Learning to Segment Breast Biopsy Whole Slide Images

We trained and applied an encoder-decoder model to semantically segment breast biopsy images into biologically meaningful tissue labels. Since conventional encoder-decoder networks cannot be applied directly on large biopsy images and the different sized structures in biopsies present novel challenges, we propose four modifications: (1) an input-aware encoding block to compensate for information loss, (2) a new dense connection pattern between encoder and decoder, (3) dense and sparse decoders to combine multi-level features, (4) a multi-resolution network that fuses the results of encoder-decoders run on different resolutions. Our model outperforms a feature-based approach and conventional encoder-decoders from the literature. We use semantic segmentations produced with our model in an automated diagnosis task and obtain higher accuracies than a baseline approach that employs an SVM for feature-based segmentation, both using the same segmentation-based diagnostic features.Comment: Added more WSI images in appendi

Automated segmentation on the entire cardiac cycle using a deep learning work-flow

The segmentation of the left ventricle (LV) from CINE MRI images is essential to infer important clinical parameters. Typically, machine learning algorithms for automated LV segmentation use annotated contours from only two cardiac phases, diastole, and systole. In this work, we present an analysis work-flow for fully-automated LV segmentation that learns from images acquired through the cardiac cycle. The workflow consists of three components: first, for each image in the sequence, we perform an automated localization and subsequent cropping of the bounding box containing the cardiac silhouette. Second, we identify the LV contours using a Temporal Fully Convolutional Neural Network (T-FCNN), which extends Fully Convolutional Neural Networks (FCNN) through a recurrent mechanism enforcing temporal coherence across consecutive frames. Finally, we further defined the boundaries using either one of two components: fully-connected Conditional Random Fields (CRFs) with Gaussian edge potentials and Semantic Flow. Our initial experiments suggest that significant improvement in performance can potentially be achieved by using a recurrent neural network component that explicitly learns cardiac motion patterns whilst performing LV segmentation.Comment: 6 pages, 2 figures, published on IEEE Xplor

Listening for Sirens: Locating and Classifying Acoustic Alarms in City Scenes

This paper is about alerting acoustic event detection and sound source localisation in an urban scenario. Specifically, we are interested in spotting the presence of horns, and sirens of emergency vehicles. In order to obtain a reliable system able to operate robustly despite the presence of traffic noise, which can be copious, unstructured and unpredictable, we propose to treat the spectrograms of incoming stereo signals as images, and apply semantic segmentation, based on a Unet architecture, to extract the target sound from the background noise. In a multi-task learning scheme, together with signal denoising, we perform acoustic event classification to identify the nature of the alerting sound. Lastly, we use the denoised signals to localise the acoustic source on the horizon plane, by regressing the direction of arrival of the sound through a CNN architecture. Our experimental evaluation shows an average classification rate of 94%, and a median absolute error on the localisation of 7.5{\deg} when operating on audio frames of 0.5s, and of 2.5{\deg} when operating on frames of 2.5s. The system offers excellent performance in particularly challenging scenarios, where the noise level is remarkably high.Comment: 6 pages, 9 figure