Stephen McKenna

Stephen McKenna, Jacob Carse

We consider calibration of convolutional classifiers for diagnostic decision making. Clinical decision makers can use calibrated classifiers to minimise expected costs given their own cost function. Such functions are usually unknown at training time. If minimising expected costs is the primary aim, algorithms should focus on tuning calibration in regions of probability simplex likely to effect decisions. We give an example, modifying temperature scaling calibration, and demonstrate improved calibration where it matters using convnets trained to classify dermoscopy images.

Jacob Carse, Frank Carey, Stephen McKenna

Digital pathology tasks have benefited greatly from modern deep learning algorithms. However, their need for large quantities of annotated data has been identified as a key challenge. This need for data can be countered by using unsupervised learning in situations where data are abundant but access to annotations is limited. Feature representations learned from unannotated data using contrastive predictive coding (CPC) have been shown to enable classifiers to obtain state of the art performance from relatively small amounts of annotated computer vision data. We present a modification to the CPC framework for use with digital pathology patches. This is achieved by introducing an alternative mask for building the latent context and using a multi-directional PixelCNN autoregressor. To demonstrate our proposed method we learn feature representations from the Patch Camelyon histology dataset. We show that our proposed modification can yield improved deep classification of histology patches.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.