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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In Alzheimer's disease (AD) diagnosis process, functional brain image modalities such as Single-Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET) have been widely used to guide the clinicians. However, the current evaluation of these images entails a succession of manual reorientations and visual interpretation steps, which attach in some way subjectivity to the diagnostic. In this work, a complete computer aided diagnosis (CAD) system for an automatic evaluation of the neuroimages is presented. Principal component analysis (PCA)-based methods are proposed as feature extraction techniques, enhanced by other linear approaches such as linear discriminant analysis (LDA) or the measure of the Fisher discriminant ratio (FDR) for feature selection. The final features allow to face up the so-called small sample size problem and subsequently they are used for the study of neural networks (NN) and support vector machine (SVM) classifiers. The combination of the presented methods achieved accuracy results of up to 96.7 and 89.52 for SPECT and PET images, respectively, which means a significant improvement over the results obtained by the classical voxels-as-features (VAF) reference approach. State-of-the-art object detection networks depend on region proposal algorithms to hypothesize object locations. Advances like SPPnet [7] and Fast R-CNN [5] have reduced the running time of these detection networks, exposing region proposal computation as a bottleneck. In this work, we introduce a Region Proposal Network (RPN) that shares full-image convolutional features with the detection network, thus enabling nearly cost-free region proposals. An RPN is a fully-convolutional network that simultaneously predicts object bounds and objectness scores at each position. RPNs are trained end-to-end to generate high-quality region proposals, which are used by Fast R-CNN for detection. With a simple alternating optimization, RPN and Fast R-CNN can be trained to share convolutional features. For the very deep VGG-16 model [19], our detection system has a frame rate of 5fps (including all steps) on a GPU, while achieving state-of-the-art object detection accuracy on PASCAL VOC 2007 (73.2 mAP) and 2012 (70.4 mAP) using 300 proposals per image. Code is available at https: github.com ShaoqingRen faster_rcnn. Current methods for training convolutional neural networks depend on large amounts of labeled samples for supervised training. In this paper we present an approach for training a convolutional neural network using only unlabeled data. We train the network to discriminate between a set of surrogate classes. Each surrogate class is formed by applying a variety of transformations to a randomly sampled 'seed' image patch. We find that this simple feature learning algorithm is surprisingly successful when applied to visual object recognition. The feature representation learned by our algorithm achieves classification results matching or outperforming the current state-of-the-art for unsupervised learning on several popular datasets (STL-10, CIFAR-10, Caltech-101). Learning representative computational models from medical imaging data requires large training data sets. Often, voxel-level annotation is unfeasible for sufficient amounts of data. An alternative to manual annotation, is to use the enormous amount of knowledge encoded in imaging data and corresponding reports generated during clinical routine. Weakly supervised learning approaches can link volume-level labels to image content but suffer from the typical label distributions in medical imaging data where only a small part consists of clinically relevant abnormal structures. In this paper we propose to use a semantic representation of clinical reports as a learning target that is predicted from imaging data by a convolutional neural network. We demonstrate how we can learn accurate voxel-level classifiers based on weak volume-level semantic descriptions on a set of 157 optical coherence tomography (OCT) volumes. We specifically show how semantic information increases classification accuracy for intraretinal cystoid fluid (IRC), subretinal fluid (SRF) and normal retinal tissue, and how the learning algorithm links semantic concepts to image content and geometry. Traditionally, when generative models of data are developed via deep architectures, greedy layer-wise pre-training is employed. In a well-trained model, the lower layer of the architecture models the data distribution conditional upon the hidden variables, while the higher layers model the hidden distribution prior. But due to the greedy scheme of the layerwise training technique, the parameters of lower layers are fixed when training higher layers. This makes it extremely challenging for the model to learn the hidden distribution prior, which in turn leads to a suboptimal model for the data distribution. We therefore investigate joint training of deep autoencoders, where the architecture is viewed as one stack of two or more single-layer autoencoders. A single global reconstruction objective is jointly optimized, such that the objective for the single autoencoders at each layer acts as a local, layer-level regularizer. We empirically evaluate the performance of this joint training scheme and observe that it not only learns a better data model, but also learns better higher layer representations, which highlights its potential for unsupervised feature learning. In addition, we find that the usage of regularizations in the joint training scheme is crucial in achieving good performance. In the supervised setting, joint training also shows superior performance when training deeper models. The joint training framework can thus provide a platform for investigating more efficient usage of different types of regularizers, especially in light of the growing volumes of available unlabeled data. We propose a deep convolutional neural network architecture codenamed Inception that achieves the new state of the art for classification and detection in the ImageNet Large-Scale Visual Recognition Challenge 2014 (ILSVRC14). The main hallmark of this architecture is the improved utilization of the computing resources inside the network. By a carefully crafted design, we increased the depth and width of the network while keeping the computational budget constant. To optimize quality, the architectural decisions were based on the Hebbian principle and the intuition of multi-scale processing. One particular incarnation used in our submission for ILSVRC14 is called GoogLeNet, a 22 layers deep network, the quality of which is assessed in the context of classification and detection. This work explores the use of spatial context as a source of free and plentiful supervisory signal for training a rich visual representation. Given only a large, unlabeled image collection, we extract random pairs of patches from each image and train a convolutional neural net to predict the position of the second patch relative to the first. We argue that doing well on this task requires the model to learn to recognize objects and their parts. We demonstrate that the feature representation learned using this within-image context indeed captures visual similarity across images. For example, this representation allows us to perform unsupervised visual discovery of objects like cats, people, and even birds from the Pascal VOC 2011 detection dataset. Furthermore, we show that the learned ConvNet can be used in the R-CNN framework [19] and provides a significant boost over a randomly-initialized ConvNet, resulting in state-of-the-art performance among algorithms which use only Pascal-provided training set annotations.