In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manually annotated data, which is expensive to acquire and limited by the available resources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.
For natural image and video analysis problems, a number of pretext tasks have been explored, including prediction of image rotation @cite_8 , relative position @cite_6 , colorisation @cite_10 and image impainting @cite_3 etc. In medical imaging domain, self-supervised learning has also been explored but to a less extent. proposed a pretext task for subject identification @cite_4 . A Siamese network was trained to classify whether two spinal MR images came from the same subject or not. The pretrained features were used to initialise a disease grade classification network. defined re-colourisation of surgical videos as a pretext task and used the pretrained features to initialise a surgical instrument segmentation network @cite_11 . used rotation prediction as a pretext task and the self-learnt features were transferred to lung lobe segmentation and nodule detection tasks @cite_2 . Different from previous works in the medical imaging domain, we propose a novel pretext task, which is to predict anatomical positions. In particular, we leverage the rich information encoded in the cardiac MR scan view planes and DICOM headers to define the anatomical positions for the task.
@cite_4 @cite_8 @cite_3 @cite_6 @cite_2 @cite_10 @cite_11
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In self-supervised learning, one trains a model to solve a so-called pretext task on a dataset without the need for human annotation. The main objective, however, is to transfer this model to a target domain and task. Currently, the most effective transfer strategy is fine-tuning, which restricts one to use the same model or parts thereof for both pretext and target tasks. In this paper, we present a novel framework for self-supervised learning that overcomes limitations in designing and comparing different tasks, models, and data domains. In particular, our framework decouples the structure of the self-supervised model from the final task-specific fine-tuned model. This allows us to: 1) quantitatively assess previously incompatible models including handcrafted features; 2) show that deeper neural network models can learn better representations from the same pretext task; 3) transfer knowledge learned with a deep model to a shallower one and thus boost its learning. We use this framework to design a novel self-supervised task, which achieves state-of-the-art performance on the common benchmarks in PASCAL VOC 2007, ILSVRC12 and Places by a significant margin. Our learned features shrink the mAP gap between models trained via self-supervised learning and supervised learning from 5.9 to 2.6 in object detection on PASCAL VOC 2007. Alterations in the geometry and function of the heart define well-established causes of cardiovascular disease. However, current approaches to the diagnosis of cardiovascular diseases often rely on subjective human assessment as well as manual analysis of medical images. Both factors limit the sensitivity in quantifying complex structural and functional phenotypes. Deep learning approaches have recently achieved success for tasks such as classification or segmentation of medical images, but lack interpretability in the feature extraction and decision processes, limiting their value in clinical diagnosis. In this work, we propose a 3D convolutional generative model for automatic classification of images from patients with cardiac diseases associated with structural remodeling. The model leverages interpretable task-specific anatomic patterns learned from 3D segmentations. It further allows to visualise and quantify the learned pathology-specific remodeling patterns in the original input space of the images. This approach yields high accuracy in the categorization of healthy and hypertrophic cardiomyopathy subjects when tested on unseen MR images from our own multi-centre dataset (100 ) as well on the ACDC MICCAI 2017 dataset (90 ). We believe that the proposed deep learning approach is a promising step towards the development of interpretable classifiers for the medical imaging domain, which may help clinicians to improve diagnostic accuracy and enhance patient risk-stratification. Deformable image registration is a fundamental task in medical image processing. Among its most important applications, one may cite: 1) multi-modality fusion, where information acquired by different imaging devices or protocols is fused to facilitate diagnosis and treatment planning; 2) longitudinal studies, where temporal structural or anatomical changes are investigated; and 3) population modeling and statistical atlases used to study normal anatomical variability. In this paper, we attempt to give an overview of deformable registration methods, putting emphasis on the most recent advances in the domain. Additional emphasis has been given to techniques applied to medical images. In order to study image registration methods in depth, their main components are identified and studied independently. The most recent techniques are presented in a systematic fashion. The contribution of this paper is to provide an extensive account of registration techniques in a systematic manner. In this paper we study the problem of image representation learning without human annotation. By following the principles of self-supervision, we build a convolutional neural network (CNN) that can be trained to solve Jigsaw puzzles as a pretext task, which requires no manual labeling, and then later repurposed to solve object classification and detection. To maintain the compatibility across tasks we introduce the context-free network (CFN), a siamese-ennead CNN. The CFN takes image tiles as input and explicitly limits the receptive field (or context) of