directions.

An Investigation about Modern Deep Learning Strategies for Colon Carcinoma Grading

Developing computer-aided approaches for cancer diagnosis and grading is currently receiving an increasing demand: this could take over intra- and inter-observer inconsistency, speed up the screening process, increase early diagnosis, and improve the accuracy and consistency of the treatment-planning processes.The third most common cancer worldwide and the second most common in women is colorectal cancer (CRC). Grading CRC is a key task in planning appropriate treatments and estimating the response to them. Unfortunately, it has not yet been fully demonstrated how the most advanced models and methodologies of machine learning can impact this crucial task.This paper systematically investigates the use of advanced deep models (convolutional neural networks and transformer architectures) to improve colon carcinoma detection and grading from histological images. To the best of our knowledge, this is the first attempt at using transformer architectures and ensemble strategies for exploiting deep learning paradigms for automatic colon cancer diagnosis. Results on the largest publicly available dataset demonstrated a substantial improvement with respect to the leading state-of-the-art methods. In particular, by exploiting a transformer architecture, it was possible to observe a 3% increase in accuracy in the detection task (two-class problem) and up to a 4% improvement in the grading task (three-class problem) by also integrating an ensemble strategy.

Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer

Pathological diagnosis of gastric cancer requires pathologists to have extensive clinical experience. To help pathologists improve diagnostic accuracy and efficiency, we collected 1,514 cases of stomach H&E-stained specimens with complete diagnostic information to establish a pathological auxiliary diagnosis system based on deep learning. At the slide level, our system achieves a specificity of 0.8878 while maintaining a high sensitivity close to 1.0 on 269 biopsy specimens (147 malignancies) and 163 surgical specimens (80 malignancies). The classified accuracy of our system is 0.9034 at the slide level for 352 biopsy specimens (201 malignancies) from 50 medical centers. With the help of our system, the pathologists' average false-negative rate and average false-positive rate on 100 biopsy specimens (50 malignancies) are reduced to 1/5 and 1/2 of the original rates, respectively. At the same time, the average uncertainty rate and the average diagnosis time are reduced by approximately 22% and 20%, respectively.

SIAN: STYLE-GUIDED INSTANCE-ADAPTIVE NORMALIZATION FOR MULTI-ORGAN HISTOPATHOLOGY IMAGE SYNTHESIS

Existing deep neural networks for histopathology image synthesis cannot generate image styles that align with different organs, and cannot produce accurate boundaries of clustered nuclei. To address these issues, we propose a style-guided instance-adaptive normalization (SIAN) approach to synthesize realistic color distributions and textures for histopathology images from different organs. SIAN contains four phases, semantization, stylization, instantiation, and modulation. The first two phases synthesize image semantics and styles by using semantic maps and learned image style vectors. The instantiation module integrates geometrical and topological information and generates accurate nuclei boundaries. We validate the proposed approach on a multiple-organ dataset, Extensive experimental results demonstrate that the proposed method generates more realistic histopathology images than four state-of-the-art approaches for five organs. By incorporating synthetic images from the proposed approach to model training, an instance segmentation network can achieve state-of-the-art performance.

Local augmentation based consistency learning for semi-supervised pathology image classification

BACKGROUND AND OBJECTIVE

Labeling pathology images is often costly and time-consuming, which is quite detrimental for supervised pathology image classification that relies heavily on sufficient labeled data during training. Exploring semi-supervised methods based on image augmentation and consistency regularization may effectively alleviate this problem. Nevertheless, traditional image-based augmentation (e.g., flip) produces only a single enhancement to an image, whereas combining multiple image sources may mix unimportant image regions resulting in poor performance. In addition, the regularization losses used in these augmentation approaches typically enforce the consistency of image level predictions, and meanwhile simply require each prediction of augmented image to be consistent bilaterally, which may force pathology image features with better predictions to be wrongly aligned towards the features with worse predictions.

METHODS

To tackle these problems, we propose a novel semi-supervised method called Semi-LAC for pathology image classification. Specifically, we first present local augmentation technique to randomly apply different augmentations produces to each local pathology patch, which can boost the diversity of pathology image and avoid mixing unimportant regions in other images. Moreover, we further propose the directional consistency loss to enforce restrictions on the consistency of both features and prediction results, thus improving the ability of the network to obtain robust representations and achieve accurate predictions.

