“Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks”の学習報告

Obtaining models that capture imaging markers relevant for disease progression and treatment monitoring is challenging. Models are typically based on large amounts of data with annotated examples of known markers aiming at automating detection. High annotation effort and the limitation to a vocabulary of known markers limit the power of such approaches. Here, we perform unsupervised learning to identify anomalies in imaging data as candidates for markers. We propose AnoGAN, a deep convolutional generative adversarial network to learn a manifold of normal anatomical variability, accompanying a novel anomaly scoring scheme based on the mapping from image space to a latent space. Applied to new data, the model labels anomalies, and scores image patches indicating their fit into the learned distribution. Results on optical coherence tomography images of the retina demonstrate that the approach correctly identifies anomalous images, such as images containing retinal fluid or hyperreflective foci.

Unsupervised Anomaly Detection with Generative Adversarial Networks to Guide Marker Discovery

GAN-based synthetic medical image augmentation for increased CNN performance in liver lesion classification

Despite the great advances made by deep learning in many machine learning problems, there is a relative dearth of deep learning approaches for anomaly detection. Those approaches which do exist involve networks trained to perform a task other than anomaly detection, namely generative models or compression, which are in turn adapted for use in anomaly detection; they are not trained on an anomaly detection based objective. In this paper we introduce a new anomaly detection method—Deep Support Vector Data Description—, which is trained on an anomaly detection based objective. The adaptation to the deep regime necessitates that our neural network and training procedure satisfy certain properties, which we demonstrate theoretically. We show the effectiveness of our method on MNIST and CIFAR-10 image benchmark datasets as well as on the detection of adversarial examples of GTSRB stop signs.

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Deep One-Class Classification

Generative adversarial network in medical imaging: A review.

f-AnoGAN: Fast unsupervised anomaly detection with generative adversarial networks.

Diagnosis and treatment guidance are aided by detecting relevant biomarkers in medical images. Although supervised deep learning can perform accurate segmentation of pathological areas, it is limited by requiring a priori definitions of these regions, large-scale annotations, and a representative patient cohort in the training set. In contrast, anomaly detection is not limited to specific definitions of pathologies and allows for training on healthy samples without annotation. Anomalous regions can then serve as candidates for biomarker discovery. Knowledge about normal anatomical structure brings implicit information for detecting anomalies. We propose to take advantage of this property using Bayesian deep learning, based on the assumption that epistemic uncertainties will correlate with anatomical deviations from a normal training set. A Bayesian U-Net is trained on a well-defined healthy environment using weak labels of healthy anatomy produced by existing methods. At test time, we capture epistemic uncertainty estimates of our model using Monte Carlo dropout. A novel post-processing technique is then applied to exploit these estimates and transfer their layered appearance to smooth blob-shaped segmentations of the anomalies. We experimentally validated this approach in retinal optical coherence tomography (OCT) images, using weak labels of retinal layers. Our method achieved a Dice index of 0.789 in an independent anomaly test set of age-related macular degeneration (AMD) cases. The resulting segmentations allowed very high accuracy for separating healthy and diseased cases with late wet AMD, dry geographic atrophy (GA), diabetic macular edema (DME) and retinal vein occlusion (RVO). Finally, we qualitatively observed that our approach can also detect other deviations in normal scans such as cut edge artifacts.

Exploiting Epistemic Uncertainty of Anatomy Segmentation for Anomaly Detection in Retinal OCT

The identification and quantification of markers in medical images is critical for diagnosis, prognosis, and disease management. Supervised machine learning enables the detection and exploitation of findings that are known a priori after annotation of training examples by experts. However, supervision does not scale well, due to the amount of necessary training examples, and the limitation of the marker vocabulary to known entities. In this proof-of-concept study, we propose unsupervised identification of anomalies as candidates for markers in retinal optical coherence tomography (OCT) imaging data without a constraint to a priori definitions. We identify and categorize marker candidates occurring frequently in the data and demonstrate that these markers show a predictive value in the task of detecting disease. A careful qualitative analysis of the identified data driven markers reveals how their quantifiable occurrence aligns with our current understanding of disease course, in early- and late age-related macular degeneration (AMD) patients. A multi-scale deep denoising autoencoder is trained on healthy images, and a one-class support vector machine identifies anomalies in new data. Clustering in the anomalies identifies stable categories. Using these markers to classify healthy-, early AMD- and late AMD cases yields an accuracy of 81.40%. In a second binary classification experiment on a publicly available data set (healthy versus intermediate AMD), the model achieves an area under the ROC curve of 0.944.

Philipp Seeböck

Papers

Unsupervised Anomaly Detection with Generative Adversarial Networks to Guide Marker Discovery

f-AnoGAN: Fast unsupervised anomaly detection with generative adversarial networks.

Unsupervised Anomaly Detection with Generative Adversarial Networks to Guide Marker Discovery

Exploiting Epistemic Uncertainty of Anatomy Segmentation for Anomaly Detection in Retinal OCT

Unsupervised Identification of Disease Marker Candidates in Retinal OCT Imaging Data