Automatic detection of invasive ductal carcinoma in whole slide images with convolutional neural networks

This paper presents a deep learning approach for automatic detection and visual analysis of invasive ductal carcinoma (IDC) tissue regions in whole slide images (WSI) of breast cancer (BCa). Deep learning approaches are learn-from-data methods involving computational modeling of the learning process. This approach is similar to how human brain works using different interpretation levels or layers of most representative and useful features resulting into a hierarchical learned representation. These methods have been shown to outpace traditional approaches of most challenging problems in several areas such as speech recognition and object detection. Invasive breast cancer detection is a time consuming and challenging task primarily because it involves a pathologist scanning large swathes of benign regions to ultimately identify the areas of malignancy. Precise delineation of IDC in WSI is crucial to the subsequent estimation of grading tumor aggressiveness and predicting patient outcome. DL approaches are particularly adept at handling these types of problems, especially if a large number of samples are available for training, which would also ensure the generalizability of the learned features and classifier. The DL framework in this paper extends a number of convolutional neural networks (CNN) for visual semantic analysis of tumor regions for diagnosis support. The CNN is trained over a large amount of image patches (tissue regions) from WSI to learn a hierarchical part-based representation. The method was evaluated over a WSI dataset from 162 patients diagnosed with IDC. 113 slides were selected for training and 49 slides were held out for independent testing. Ground truth for quantitative evaluation was provided via expert delineation of the region of cancer by an expert pathologist on the digitized slides. The experimental evaluation was designed to measure classifier accuracy in detecting IDC tissue regions in WSI. Our method yielded the best quantitative results for automatic detection of IDC regions in WSI in terms of F-measure and balanced accuracy (71.80%, 84.23%), in comparison with an approach using handcrafted image features (color, texture and edges, nuclear textural and architecture), and a machine learning classifier for invasive tumor classification using a Random Forest. The best performing handcrafted features were fuzzy color histogram (67.53%, 78.74%) and RGB histogram (66.64%, 77.24%). Our results also suggest that at least some of the tissue classification mistakes (false positives and false negatives) were less due to any fundamental problems associated with the approach, than the inherent limitations in obtaining a very highly granular annotation of the diseased area of interest by an expert pathologist.