RESULTS

The proposed method is evaluated on Bioimaging2015 and BACH datasets, and the extensive experiments show the superior performance of our Semi-LAC compared with state-of-the-art methods for pathology image classification.

CONCLUSIONS

We conclude that using the Semi-LAC method can effectively reduce the cost for annotating pathology images, and enhance the ability of classification networks to represent pathology images by using local augmentation techniques and directional consistency loss.

Interpretable classification of pathology whole-slide images using attention based context-aware graph convolutional neural network

BACKGROUND AND OBJECTIVE

Whole slide image (WSI) classification and lesion localization within giga-pixel slide are challenging tasks in computational pathology that requires context-aware representations of histological features to adequately infer nidus. The existing weakly supervised learning methods mainly treat different locations in the slide as independent regions and cannot learn potential nonlinear interactions between instances based on i.i.d assumption, resulting in the model unable to effectively utilize context-ware information to predict the labels of WSIs and locate the region of interest (ROI).

METHODS

Here, we propose an interpretable classification model named bidirectional Attention-based Multiple Instance Learning Graph Convolutional Network (ABMIL-GCN), which hierarchically aggregates context-aware features of instances into a global representation in a topology fashion to predict the slide labels and localize the region of lymph node metastasis in WSIs.

RESULTS

We verified the superiority of this method on the Camelyon16 dataset, and the results show that the average predicted ACC and AUC of the proposed model after flooding optimization can reach 90.89% and 0.9149, respectively. The average accuracy and ACC score are improved by more than 7% and 4% compared with the existing state-of-the-art algorithms.

CONCLUSIONS

The results demonstrate that context-aware GCN outperforms existing weakly supervised learning methods by introducing spatial correlations between the neighbor image patches, which also addresses the 'accuracy-interpretability trade-off' problem. The framework provides a novel paradigm for the clinical application of computer-aided diagnosis and intelligent systems.

One model is all you need: Multi-task learning enables simultaneous histology image segmentation and classification

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600 thousand objects for segmentation and 440 thousand patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900 thousand and 2.1 million nuclei, glands and lumina respectively. We make this resource available to remove a major barrier in the development of explainable models for computational pathology.

A semi-supervised multi-task learning framework for cancer classification with weak annotation in whole-slide images

Cancer region detection (CRD) and subtyping are two fundamental tasks in digital pathology image analysis. The development of data-driven models for CRD and subtyping on whole-slide images (WSIs) would mitigate the burden of pathologists and improve their accuracy in diagnosis. However, the existing models are facing two major limitations. Firstly, they typically require large-scale datasets with precise annotations, which contradicts with the original intention of reducing labor effort. Secondly, for the subtyping task, the non-cancerous regions are treated as the same as cancerous regions within a WSI, which confuses a subtyping model in its training process. To tackle the latter limitation, the previous research proposed to perform CRD first for ruling out the non-cancerous region, then train a subtyping model based on the remaining cancerous patches. However, separately training ignores the interaction of these two tasks, also leads to propagating the error of the CRD task to the subtyping task. To address these issues and concurrently improve the performance on both CRD and subtyping tasks, we propose a semi-supervised multi-task learning (MTL) framework for cancer classification. Our framework consists of a backbone feature extractor, two task-specific classifiers, and a weight control mechanism. The backbone feature extractor is shared by two task-specific classifiers, such that the interaction of CRD and subtyping tasks can be captured. The weight control mechanism preserves the sequential relationship of these two tasks and guarantees the error back-propagation from the subtyping task to the CRD task under the MTL framework. We train the overall framework in a semi-supervised setting, where datasets only involve small quantities of annotations produced by our minimal point-based (min-point) annotation strategy. Extensive experiments on four large datasets with different cancer types demonstrate the effectiveness of the proposed framework in both accuracy and generalization.

