Informative sample generation using class aware generative adversarial networks for classification of chest Xrays

Training robust deep learning (DL) systems for disease detection from medical images is challenging due to limited images covering different disease types and severity. The problem is especially acute, where there is a severe class imbalance. We propose an active learning (AL) framework to select most informative samples for training our model using a Bayesian neural network. Informative samples are then used within a novel class aware generative adversarial network (CAGAN) to generate realistic chest xray images for data augmentation by transferring characteristics from one class label to another. Experiments show our proposed AL framework is able to achieve state-of-the-art performance by using about $35\%$ of the full dataset, thus saving significant time and effort over conventional methods

MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images

The analysis of glandular morphology within colon histopathology images is an important step in determining the grade of colon cancer. Despite the importance of this task, manual segmentation is laborious, time-consuming and can suffer from subjectivity among pathologists. The rise of computational pathology has led to the development of automated methods for gland segmentation that aim to overcome the challenges of manual segmentation. However, this task is non-trivial due to the large variability in glandular appearance and the difficulty in differentiating between certain glandular and non-glandular histological structures. Furthermore, a measure of uncertainty is essential for diagnostic decision making. To address these challenges, we propose a fully convolutional neural network that counters the loss of information caused by max-pooling by re-introducing the original image at multiple points within the network. We also use atrous spatial pyramid pooling with varying dilation rates for preserving the resolution and multi-level aggregation. To incorporate uncertainty, we introduce random transformations during test time for an enhanced segmentation result that simultaneously generates an uncertainty map, highlighting areas of ambiguity. We show that this map can be used to define a metric for disregarding predictions with high uncertainty. The proposed network achieves state-of-the-art performance on the GlaS challenge dataset and on a second independent colorectal adenocarcinoma dataset. In addition, we perform gland instance segmentation on whole-slide images from two further datasets to highlight the generalisability of our method. As an extension, we introduce MILD-Net+ for simultaneous gland and lumen segmentation, to increase the diagnostic power of the network.Comment: Initial version published at Medical Imaging with Deep Learning (MIDL) 201

Guided Curriculum Model Adaptation and Uncertainty-Aware Evaluation for Semantic Nighttime Image Segmentation

Most progress in semantic segmentation reports on daytime images taken under favorable illumination conditions. We instead address the problem of semantic segmentation of nighttime images and improve the state-of-the-art, by adapting daytime models to nighttime without using nighttime annotations. Moreover, we design a new evaluation framework to address the substantial uncertainty of semantics in nighttime images. Our central contributions are: 1) a curriculum framework to gradually adapt semantic segmentation models from day to night via labeled synthetic images and unlabeled real images, both for progressively darker times of day, which exploits cross-time-of-day correspondences for the real images to guide the inference of their labels; 2) a novel uncertainty-aware annotation and evaluation framework and metric for semantic segmentation, designed for adverse conditions and including image regions beyond human recognition capability in the evaluation in a principled fashion; 3) the Dark Zurich dataset, which comprises 2416 unlabeled nighttime and 2920 unlabeled twilight images with correspondences to their daytime counterparts plus a set of 151 nighttime images with fine pixel-level annotations created with our protocol, which serves as a first benchmark to perform our novel evaluation. Experiments show that our guided curriculum adaptation significantly outperforms state-of-the-art methods on real nighttime sets both for standard metrics and our uncertainty-aware metric. Furthermore, our uncertainty-aware evaluation reveals that selective invalidation of predictions can lead to better results on data with ambiguous content such as our nighttime benchmark and profit safety-oriented applications which involve invalid inputs.Comment: ICCV 2019 camera-read

Map-Guided Curriculum Domain Adaptation and Uncertainty-Aware Evaluation for Semantic Nighttime Image Segmentation

We address the problem of semantic nighttime image segmentation and improve the state-of-the-art, by adapting daytime models to nighttime without using nighttime annotations. Moreover, we design a new evaluation framework to address the substantial uncertainty of semantics in nighttime images. Our central contributions are: 1) a curriculum framework to gradually adapt semantic segmentation models from day to night through progressively darker times of day, exploiting cross-time-of-day correspondences between daytime images from a reference map and dark images to guide the label inference in the dark domains; 2) a novel uncertainty-aware annotation and evaluation framework and metric for semantic segmentation, including image regions beyond human recognition capability in the evaluation in a principled fashion; 3) the Dark Zurich dataset, comprising 2416 unlabeled nighttime and 2920 unlabeled twilight images with correspondences to their daytime counterparts plus a set of 201 nighttime images with fine pixel-level annotations created with our protocol, which serves as a first benchmark for our novel evaluation. Experiments show that our map-guided curriculum adaptation significantly outperforms state-of-the-art methods on nighttime sets both for standard metrics and our uncertainty-aware metric. Furthermore, our uncertainty-aware evaluation reveals that selective invalidation of predictions can improve results on data with ambiguous content such as our benchmark and profit safety-oriented applications involving invalid inputs.Comment: IEEE T-PAMI 202

An information assistant system for the prevention of tunnel vision in crisis management

In the crisis management environment, tunnel vision is a set of bias in decision makers’ cognitive process which often leads to incorrect understanding of the real crisis situation, biased perception of information, and improper decisions. The tunnel vision phenomenon is a consequence of both the challenges in the task and the natural limitation in a human being’s cognitive process. An information assistant system is proposed with the purpose of preventing tunnel vision. The system serves as a platform for monitoring the on-going crisis event. All information goes through the system before arrives at the user. The system enhances the data quality, reduces the data quantity and presents the crisis information in a manner that prevents or repairs the user’s cognitive overload. While working with such a system, the users (crisis managers) are expected to be more likely to stay aware of the actual situation, stay open minded to possibilities, and make proper decisions