Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease

GNCnn: A QuPath extension for glomerulosclerosis and glomerulonephritis characterization based on deep learning

The digitalization of traditional glass slide microscopy into whole slide images has opened up new opportunities for pathology, such as the application of artificial intelligence techniques. Specialized software is necessary to visualize and analyze these images. One of these applications is QuPath, a popular bioimage analysis tool. This study proposes GNCnn, the first open-source QuPath extension specifically designed for nephropathology. It integrates deep learning models to provide nephropathologists with an accessible, automatic detector and classifier of glomeruli, the basic filtering units of the kidneys. The aim is to offer nephropathologists a freely available application to measure and analyze glomeruli to identify conditions such as glomerulosclerosis and glomerulonephritis. GNCnn offers a user-friendly interface that enables nephropathologists to detect glomeruli with high accuracy (Dice coefficient of 0.807) and categorize them as either sclerotic or non-sclerotic, achieving a balanced accuracy of 98.46%. Furthermore, it facilitates the classification of non-sclerotic glomeruli into 12 commonly diagnosed types of glomerulonephritis, with a top-3 balanced accuracy of 84.41%. GNCnn provides real-time updates of results, which are available at both the glomerulus and slide levels. This allows users to complete a typical analysis task without leaving the main application, QuPath. This tool is the first to integrate the entire workflow for the assessment of glomerulonephritis directly into the nephropathologists' workspace, accelerating and supporting their diagnosis.

LVI-PathNet: Segmentation-classification pipeline for detection of lymphovascular invasion in whole slide images of lung adenocarcinoma

Lymphovascular invasion (LVI) in lung cancer is a significant prognostic factor that influences treatment and outcomes, yet its reliable detection is challenging due to interobserver variability. This study aims to develop a deep learning model for LVI detection using whole slide images (WSIs) and evaluate its effectiveness within a pathologist's information system. Experienced pathologists annotated blood vessels and invading tumor cells in 162 WSIs of non-mucinous lung adenocarcinoma sourced from two external and one internal datasets. Two models were trained to segment vessels and identify images with LVI features. DeepLabV3+ model achieved an Intersection-over-Union of 0.8840 and an area under the receiver operating characteristic curve (AUC-ROC) of 0.9869 in vessel segmentation. For LVI classification, the ensemble model achieved a F1-score of 0.9683 and an AUC-ROC of 0.9987. The model demonstrated robustness and was unaffected by variations in staining and image quality. The pilot study showed that pathologists' evaluation time for LVI detecting decreased by an average of 16.95%, and by 21.5% in "hard cases". The model facilitated consistent diagnostic assessments, suggesting potential for broader applications in detecting pathological changes in blood vessels and other lung pathologies.

Novel statistically equivalent signature-based hybrid feature selection and ensemble deep learning LSTM and GRU for chronic kidney disease classification

Chronic kidney disease (CKD) involves numerous variables, but only a few significantly impact the classification task. The statistically equivalent signature (SES) method, inspired by constraint-based learning of Bayesian networks, is employed to identify essential features in CKD. Unlike conventional feature selection methods, which typically focus on a single set of features with the highest predictive potential, the SES method can identify multiple predictive feature subsets with similar performance. However, most feature selection (FS) classifiers perform suboptimally with strongly correlated data. The FS approach faces challenges in identifying crucial features and selecting the most effective classifier, particularly in high-dimensional data. This study proposes using the Least Absolute Shrinkage and Selection Operator (LASSO) in conjunction with the SES method for feature selection in CKD identification. Following this, an ensemble deep-learning model combining long short-term memory (LSTM) and gated recurrent unit (GRU) networks is proposed for CKD classification. The features selected by the hybrid feature selection method are fed into the ensemble deep-learning model. The model's performance is evaluated using accuracy, precision, recall, and F1 score metrics. The experimental results are compared with individual classifiers, including decision tree (DT), Random Forest (RF), logistic regression (LR), and support vector machine (SVM). The findings indicate a 2% improvement in classification accuracy when using the proposed hybrid feature selection method combined with the LSTM and GRU ensemble deep-learning model. Further analysis reveals that certain features, such as HEMO, POT, bacteria, and coronary artery disease, contribute minimally to the classification task. Future research could explore additional feature selection methods, including dynamic feature selection that adapts to evolving datasets and incorporates clinical knowledge to enhance CKD classification accuracy further.

