Deep Learning for Automatic Subclassification of Gastric Carcinoma Using Whole-Slide Histopathology Images.
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ABSTRACT:
SUBMITTER: Jang HJ
PROVIDER: S-EPMC8345042 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Breast cancer tumor grade is strongly associated with patient survival. In current clinical practice, pathologists assign tumor grade after visual analysis of tissue specimens. However, different studies show significant inter-observer variation in breast cancer grading. Computer-based breast cancer grading methods have been proposed but only work on specifically selected tissue areas and/or require labor-intensive annotations to be applied to new datasets. In this study, we trained and evaluated a deep learning-based breast cancer grading model that works on whole-slide histopathology images. The model was developed using whole-slide images from 706 young (< 40 years) invasive breast cancer patients with corresponding tumor grade (low/intermediate vs. high), and its constituents nuclear grade, tubule formation and mitotic rate. The performance of the model was evaluated using Cohen's kappa on an independent test set of 686 patients using annotations by expert pathologists as ground truth. The predicted low/intermediate (n = 327) and high (n = 359) grade groups were used to perform survival analysis. The deep learning system distinguished low/intermediate versus high tumor grade with a Cohen's Kappa of 0.59 (80% accuracy) compared to expert pathologists. In subsequent survival analysis the two groups predicted by the system were found to have a significantly different overall survival (OS) and disease/recurrence-free survival (DRFS/RFS) (p < 0.05). Univariate Cox hazard regression analysis showed statistically significant hazard ratios (p < 0.05). After adjusting for clinicopathologic features and stratifying for molecular subtype the hazard ratios showed a trend but lost statistical significance for all endpoints. In conclusion, we developed a deep learning-based model for automated grading of breast cancer on whole-slide images. The model distinguishes between low/intermediate and high grade tumors and finds a trend in the survival of the two predicted groups.
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Project description:Renal cell carcinoma is the most common type of kidney cancer. There are several subtypes of renal cell carcinoma with distinct clinicopathologic features. Among the subtypes, clear cell renal cell carcinoma is the most common and tends to portend poor prognosis. In contrast, clear cell papillary renal cell carcinoma has an excellent prognosis. These two subtypes are primarily classified based on the histopathologic features. However, a subset of cases can a have a significant degree of histopathologic overlap. In cases with ambiguous histologic features, the correct diagnosis is dependent on the pathologist's experience and usage of immunohistochemistry. We propose a new method to address this diagnostic task based on a deep learning pipeline for automated classification. The model can detect tumor and non-tumoral portions of kidney and classify the tumor as either clear cell renal cell carcinoma or clear cell papillary renal cell carcinoma. Our framework consists of three convolutional neural networks and the whole slide images of kidney which were divided into patches of three different sizes for input into the networks. Our approach can provide patchwise and pixelwise classification. The kidney histology images consist of 64 whole slide images. Our framework results in an image map that classifies the slide image on the pixel-level. Furthermore, we applied generalized Gauss-Markov random field smoothing to maintain consistency in the map. Our approach classified the four classes accurately and surpassed other state-of-the-art methods, such as ResNet (pixel accuracy: 0.89 Resnet18, 0.92 proposed). We conclude that deep learning has the potential to augment the pathologist's capabilities by providing automated classification for histopathological images.
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Project description:Breast carcinoma is the most common cancer among women worldwide that consists of a heterogeneous group of subtype diseases. The whole-slide images (WSIs) can capture the cell-level heterogeneity, and are routinely used for cancer diagnosis by pathologists. However, key driver genetic mutations related to targeted therapies are identified by genomic analysis like high-throughput molecular profiling. In this study, we develop a deep-learning model to predict the genetic mutations and biological pathway activities directly from WSIs. Our study offers unique insights into WSI visual interactions between mutation and its related pathway, enabling a head-to-head comparison to reinforce our major findings. Using the histopathology images from the Genomic Data Commons Database, our model can predict the point mutations of six important genes (AUC 0.68-0.85) and copy number alteration of another six genes (AUC 0.69-0.79). Additionally, the trained models can predict the activities of three out of ten canonical pathways (AUC 0.65-0.79). Next, we visualized the weight maps of tumor tiles in WSI to understand the decision-making process of deep-learning models via a self-attention mechanism. We further validated our models on liver and lung cancers that are related to metastatic breast cancer. Our results provide insights into the association between pathological image features, molecular outcomes, and targeted therapies for breast cancer patients.
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Project description:BackgroundDeep learning has the potential to improve diagnostic accuracy and efficiency in medical image recognition. In the current study, we developed a deep learning algorithm and assessed its performance in discriminating melanoma from nevus using whole-slide pathological images (WSIs).MethodsThe deep learning algorithm was trained and validated using a set of 781 WSIs (86 melanomas, 695 nevi) from PLA General Hospital. The diagnostic performance of the algorithm was tested on an independent test set of 104 WSIs (29 melanomas, 75 nevi) from Tianjin Chang Zheng Hospital. The same test set was also diagnostically classified by 7 expert dermatopathologists.ResultsThe deep learning algorithm receiver operating characteristic (ROC) curve achieved a sensitivity 100% at the specificity of 94.7% in the classification of melanoma and nevus on the test set. The area under ROC curve was 0.99. Dermatopathologists achieved a mean sensitivity and specificity of 95.1% (95% confidence interval [CI]: 92.0%-98.2%) and 96.0% (95% CI: 94.2%-97.8%), respectively. At the operating point of sensitivity of 95.1%, the algorithm revealed a comparable specificity with 7 dermatopathologists (97.3% vs. 96.0%, P = 0.11). At the operating point of specificity of 96.0%, the algorithm also achieved a comparable sensitivity with 7 dermatopathologists (96.5% vs. 95.1%, P = 0.30). A more transparent and interpretable diagnosis could be generated by highlighting the regions of interest recognized by the algorithm in WSIs.ConclusionThe performance of the deep learning algorithm was on par with that of 7 expert dermatopathologists in interpreting WSIs with melanocytic lesions. By pre-screening the suspicious melanoma regions, it might serve as a supplemental diagnostic tool to improve working efficiency of pathologists.
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