Colon Cancer Diagnosis Based on Machine Learning and Deep Learning: Modalities and Analysis Techniques

The treatment and diagnosis of colon cancer are considered to be social and economic challenges due to the high mortality rates. Every year, around the world, almost half a million people contract cancer, including colon cancer. Determining the grade of colon cancer mainly depends on analyzing the gland's structure by tissue region, which has led to the existence of various tests for screening that can be utilized to investigate polyp images and colorectal cancer. This article presents a comprehensive survey on the diagnosis of colon cancer. This covers many aspects related to colon cancer, such as its symptoms and grades as well as the available imaging modalities (particularly, histopathology images used for analysis) in addition to common diagnosis systems. Furthermore, the most widely used datasets and performance evaluation metrics are discussed. We provide a comprehensive review of the current studies on colon cancer, classified into deep-learning (DL) and machine-learning (ML) techniques, and we identify their main strengths and limitations. These techniques provide extensive support for identifying the early stages of cancer that lead to early treatment of the disease and produce a lower mortality rate compared with the rate produced after symptoms develop. In addition, these methods can help to prevent colorectal cancer from progressing through the removal of pre-malignant polyps, which can be achieved using screening tests to make the disease easier to diagnose. Finally, the existing challenges and future research directions that open the way for future work in this field are presented.

HCCANet: histopathological image grading of colorectal cancer using CNN based on multichannel fusion attention mechanism

Histopathological image analysis is the gold standard for pathologists to grade colorectal cancers of different differentiation types. However, the diagnosis by pathologists is highly subjective and prone to misdiagnosis. In this study, we constructed a new attention mechanism named MCCBAM based on channel attention mechanism and spatial attention mechanism, and developed a computer-aided diagnosis (CAD) method based on CNN and MCCBAM, called HCCANet. In this study, 630 histopathology images processed with Gaussian filtering denoising were included and gradient-weighted class activation map (Grad-CAM) was used to visualize regions of interest in HCCANet to improve its interpretability. The experimental results show that the proposed HCCANet model outperforms four advanced deep learning (ResNet50, MobileNetV2, Xception, and DenseNet121) and four classical machine learning (KNN, NB, RF, and SVM) techniques, achieved 90.2%, 85%, and 86.7% classification accuracy for colorectal cancers with high, medium, and low differentiation levels, respectively, with an overall accuracy of 87.3% and an average AUC value of 0.9.In addition, the MCCBAM constructed in this study outperforms several commonly used attention mechanisms SAM, SENet, SKNet, Non_Local, CBAM, and BAM on the backbone network. In conclusion, the HCCANet model proposed in this study is feasible for postoperative adjuvant diagnosis and grading of colorectal cancer.

Artificial intelligence in histopathology: enhancing cancer research and clinical oncology

Artificial intelligence (AI) methods have multiplied our capabilities to extract quantitative information from digital histopathology images. AI is expected to reduce workload for human experts, improve the objectivity and consistency of pathology reports, and have a clinical impact by extracting hidden information from routinely available data. Here, we describe how AI can be used to predict cancer outcome, treatment response, genetic alterations and gene expression from digitized histopathology slides. We summarize the underlying technologies and emerging approaches, noting limitations, including the need for data sharing and standards. Finally, we discuss the broader implications of AI in cancer research and oncology.

Divide-and-Attention Network for HE-Stained Pathological Image Classification

Simple Summary

We propose a Divide-and-Attention network that can learn representative pathological image features with respect to different tissue structures and adaptively focus on the most important ones. In addition, we introduce deep canonical correlation analysis constraints in the feature fusion process of different branches, so as to maximize the correlation of different branches and ensure that the fused branches emphasize specific tissue structures. Extensive experiments on three different pathological image datasets show that the proposed method achieved competitive results.

Abstract

Since pathological images have some distinct characteristics that are different from natural images, the direct application of a general convolutional neural network cannot achieve good classification performance, especially for fine-grained classification problems (such as pathological image grading). Inspired by the clinical experience that decomposing a pathological image into different components is beneficial for diagnosis, in this paper, we propose a Divide-and-Attention Network (DANet) for Hematoxylin-and-Eosin (HE)-stained pathological image classification. The DANet utilizes a deep-learning method to decompose a pathological image into nuclei and non-nuclei parts. With such decomposed pathological images, the DANet first performs feature learning independently in each branch, and then focuses on the most important feature representation through the branch selection attention module. In this way, the DANet can learn representative features with respect to different tissue structures and adaptively focus on the most important ones, thereby improving classification performance. In addition, we introduce deep canonical correlation analysis (DCCA) constraints in the feature fusion process of different branches. The DCCA constraints play the role of branch fusion attention, so as to maximize the correlation of different branches and ensure that the fused branches emphasize specific tissue structures. The experimental results of three datasets demonstrate the superiority of the DANet, with an average classification accuracy of 92.5% on breast cancer classification, 95.33% on colorectal cancer grading, and 91.6% on breast cancer grading tasks.