Vortex-like vs. turbulent mixing of a Viscum album preparation affects crystalline structures formed in dried droplets

Various types of motion introduced into a solution can affect, among other factors, the alignment and positioning of molecules, the agglomeration of large molecules, oxidation processes, and the production of microparticles and microbubbles. We employed turbulent mixing vs. laminar flow induced by a vortex vs. diffusion-based mixing during the production of Viscum album Quercus L. 10-3 following the guidelines for manufacturing homeopathic preparations. The differently mixed preparation variants were analyzed using the droplet evaporation method. The crystalline structures formed in dried droplets were photographed and analyzed using computer-supported image analysis and deep learning. Computer-supported evaluation and deep learning revealed that the patterns of the variant succussed under turbulence are characterized by lower complexity, whereas those obtained from the vortex-mixed variant are characterized by greater complexity compared to the diffusion-based mixed control variant. The droplet evaporation method could provide a relatively inexpensive means of testing the effects of liquid flow and serve as an alternative to currently used methods.

The relationship between histopathological features, immunosuppression and outcome in patients undergoing native kidney biopsies

AIMS

To assess retrospectively the association between histopathological lesions on renal biopsy and subsequent impairment of renal function across the spectrum of kidney diseases and to explore the influence of immunosuppressive therapy within the first 6 months after biopsy on this association.

METHODS AND RESULTS

Clinical data from 488 adult patients having a renal biopsy reported at a single centre from 2017 to 2019 were obtained during a median follow-up period of 786 days. Seventeen semi-quantitative histology parameters were recorded at the time of biopsy, 14 of which were suitable for assessment of association with loss of eGFR by multivariable Cox regression analysis, measurement of eGFR slope and measurement of eGFR 12 months after biopsy. A widely used histopathological chronicity score was also assessed. Clinical baseline variables including prescription of immunosuppression were recorded. Seven of 14 histology parameters: mesangial matrix expansion, global glomerulosclerosis, tubular atrophy, interstitial fibrosis, arteriolosclerosis, mesangial hypercellularity and acute tubular injury; and the chronicity score, predicted loss of kidney function by all three measures. Prescription of immunosuppression was more likely in patients with active inflammatory pathology and less likely in patients with chronic fibrotic pathology, and was associated with reduced risk of loss of eGFR.

CONCLUSIONS

This retrospective study demonstrates the prognostic significance and complex relationship with immunosuppression of routinely reported histopathological variables in patients having native kidney biopsies, across the spectrum of kidney diseases. It provides useful information for renal biopsy prognostication and design of retrospective studies, including machine learning models.

AI's Threat to the Medical Profession

This Viewpoint discusses the potential drawbacks of the use of artificial intelligence (AI) in medicine, for example, the loss of certain skills due to the reliance on AI, and how physicians should consider how to take advantage of the potential benefits of AI without losing control over their profession.

Time for a full digital approach in nephropathology: a systematic review of current artificial intelligence applications and future directions

INTRODUCTION

Artificial intelligence (AI) integration in nephropathology has been growing rapidly in recent years, facing several challenges including the wide range of histological techniques used, the low occurrence of certain diseases, and the need for data sharing. This narrative review retraces the history of AI in nephropathology and provides insights into potential future developments.

METHODS

Electronic searches in PubMed-MEDLINE and Embase were made to extract pertinent articles from the literature. Works about automated image analysis or the application of an AI algorithm on non-neoplastic kidney histological samples were included and analyzed to extract information such as publication year, AI task, and learning type. Prepublication servers and reviews were not included.

RESULTS

Seventy-six (76) original research articles were selected. Most of the studies were conducted in the United States in the last 7 years. To date, research has been mainly conducted on relatively easy tasks, like single-stain glomerular segmentation. However, there is a trend towards developing more complex tasks such as glomerular multi-stain classification.

CONCLUSION

Deep learning has been used to identify patterns in complex histopathology data and looks promising for the comprehensive assessment of renal biopsy, through the use of multiple stains and virtual staining techniques. Hybrid and collaborative learning approaches have also been explored to utilize large amounts of unlabeled data. A diverse team of experts, including nephropathologists, computer scientists, and clinicians, is crucial for the development of AI systems for nephropathology. Collaborative efforts among multidisciplinary experts result in clinically relevant and effective AI tools.

