Classification of non-small-cell lung cancer (NSCLC) into adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) via histopathology is a vital prerequisite to select the appropriate treatment for lung cancer patients. Most machine learning approaches rely on manually annotating large numbers of whole slide images (WSI) for training. However, manually delineating cancer areas or even single cancer cells on hundreds or thousands of slides is tedious, subjective and requires highly trained pathologists. We propose to use Neural Image Compression (NIC), which requires only slide-level labels, to classify NSCLC into LUSC and LUAD. NIC consists of two phases/networks. In the first phase the slides are compressed with a convolutional neural network (CNN) acting as an encoder. In the second phase the compressed slides are classified with a second CNN. We trained our classification model on >2,000 NIC-compressed slides from the TCGA and TCIA databases and evaluated the model performance additionally on several internal and external cohorts. We show that NIC approaches state of the art performance on lung cancer classification, with an average AUC of 0.94 on the TCGA and TCIA testdata, and AUCs between 0.84 and 0.98 on other independent datasets.
When diagnosing and reporting lung adenocarcinoma (LAC), pathologists currently include an assessment of histologic tumor growth patterns because the predominant growth pattern has been reported to impact prognosis. However, the subjective nature of manual slide evaluation contributes to suboptimal inter-pathologist variability in tumor growth pattern assessment. We applied a deep learning approach to identify and automatically delineate areas of four tumor growth patterns (solid, acinar, micropapillary, and cribriform) and non-tumor areas in whole slide images (WSI) from resected LAC specimens. We trained a DenseNet model using patches from 109 slides collected at two institutions. The model was tested using 56 WSIs including 20 that were collected at a third institution. Using the same slide set, the concordance between the DenseNet model and an experienced pathologist (blinded to the DenseNet results) in determining the predominant tumor growth pattern was substantial (kappa score = 0.603). Using a subset of 36 test slides that were manually annotated for tumor growth patterns, we also measured the F1-score for each growth pattern: 0.95 (solid), 0.78 (acinar), 0.76 (micropapillary), 0.28 (cribriform) and 0.97 (non-tumor). Our results suggest that DenseNet assessment of WSIs with solid, acinar, and micropapillary predominant tumor growth is more robust than for the WSIs with predominant cribriform growth which are less frequently encountered.
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