its early processing units to one tile at a time. We show that the CFN includes fewer parameters than AlexNet while preserving the same semantic learning capabilities. By training the CFN to solve Jigsaw puzzles, we learn both a feature mapping of object parts as well as their correct spatial arrangement. Our experimental evaluations show that the learned features capture semantically relevant content. Our proposed method for learning visual representations outperforms state of the art methods in several transfer learning benchmarks. A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. Automatic and accurate whole-heart and great vessel segmentation from 3D cardiac magnetic resonance (MR) images plays an important role in the computer-assisted diagnosis and treatment of cardiovascular disease. However, this task is very challenging due to ambiguous cardiac borders and large anatomical variations among different subjects. In this paper, we propose a novel densely-connected volumetric convolutional neural network, referred as DenseVoxNet, to automatically segment the cardiac and vascular structures from 3D cardiac MR images. The DenseVoxNet adopts the 3D fully convolutional architecture for effective volume-to-volume prediction. From the learning perspective, our DenseVoxNet has three compelling advantages. First, it preserves the maximum information flow between layers by a densely-connected mechanism and hence eases the network training. Second, it avoids learning redundant feature maps by encouraging feature reuse and hence requires fewer parameters to achieve high performance, which is essential for medical applications with limited training data. Third, we add auxiliary side paths to strengthen the gradient propagation and stabilize the learning process. We demonstrate the effectiveness of DenseVoxNet by comparing it with the state-of-the-art approaches from HVSMR 2016 challenge in conjunction with MICCAI, and our network achieves the best dice coefficient. We also show that our network can achieve better performance than other 3D ConvNets but with fewer parameters. This paper presents a novel yet intuitive approach to unsupervised feature learning. Inspired by the human visual system, we explore whether low-level motion-based grouping cues can be used to learn an effective visual representation. Specifically, we use unsupervised motion-based segmentation on videos to obtain segments, which we use as pseudo ground truth to train a convolutional network to segment objects from a single frame. Given the extensive evidence that motion plays a key role in the development of the human visual system, we hope that this straightforward approach to unsupervised learning will be more effective than cleverly designed pretext tasks studied in the literature. Indeed, our extensive experiments show that this is the case. When used for transfer learning on object detection, our representation significantly outperforms previous unsupervised approaches across multiple settings, especially when training data for the target task is scarce. This paper presents a novel yet intuitive approach to unsupervised feature learning. Inspired by the human visual system, we explore whether low-level motion-based grouping cues can be used to learn an effective visual representation. Specifically, we use unsupervised motion-based segmentation on videos to obtain segments, which we use as 'pseudo ground truth' to train a convolutional network to segment objects from a single frame. Given the extensive evidence that motion plays a key role in the development of the human visual system, we hope that this straightforward approach to unsupervised learning will be more effective than cleverly designed 'pretext' tasks studied in the literature. Indeed, our extensive experiments show that this is the case. When used for transfer learning on object detection, our representation significantly outperforms previous unsupervised approaches across multiple settings, especially when training data for the target task is scarce. Citation relationship between scientific publications has been successfully used for scholarly bibliometrics, information retrieval and data mining tasks, and citation-based recommendation algorithms are well documented. While previous studies investigated citation relations from various viewpoints, most of them share the same assumption that, if paper1 cites paper2 (or author1 cites author2), they are connected, regardless of citation importance, sentiment, reason, topic, or motivation. However, this assumption is oversimplified. In this study, we employ an innovative "context-rich heterogeneous network" approach, which paves a new way for citation recommendation task. In the network, we characterize 1) the importance of citation relationships between citing and cited papers, and 2) the topical citation motivation. Unlike earlier studies, the citation information, in this paper, is characterized by citation textual contexts extracted from the full-text citing paper. We also propose algorithm to cope with the situation when large portion of full-text missing information exists in the bibliographic repository. Evaluation results show that, context-rich heterogeneous network can significantly enhance the citation recommendation performance. The anatomical location of imaging features is of crucial importance for accurate diagnosis in many medical tasks. Convolutional neural networks (CNN) have had huge successes in computer vision, but they lack the natural ability to incorporate the anatomical location in their decision making process, hindering success in some medical image analysis tasks. In this paper, to integrate the anatomical location information into the network, we propose several deep CNN architectures that consider multi-scale patches or take explicit location features while training. We apply and compare the