Artificial Intelligence Assists in the Detection of Blood Vessels in Whole Slide Images: Practical Benefits for Oncological Pathology

The analysis of the microvasculature and the assessment of angiogenesis have significant prognostic value in various diseases, including cancer. The search for invasion into the blood and lymphatic vessels and the assessment of angiogenesis are important aspects of oncological diagnosis. These features determine the prognosis and aggressiveness of the tumor. Traditional manual evaluation methods are time consuming and subject to inter-observer variability. Blood vessel detection is a perfect task for artificial intelligence, which is capable of rapid analyzing thousands of tissue structures in whole slide images. The development of computer vision solutions requires the segmentation of tissue regions, the extraction of features and the training of machine learning models. In this review, we focus on the methodologies employed by researchers to identify blood vessels and vascular invasion across a range of tumor localizations, including breast, lung, colon, brain, renal, pancreatic, gastric and oral cavity cancers. Contemporary models herald a new era of computational pathology in morphological diagnostics.

Clustering-based spatial analysis (CluSA) framework through graph neural network for chronic kidney disease prediction using histopathology images

Machine learning applied to digital pathology has been increasingly used to assess kidney function and diagnose the underlying cause of chronic kidney disease (CKD). We developed a novel computational framework, clustering-based spatial analysis (CluSA), that leverages unsupervised learning to learn spatial relationships between local visual patterns in kidney tissue. This framework minimizes the need for time-consuming and impractical expert annotations. 107,471 histopathology images obtained from 172 biopsy cores were used in the clustering and in the deep learning model. To incorporate spatial information over the clustered image patterns on the biopsy sample, we spatially encoded clustered patterns with colors and performed spatial analysis through graph neural network. A random forest classifier with various groups of features were used to predict CKD. For predicting eGFR at the biopsy, we achieved a sensitivity of 0.97, specificity of 0.90, and accuracy of 0.95. AUC was 0.96. For predicting eGFR changes in one-year, we achieved a sensitivity of 0.83, specificity of 0.85, and accuracy of 0.84. AUC was 0.85. This study presents the first spatial analysis based on unsupervised machine learning algorithms. Without expert annotation, CluSA framework can not only accurately classify and predict the degree of kidney function at the biopsy and in one year, but also identify novel predictors of kidney function and renal prognosis.

Artificial Intelligence-Assisted Renal Pathology: Advances and Prospects

Digital imaging and advanced microscopy play a pivotal role in the diagnosis of kidney diseases. In recent years, great achievements have been made in digital imaging, providing novel approaches for precise quantitative assessments of nephropathology and relieving burdens of renal pathologists. Developing novel methods of artificial intelligence (AI)-assisted technology through multidisciplinary interaction among computer engineers, renal specialists, and nephropathologists could prove beneficial for renal pathology diagnoses. An increasing number of publications has demonstrated the rapid growth of AI-based technology in nephrology. In this review, we offer an overview of AI-assisted renal pathology, including AI concepts and the workflow of processing digital image data, focusing on the impressive advances of AI application in disease-specific backgrounds. In particular, this review describes the applied computer vision algorithms for the segmentation of kidney structures, diagnosis of specific pathological changes, and prognosis prediction based on images. Lastly, we discuss challenges and prospects to provide an objective view of this topic.

Unsupervised Learning Based on Multiple Descriptors for WSIs Diagnosis

An automatic pathological diagnosis is a challenging task because histopathological images with different cellular heterogeneity representations are sometimes limited. To overcome this, we investigated how the holistic and local appearance features with limited information can be fused to enhance the analysis performance. We propose an unsupervised deep learning model for whole-slide image diagnosis, which uses stacked autoencoders simultaneously feeding multiple-image descriptors such as the histogram of oriented gradients and local binary patterns along with the original image to fuse the heterogeneous features. The pre-trained latent vectors are extracted from each autoencoder, and these fused feature representations are utilized for classification. We observed that training with additional descriptors helps the model to overcome the limitations of multiple variants and the intricate cellular structure of histopathology data by various experiments. Our model outperforms existing state-of-the-art approaches by achieving the highest accuracies of 87.2 for ICIAR2018, 94.6 for Dartmouth, and other significant metrics for public benchmark datasets. Our model does not rely on a specific set of pre-trained features based on classifiers to achieve high performance. Unsupervised spaces are learned from the number of independent multiple descriptors and can be used with different variants of classifiers to classify cancer diseases from whole-slide images. Furthermore, we found that the proposed model classifies the types of breast and lung cancer similar to the viewpoint of pathologists by visualization. We also designed our whole-slide image processing toolbox to extract and process the patches from whole-slide images.