A Novel Hybrid Convolutional Neural Network Approach for the Stomach Intestinal Early Detection Cancer Subtype Classification

There may be different types of cancer that cause fatal effects in the human body. In general, cancer is nothing but the unnatural growth of blood cells in different parts of the body and is named accordingly. It may be skin cancer, breast cancer, uterus cancer, intestinal cancer, stomach cancer, etc. However, every type of cancer consists of unwanted blood cells which cause issues in the body starting from the minor to death. Cancer cells have the common features in them, and these common features we have used in our work for the processing. Cancer has a significant death rate; however, it is frequently curable with simple surgery if detected in its early stages. A quick and correct diagnosis may be extremely beneficial to both doctors and patients. In several medical domains, the latest deep-learning-based model’s performance is comparable to or even exceeds that of human specialists. We have proposed a novel methodology based on a convolutional neural network that may be used for almost all types of cancer detection. We have collected different datasets of different types of common cancer from different sources and used 90% of the sample data for the training purpose, then we reduced it by 10%, and an 80% image set was used for the validation of the model. After that for testing purposes, we fed a sample dataset and obtain the results. The final output clearly shows that the proposed model outperforms the previous model when we compared our methodology with the existing work.

MixPatch: A New Method for Training Histopathology Image Classifiers

CNN-based image processing has been actively applied to histopathological analysis to detect and classify cancerous tumors automatically. However, CNN-based classifiers generally predict a label with overconfidence, which becomes a serious problem in the medical domain. The objective of this study is to propose a new training method, called MixPatch, designed to improve a CNN-based classifier by specifically addressing the prediction uncertainty problem and examine its effectiveness in improving diagnosis performance in the context of histopathological image analysis. MixPatch generates and uses a new sub-training dataset, which consists of mixed-patches and their predefined ground-truth labels, for every single mini-batch. Mixed-patches are generated using a small size of clean patches confirmed by pathologists while their ground-truth labels are defined using a proportion-based soft labeling method. Our results obtained using a large histopathological image dataset shows that the proposed method performs better and alleviates overconfidence more effectively than any other method examined in the study. More specifically, our model showed 97.06% accuracy, an increase of 1.6% to 12.18%, while achieving 0.76% of expected calibration error, a decrease of 0.6% to 6.3%, over the other models. By specifically considering the mixed-region variation characteristics of histopathology images, MixPatch augments the extant mixed image methods for medical image analysis in which prediction uncertainty is a crucial issue. The proposed method provides a new way to systematically alleviate the overconfidence problem of CNN-based classifiers and improve their prediction accuracy, contributing toward more calibrated and reliable histopathology image analysis.

Usability of deep learning and H&E images predict disease outcome-emerging tool to optimize clinical trials

Understanding factors that impact prognosis for cancer patients have high clinical relevance for treatment decisions and monitoring of the disease outcome. Advances in artificial intelligence (AI) and digital pathology offer an exciting opportunity to capitalize on the use of whole slide images (WSIs) of hematoxylin and eosin (H&E) stained tumor tissue for objective prognosis and prediction of response to targeted therapies. AI models often require hand-delineated annotations for effective training which may not be readily available for larger data sets. In this study, we investigated whether AI models can be trained without region-level annotations and solely on patient-level survival data. We present a weakly supervised survival convolutional neural network (WSS-CNN) approach equipped with a visual attention mechanism for predicting overall survival. The inclusion of visual attention provides insights into regions of the tumor microenvironment with the pathological interpretation which may improve our understanding of the disease pathomechanism. We performed this analysis on two independent, multi-center patient data sets of lung (which is publicly available data) and bladder urothelial carcinoma. We perform univariable and multivariable analysis and show that WSS-CNN features are prognostic of overall survival in both tumor indications. The presented results highlight the significance of computational pathology algorithms for predicting prognosis using H&E stained images alone and underpin the use of computational methods to improve the efficiency of clinical trial studies.

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.