proposed architectures for segmentation of white matter hyperintensities in brain MR images on a large dataset. As a result, we observe that the CNNs that incorporate location information substantially outperform a conventional segmentation method with handcrafted features as well as CNNs that do not integrate location information. On a test set of 50 scans, the best configuration of our networks obtained a Dice score of 0.792, compared to 0.805 for an independent human observer. Performance levels of the machine and the independent human observer were not statistically significantly different (p-value = 0.06). In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively. Given a grayscale photograph as input, this paper attacks the problem of hallucinating a plausible color version of the photograph. This problem is clearly underconstrained, so previous approaches have either relied on significant user interaction or resulted in desaturated colorizations. We propose a fully automatic approach that produces vibrant and realistic colorizations. We embrace the underlying uncertainty of the problem by posing it as a classification task and use class-rebalancing at training time to increase the diversity of colors in the result. The system is implemented as a feed-forward pass in a CNN at test time and is trained on over a million color images. We evaluate our algorithm using a “colorization Turing test,” asking human participants to choose between a generated and ground truth color image. Our method successfully fools humans on 32 of the trials, significantly higher than previous methods. Moreover, we show that colorization can be a powerful pretext task for self-supervised feature learning, acting as a cross-channel encoder. This approach results in state-of-the-art performance on several feature learning benchmarks. Given a grayscale photograph as input, this paper attacks the problem of hallucinating a plausible color version of the photograph. This problem is clearly underconstrained, so previous approaches have either relied on significant user interaction or resulted in desaturated colorizations. We propose a fully automatic approach that produces vibrant and realistic colorizations. We embrace the underlying uncertainty of the problem by posing it as a classification task and use class-rebalancing at training time to increase the diversity of colors in the result. The system is implemented as a feed-forward pass in a CNN at test time and is trained on over a million color images. We evaluate our algorithm using a "colorization Turing test," asking human participants to choose between a generated and ground truth color image. Our method successfully fools humans on 32 of the trials, significantly higher than previous methods. Moreover, we show that colorization can be a powerful pretext task for self-supervised feature learning, acting as a cross-channel encoder. This approach results in state-of-the-art performance on several feature learning benchmarks. The success and generalisation of deep learning algorithms heavily depend on learning good feature representations. In medical imaging this entails representing anatomical information, as well as properties related to the specific imaging setting. Anatomical information is required to perform further analysis, whereas imaging information is key to disentangle scanner variability and potential artefacts. The ability to factorise these would allow for training algorithms only on the relevant information according to the task. To date, such factorisation has not been attempted. In this paper, we propose a methodology of latent space factorisation relying on the cycle-consistency principle. As an example application, we consider cardiac MR segmentation, where we separate information related to the myocardium from other features related to imaging and surrounding substructures. We demonstrate the proposed method’s utility in a semi-supervised setting: we use very few labelled images together with many unlabelled images to train a myocardium segmentation neural network. Specifically, we achieve comparable performance to fully supervised networks using a fraction of labelled images in experiments on ACDC and a dataset from Edinburgh Imaging Facility QMRI. Code will be made available at https: github.com agis85 spatial_factorisation. In this paper we aim to determine the location and orientation of a ground-level query image by matching to a reference database of overhead (e.g. satellite) images. For this task we collect a new dataset with one million pairs of street view and overhead images sampled from eleven U.S. cities. We explore several deep CNN architectures for cross-domain matching – Classification, Hybrid, Siamese, and Triplet networks. Classification and Hybrid architectures are accurate but slow since they allow only partial feature precomputation. We propose a new loss function which significantly improves the accuracy of Siamese and Triplet embedding networks while maintaining their applicability to large-scale retrieval tasks like image geolocalization. This image matching task is challenging not just because of the dramatic viewpoint difference between ground-level and overhead imagery but because the orientation (i.e. azimuth) of the street views is unknown making correspondence even more difficult. We examine several mechanisms to match in spite of this – training for rotation invariance, sampling possible rotations at query time, and explicitly predicting relative rotation of ground and overhead images with our deep networks. It turns out that explicit orientation supervision also improves location prediction accuracy. Our best performing architectures are roughly 2.5 times as accurate as the commonly used Siamese network baseline. 