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.
Anomaly detection can be a crucial first step in the process of biomarker detection. The results of these algorithms are affected by the quality of the features used for characterizing the data. Supervised deep learning has recently improved the state-of-the-art in various tasks, such as image classification @cite_5 , object detection @cite_4 or weakly supervised learning linking semantic descriptions to image content @cite_0 . It results in rich feature representations, although at the cost of requiring large amounts of annotated training samples and the limitation to known markers. On the other hand, unsupervised learning enables the exploitation of unlabeled data, capturing the structure of its underlying distribution @cite_16 @cite_28 @cite_8 @cite_19 . A well-known and widely used technique for feature learning is Principal Component Analysis (PCA) @cite_14 , which is computationally efficient, but limited to a linear embedding. In contrast, unsupervised deep learning of convolutional neural networks (CNNs) is computationally more expensive, but can learn a non-linear embedding.
@cite_14 @cite_4 @cite_8 @cite_28 @cite_0 @cite_19 @cite_5 @cite_16
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Over the last years, deep convolutional neural networks (ConvNets) have transformed the field of computer vision thanks to their unparalleled capacity to learn high level semantic image features. However, in order to successfully learn those features, they usually require massive amounts of manually labeled data, which is both expensive and impractical to scale. Therefore, unsupervised semantic feature learning, i.e., learning without requiring manual annotation effort, is of crucial importance in order to successfully harvest the vast amount of visual data that are available today. In our work we propose to learn image features by training ConvNets to recognize the 2d rotation that is applied to the image that it gets as input. We demonstrate both qualitatively and quantitatively that this apparently simple task actually provides a very powerful supervisory signal for semantic feature learning. We exhaustively evaluate our method in various unsupervised feature learning benchmarks and we exhibit in all of them state-of-the-art performance. Specifically, our results on those benchmarks demonstrate dramatic improvements w.r.t. prior state-of-the-art approaches in unsupervised representation learning and thus significantly close the gap with supervised feature learning. For instance, in PASCAL VOC 2007 detection task our unsupervised pre-trained AlexNet model achieves the state-of-the-art (among unsupervised methods) mAP of 54.4 that is only 2.4 points lower from the supervised case. We get similarly striking results when we transfer our unsupervised learned features on various other tasks, such as ImageNet classification, PASCAL classification, PASCAL segmentation, and CIFAR-10 classification. The code and models of our paper will be published on: this https URL . Over the last years, deep convolutional neural networks (ConvNets) have transformed the field of computer vision thanks to their unparalleled capacity to learn high level semantic image features. However, in order to successfully learn those features, they usually require massive amounts of manually labeled data, which is both expensive and impractical to scale. Therefore, unsupervised semantic feature learning, i.e., learning without requiring manual annotation effort, is of crucial importance in order to successfully harvest the vast amount of visual data that are available today. In our work we propose to learn image features by training ConvNets to recognize the 2d rotation that is applied to the image that it gets as input. We demonstrate both qualitatively and quantitatively that this apparently simple task actually provides a very powerful supervisory signal for semantic feature learning. We exhaustively evaluate our method in various unsupervised feature learning benchmarks and we exhibit in all of them state-of-the-art performance. Specifically, our results on those benchmarks demonstrate dramatic improvements w.r.t. prior state-of-the-art approaches in unsupervised representation learning and thus significantly close the gap with supervised feature learning. For instance, in PASCAL VOC 2007 detection task our unsupervised pre-trained AlexNet model achieves the state-of-the-art (among unsupervised methods) mAP of 54.4 that is only 2.4 points lower from the supervised case. We get similar striking results when we transfer our unsupervised learned features on various other tasks, such as ImageNet classification, PASCAL classification, PASCAL segmentation, and CIFAR-10 classification. Remarkable progress has been made in image recognition, primarily due to the availability of large-scale annotated datasets and deep convolutional neural networks (CNNs). CNNs enable learning data-driven, highly representative, hierarchical image features from sufficient training data. However, obtaining datasets as comprehensively annotated as ImageNet in the medical imaging domain remains a challenge. There are currently three major techniques that successfully employ CNNs to medical image classification: training the CNN from scratch, using off-the-shelf pre-trained CNN features, and conducting unsupervised CNN pre-training with supervised fine-tuning. Another effective method is transfer learning, i.e., fine-tuning CNN models pre-trained from natural image dataset to medical image tasks. In this paper, we exploit three important, but previously understudied factors of employing deep convolutional neural networks to computer-aided detection problems. We first explore and evaluate different CNN architectures. The studied models contain 5 thousand to 160 million parameters, and vary in numbers of layers. We then evaluate the influence of dataset scale and spatial image context on performance. Finally, we examine when and why transfer learning from pre-trained ImageNet (via fine-tuning) can be useful. We study two specific computer-aided detection (CADe) problems, namely thoraco-abdominal lymph node (LN) detection and interstitial lung disease (ILD) classification. We achieve the state-of-the-art performance on the mediastinal LN detection, and report the first five-fold cross-validation classification results on predicting axial CT slices with ILD categories. Our extensive empirical evaluation, CNN model analysis and valuable insights can be extended to the design of high performance CAD systems for other medical imaging tasks. Recent deep learning models have demonstrated strong capabilities for classifying text and non-text components in natural images. They extract a high-level feature globally computed from a whole image component (patch), where the cluttered background information may dominate true text features in the deep representation. This leads to less discriminative power and poorer robustness. In this paper, we present a new system for scene text detection by proposing a novel text-attentional convolutional neural network (Text-CNN) that particularly focuses on extracting text-related regions and features from the image components. We develop a new learning mechanism to train the Text-CNN with multi-level and rich supervised information, including text region mask, character label, and binary text non-text information. The rich supervision information enables the Text-CNN with a strong capability for discriminating ambiguous texts, and also increases its robustness against complicated background components. The training process is formulated as a multi-task learning problem, where low-level supervised information greatly facilitates the main task of text non-text classification. In addition, a powerful low-level detector called contrast-enhancement maximally stable extremal regions (MSERs) is developed, which extends the widely used MSERs by enhancing intensity contrast between text patterns and background. This allows it to detect highly challenging text patterns, resulting in a higher recall. Our approach achieved promising results on the ICDAR 2013 data set, with an F-measure of 0.82, substantially improving the state-of-the-art results.