SAFRON: Stitching Across the Frontier Network for Generating Colorectal Cancer Histology Images

Automated synthesis of histology images has several potential applications including the development of data-efficient deep learning algorithms. In the field of computational pathology, where histology images are large in size and visual context is crucial, synthesis of large high-resolution images via generative modeling is an important but challenging task due to memory and computational constraints. To address this challenge, we propose a novel framework called SAFRON (Stitching Across the FROntier Network) to construct realistic, large high-resolution tissue images conditioned on input tissue component masks. The main novelty in the framework is integration of stitching in its loss function which enables generation of images of arbitrarily large sizes after training on relatively small image patches while preserving morphological features with minimal boundary artifacts. We have used the proposed framework for generating, to the best of our knowledge, the largest-sized synthetic histology images to date (up to 11K×8K pixels). Compared to existing approaches, our framework is efficient in terms of the memory required for training and computations needed for synthesizing large high-resolution images. The quality of generated images was assessed quantitatively using Frechet Inception Distance as well as by 7 trained pathologists, who assigned a realism score to a set of images generated by SAFRON. The average realism score across all pathologists for synthetic images was as high as that of real images. We also show that training with additional synthetic data generated by SAFRON can significantly boost prediction performance of gland segmentation and cancer detection algorithms in colorectal cancer histology images.

Development and validation of a weakly supervised deep learning framework to predict the status of molecular pathways and key mutations in colorectal cancer from routine histology images: a retrospective study

BACKGROUND

Determining the status of molecular pathways and key mutations in colorectal cancer is crucial for optimal therapeutic decision making. We therefore aimed to develop a novel deep learning pipeline to predict the status of key molecular pathways and mutations from whole-slide images of haematoxylin and eosin-stained colorectal cancer slides as an alternative to current tests.

METHODS

In this retrospective study, we used 502 diagnostic slides of primary colorectal tumours from 499 patients in The Cancer Genome Atlas colon and rectal cancer (TCGA-CRC-DX) cohort and developed a weakly supervised deep learning framework involving three separate convolutional neural network models. Whole-slide images were divided into equally sized tiles and model 1 (ResNet18) extracted tumour tiles from non-tumour tiles. These tumour tiles were inputted into model 2 (adapted ResNet34), trained by iterative draw and rank sampling to calculate a prediction score for each tile that represented the likelihood of a tile belonging to the molecular labels of high mutation density (vs low mutation density), microsatellite instability (vs microsatellite stability), chromosomal instability (vs genomic stability), CpG island methylator phenotype (CIMP)-high (vs CIMP-low), BRAFmut (vs BRAFWT), TP53mut (vs TP53WT), and KRASWT (vs KRASmut). These scores were used to identify the top-ranked titles from each slide, and model 3 (HoVer-Net) segmented and classified the different types of cell nuclei in these tiles. We calculated the area under the convex hull of the receiver operating characteristic curve (AUROC) as a model performance measure and compared our results with those of previously published methods.

FINDINGS

Our iterative draw and rank sampling method yielded mean AUROCs for the prediction of hypermutation (0·81 [SD 0·03] vs 0·71), microsatellite instability (0·86 [0·04] vs 0·74), chromosomal instability (0·83 [0·02] vs 0·73), BRAFmut (0·79 [0·01] vs 0·66), and TP53mut (0·73 [0·02] vs 0·64) in the TCGA-CRC-DX cohort that were higher than those from previously published methods, and an AUROC for KRASmut that was similar to previously reported methods (0·60 [SD 0·04] vs 0·60). Mean AUROC for predicting CIMP-high status was 0·79 (SD 0·05). We found high proportions of tumour-infiltrating lymphocytes and necrotic tumour cells to be associated with microsatellite instability, and high proportions of tumour-infiltrating lymphocytes and a low proportion of necrotic tumour cells to be associated with hypermutation.

INTERPRETATION

After large-scale validation, our proposed algorithm for predicting clinically important mutations and molecular pathways, such as microsatellite instability, in colorectal cancer could be used to stratify patients for targeted therapies with potentially lower costs and quicker turnaround times than sequencing-based or immunohistochemistry-based approaches.

FUNDING

The UK Medical Research Council.