7T MRI scanner provides MR images with higher resolution and better contrast than 3T MR scanners. This helps many medical analysis tasks, including tissue segmentation. However, currently there is a very limited number of 7T MRI scanners worldwide. This motivates us to propose a novel image post-processing framework that can jointly generate high-resolution 7T-like images and their corresponding high-quality 7T-like tissue segmentation maps, solely from the routine 3T MR images. Our proposed framework comprises two parallel components, namely (1) reconstruction and (2) segmentation. The reconstruction component includes the multi-step cascaded convolutional neural networks (CNNs) that map the input 3T MR image to a 7T-like MR image, in terms of both resolution and contrast. Similarly, the segmentation component involves another paralleled cascaded CNNs, with a different architecture, to generate high-quality segmentation maps. These cascaded feedbacks between the two designed paralleled CNNs allow both tasks to mutually benefit from each another when learning the respective reconstruction and segmentation mappings. For evaluation, we have tested our framework on 15 subjects (with paired 3T and 7T images) using a leave-one-out cross-validation. The experimental results show that our estimated 7T-like images have richer anatomical details and better segmentation results, compared to the 3T MRI. Furthermore, our method also achieved better results in both reconstruction and segmentation tasks, compared to the state-of-the-art methods. In a document network such as a citation network of scientific documents, web-logs, etc., the content produced by authors exhibits their interest in certain topics. In addition some authors influence other authors' interests. In this work, we propose to model the influence of cited authors along with the interests of citing authors. Moreover, we hypothesize that apart from the citations present in documents, the context surrounding the citation mention provides extra topical information about the cited authors. However, associating terms in the context to the cited authors remains an open problem. We propose novel document generation schemes that incorporate the context while simultaneously modeling the interests of citing authors and influence of the cited authors. Our experiments show significant improvements over baseline models for various evaluation criteria such as link prediction between document and cited author, and quantitatively explaining unseen text. We investigate the effectiveness of a simple solution to the common problem of deep learning in medical image analysis with limited quantities of labeled training data. The underlying idea is to assign artificial labels to abundantly available unlabeled medical images and, through a process known as surrogate supervision, pre-train a deep neural network model for the target medical image analysis task lacking sufficient labeled training data. In particular, we employ 3 surrogate supervision schemes, namely rotation, reconstruction, and colorization, in 4 different medical imaging applications representing classification and segmentation for both 2D and 3D medical images. 3 key findings emerge from our research: 1) pre-training with surrogate supervision is effective for small training sets; 2) deep models trained from initial weights pre-trained through surrogate supervision outperform the same models when trained from scratch, suggesting that pre-training with surrogate supervision should be considered prior to training any deep 3D models; 3) pre-training models in the medical domain with surrogate supervision is more effective than transfer learning from an unrelated domain (e.g., natural images), indicating the practical value of abundant unlabeled medical image data. Automatic liver segmentation in 3D medical images is essential in many clinical applications, such as pathological diagnosis of hepatic diseases, surgical planning, and postoperative assessment. However, it is still a very challenging task due to the complex background, fuzzy boundary, and various appearance of liver. In this paper, we propose an automatic and efficient algorithm to segment liver from 3D CT volumes. A deep image-to-image network (DI2IN) is first deployed to generate the liver segmentation, employing a convolutional encoder-decoder architecture combined with multi-level feature concatenation and deep supervision. Then an adversarial network is utilized during training process to discriminate the output of DI2IN from ground truth, which further boosts the performance of DI2IN. The proposed method is trained on an annotated dataset of 1000 CT volumes with various different scanning protocols (e.g., contrast and non-contrast, various resolution and position) and large variations in populations (e.g., ages and pathology). Our approach outperforms the state-of-the-art solutions in terms of segmentation accuracy and computing efficiency. We work towards efficient methods of categorizing visual content in medical images as a precursor step to segmentation and anatomy recognition. In this paper, we address the problem of automatic detection of level position for a given cardiac CT slice. Specifically, we divide the body area depicted in chest CT into nine semantic categories each representing an area most relevant to the study of a disease and or key anatomic cardiovascular feature. Using a set of handcrafted image features together with features derived form a deep convolutional neural network (CNN), we build a classification scheme to map a given CT slice to the relevant level. Each feature group is used to train a separate support vector machine classifier. The resulting labels are then combined in a linear model, also learned from training data. We report margin zero and margin one accuracy of 91.7 and 98.8 and show that this hybrid approach is a very effective methodology for assigning a given CT image to a relatively narrow anatomic window.