The Lov\'asz-Softmax loss: A tractable surrogate for the optimization of the intersection-over-union measure in neural networks

The Jaccard index, also referred to as the intersection-over-union score, is commonly employed in the evaluation of image segmentation results given its perceptual qualities, scale invariance - which lends appropriate relevance to small objects, and appropriate counting of false negatives, in comparison to per-pixel losses. We present a method for direct optimization of the mean intersection-over-union loss in neural networks, in the context of semantic image segmentation, based on the convex Lov\'asz extension of submodular losses. The loss is shown to perform better with respect to the Jaccard index measure than the traditionally used cross-entropy loss. We show quantitative and qualitative differences between optimizing the Jaccard index per image versus optimizing the Jaccard index taken over an entire dataset. We evaluate the impact of our method in a semantic segmentation pipeline and show substantially improved intersection-over-union segmentation scores on the Pascal VOC and Cityscapes datasets using state-of-the-art deep learning segmentation architectures.Comment: Accepted as a conference paper at CVPR 201

Feature Tracking Cardiac Magnetic Resonance via Deep Learning and Spline Optimization

Feature tracking Cardiac Magnetic Resonance (CMR) has recently emerged as an area of interest for quantification of regional cardiac function from balanced, steady state free precession (SSFP) cine sequences. However, currently available techniques lack full automation, limiting reproducibility. We propose a fully automated technique whereby a CMR image sequence is first segmented with a deep, fully convolutional neural network (CNN) architecture, and quadratic basis splines are fitted simultaneously across all cardiac frames using least squares optimization. Experiments are performed using data from 42 patients with hypertrophic cardiomyopathy (HCM) and 21 healthy control subjects. In terms of segmentation, we compared state-of-the-art CNN frameworks, U-Net and dilated convolution architectures, with and without temporal context, using cross validation with three folds. Performance relative to expert manual segmentation was similar across all networks: pixel accuracy was ~97%, intersection-over-union (IoU) across all classes was ~87%, and IoU across foreground classes only was ~85%. Endocardial left ventricular circumferential strain calculated from the proposed pipeline was significantly different in control and disease subjects (-25.3% vs -29.1%, p = 0.006), in agreement with the current clinical literature.Comment: Accepted to Functional Imaging and Modeling of the Heart (FIMH) 201

Augmented Mitotic Cell Count using Field Of Interest Proposal

Histopathological prognostication of neoplasia including most tumor grading systems are based upon a number of criteria. Probably the most important is the number of mitotic figures which are most commonly determined as the mitotic count (MC), i.e. number of mitotic figures within 10 consecutive high power fields. Often the area with the highest mitotic activity is to be selected for the MC. However, since mitotic activity is not known in advance, an arbitrary choice of this region is considered one important cause for high variability in the prognostication and grading. In this work, we present an algorithmic approach that first calculates a mitotic cell map based upon a deep convolutional network. This map is in a second step used to construct a mitotic activity estimate. Lastly, we select the image segment representing the size of ten high power fields with the overall highest mitotic activity as a region proposal for an expert MC determination. We evaluate the approach using a dataset of 32 completely annotated whole slide images, where 22 were used for training of the network and 10 for test. We find a correlation of r=0.936 in mitotic count estimate.Comment: 6 pages, submitted to BVM 2019 (bvm-workshop.org