Improving automated prostate pathological grading via confidence filtering

There have been many promising developments in deep learning to identify degrees of malignancies in prostate cancer pathologies. Deep network models have been shown to be useful in identifying patterns in histology images assessed at different scales. Prostate pathological grade identification has been a challenge among clinical experts due to complex patterns on the whole slide level, for hematoxylin and eosin (H&E) stained samples. In this study, we identify primary patterns (Gleason) in small sections of the whole slide composed of uniform glandular patterns. We then follow sample selection methods that eliminate ambiguous regions or tiled-samples by confidence filtering. A pseudo-confidence is derived from the predicted output of the network, which is used as a quality indicator to consider the sample for discriminatory analysis. We provide further evidence that using highly calibrated confidence sample selection, these gland-level features on the prostate biopsy sections can discriminate degrees of malignancy following primary Gleason patterns. We used an optimized deep network (convolutional neural network, CNN) discriminating glandular regions with aggressive grades (Gleason 3 from 4) showed an accuracy of 0.68(0.04), F1 of 0.66(0.06) and AUC of 0.74(0.04). We further improve this result using confidence filtering, with a sample fraction of 0.35 (with a calibrated confidence of greater than 0.85), achieving an accuracy of 0.74 (0.08), F1 of 0.72 (0.12), and AUC 0.79 (0.08) averaged from holdout sets over multiple reshuffled experiments.