Deep Learning Approaches to Colorectal Cancer Diagnosis: A Review

Unprecedented breakthroughs in the development of graphical processing systems have led to great potential for deep learning (DL) algorithms in analyzing visual anatomy from high-resolution medical images. Recently, in digital pathology, the use of DL technologies has drawn a substantial amount of attention for use in the effective diagnosis of various cancer types, especially colorectal cancer (CRC), which is regarded as one of the dominant causes of cancer-related deaths worldwide. This review provides an in-depth perspective on recently published research articles on DL-based CRC diagnosis and prognosis. Overall, we provide a retrospective synopsis of simple image-processing-based and machine learning (ML)-based computer-aided diagnosis (CAD) systems, followed by a comprehensive appraisal of use cases with different types of state-of-the-art DL algorithms for detecting malignancies. We first list multiple standardized and publicly available CRC datasets from two imaging types: colonoscopy and histopathology. Secondly, we categorize the studies based on the different types of CRC detected (tumor tissue, microsatellite instability, and polyps), and we assess the data preprocessing steps and the adopted DL architectures before presenting the optimum diagnostic results. CRC diagnosis with DL algorithms is still in the preclinical phase, and therefore, we point out some open issues and provide some insights into the practicability and development of robust diagnostic systems in future health care and oncology.

Hierarchical graph representations in digital pathology

Cancer diagnosis, prognosis, and therapy response predictions from tissue specimens highly depend on the phenotype and topological distribution of constituting histological entities. Thus, adequate tissue representations for encoding histological entities is imperative for computer aided cancer patient care. To this end, several approaches have leveraged cell-graphs, capturing the cell-microenvironment, to depict the tissue. These allow for utilizing graph theory and machine learning to map the tissue representation to tissue functionality, and quantify their relationship. Though cellular information is crucial, it is incomplete alone to comprehensively characterize complex tissue structure. We herein treat the tissue as a hierarchical composition of multiple types of histological entities from fine to coarse level, capturing multivariate tissue information at multiple levels. We propose a novel multi-level hierarchical entity-graph representation of tissue specimens to model the hierarchical compositions that encode histological entities as well as their intra- and inter-entity level interactions. Subsequently, a hierarchical graph neural network is proposed to operate on the hierarchical entity-graph and map the tissue structure to tissue functionality. Specifically, for input histology images, we utilize well-defined cells and tissue regions to build HierArchical Cell-to-Tissue (HACT) graph representations, and devise HACT-Net, a message passing graph neural network, to classify the HACT representations. As part of this work, we introduce the BReAst Carcinoma Subtyping (BRACS) dataset, a large cohort of Haematoxylin & Eosin stained breast tumor regions-of-interest, to evaluate and benchmark our proposed methodology against pathologists and state-of-the-art computer-aided diagnostic approaches. Through comparative assessment and ablation studies, our proposed method is demonstrated to yield superior classification results compared to alternative methods as well as individual pathologists. The code, data, and models can be accessed at https://github.com/histocartography/hact-net.

A digital score of tumour-associated stroma infiltrating lymphocytes predicts survival in head and neck squamous cell carcinoma

The infiltration of T-lymphocytes in the stroma and tumour is an indication of an effective immune response against the tumour, resulting in better survival. In this study, our aim was to explore the prognostic significance of tumour-associated stroma infiltrating lymphocytes (TASILs) in head and neck squamous cell carcinoma (HNSCC) through an AI-based automated method. A deep learning-based automated method was employed to segment tumour, tumour-associated stroma, and lymphocytes in digitally scanned whole slide images of HNSCC tissue slides. The spatial patterns of lymphocytes and tumour-associated stroma were digitally quantified to compute the tumour-associated stroma infiltrating lymphocytes score (TASIL-score). Finally, the prognostic significance of the TASIL-score for disease-specific and disease-free survival was investigated using the Cox proportional hazard analysis. Three different cohorts of haematoxylin and eosin (H&E)-stained tissue slides of HNSCC cases (n = 537 in total) were studied, including publicly available TCGA head and neck cancer cases. The TASIL-score carries prognostic significance (p = 0.002) for disease-specific survival of HNSCC patients. The TASIL-score also shows a better separation between low- and high-risk patients compared with the manual tumour-infiltrating lymphocytes (TILs) scoring by pathologists for both disease-specific and disease-free survival. A positive correlation of TASIL-score with molecular estimates of CD8⁺ T cells was also found, which is in line with existing findings. To the best of our knowledge, this is the first study to automate the quantification of TASILs from routine H&E slides of head and neck cancer. Our TASIL-score-based findings are aligned with the clinical knowledge, with the added advantages of objectivity, reproducibility, and strong prognostic value. Although we validated our method on three different cohorts (n = 537 cases in total), a comprehensive evaluation on large multicentric cohorts is required before the proposed digital score can be adopted in clinical practice. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.