This paper presents a new method for medical diagnosis of neurodegenerative diseases, such as Parkinson's, by extracting and using latent information from trained Deep convolutional, or convolutional-recurrent Neural Networks (DNNs). In particular, our approach adopts a combination of transfer learning, k-means clustering and k-Nearest Neighbour classification of deep neural network learned representations to provide enriched prediction of the disease based on MRI and or DaT Scan data. A new loss function is introduced and used in the training of the DNNs, so as to perform adaptation of the generated learned representations between data from different medical environments. Results are presented using a recently published database of Parkinson's related information, which was generated and evaluated in a hospital environment.
Recent advances in deep neural networks @cite_4 , @cite_6 , @cite_8 , @cite_16 have been explored in @cite_0 , where convolutional (CNN) and convolutional-recurrent (CNN-RNN) neural networks were developed and trained to classify the information in the above Parkinson's database in two categories, i.e., patients and non patients, based on either MRI inputs, or DaT Scan inputs, or together MRI and DaT Scan inputs.
@cite_4 @cite_8 @cite_6 @cite_0 @cite_16
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We adopt Convolutional Neural Networks (CNN) to learn discriminative features for local patch classification. We further introduce quaddirectional 2D Recurrent Neural Networks to model the long range dependencies among pixels. Our quaddirectional 2D-RNN is able to embed the global image context into the compact local representation, which significantly enhance their discriminative power. Our experiments demonstrate that the integration of CNN and quaddirectional 2D-RNN achieves very promising results which are comparable to state-of-the-art on real-world image labeling benchmarks. In existing convolutional neural networks (CNNs), both convolution and pooling are locally performed for image regions separately, no contextual dependencies between different image regions have been taken into consideration. Such dependencies represent useful spatial structure information in images. Whereas recurrent neural networks (RNNs) are designed for learning contextual dependencies among sequential data by using the recurrent (feedback) connections. In this work, we propose the convolutional recurrent neural network (C-RNN), which learns the spatial dependencies between image regions to enhance the discriminative power of image representation. The C-RNN is trained in an end-to-end manner from raw pixel images. CNN layers are firstly processed to generate middle level features. RNN layer is then learned to encode spatial dependencies. The C-RNN can learn better image representation, especially for images with obvious spatial contextual dependencies. Our method achieves competitive performance on ILSVRC 2012, SUN 397, and MIT indoor. Despite the recent advances in automatically describing image contents, their applications have been mostly limited to image caption datasets containing natural images (e.g., Flickr 30k, MSCOCO). In this paper, we present a deep learning model to efficiently detect a disease from an image and annotate its contexts (e.g., location, severity and the affected organs). We employ a publicly available radiology dataset of chest x-rays and their reports, and use its image annotations to mine disease names to train convolutional neural networks (CNNs). In doing so, we adopt various regularization techniques to circumvent the large normal-vs-diseased cases bias. Recurrent neural networks (RNNs) are then trained to describe the contexts of a detected disease, based on the deep CNN features. Moreover, we introduce a novel approach to use the weights of the already trained pair of CNN RNN on the domain-specific image text dataset, to infer the joint image text contexts for composite image labeling. Significantly improved image annotation results are demonstrated using the recurrent neural cascade model by taking the joint image text contexts into account. The 3D convolutional neural network (CNN) is able to make full use of the spatial 3D context information of lung nodules, and the multi-view strategy has been shown to be useful for improving the performance of 2D CNN in classifying lung nodules. In this paper, we explore the classification of lung nodules using the 3D multi-view convolutional neural networks (MV-CNN) with both chain architecture and directed acyclic graph architecture, including 3D Inception and 3D Inception-ResNet. All networks employ the multi-view-one-network strategy. We conduct a binary classification (benign and malignant) and a ternary classification (benign, primary malignant and metastatic malignant) on Computed Tomography (CT) images from Lung Image Database Consortium and Image Database Resource Initiative database (LIDC-IDRI). All results are obtained via 10-fold cross validation. As regards the MV-CNN with chain architecture, results show that the performance of 3D MV-CNN surpasses that of 2D MV-CNN by a significant margin. Finally, a 3D Inception network achieved an error rate of 4.59 for the binary classification and 7.70 for the ternary classification, both of which represent superior results for the corresponding task. We compare the multi-view-one-network strategy with the one-view-one-network strategy. The results reveal that the multi-view-one-network strategy can achieve a lower error rate than the one-view-one-network strategy. In this paper, we consider numerous low-level vision problems (e.g., edge-preserving filtering and denoising) as recursive image filtering via a hybrid neural network. The network contains several spatially variant recurrent neural networks (RNN) as equivalents of a group of distinct recursive filters for each pixel, and a deep convolutional neural network (CNN) that learns the weights of RNNs. The deep CNN can learn regulations of recurrent propagation for various tasks and effectively guides recurrent propagation over an entire image. The proposed model does not need a large number of convolutional channels nor big kernels to learn features for low-level vision filters. It is significantly smaller and faster in comparison with a deep CNN based image filter. Experimental results show that many low-level vision tasks can be effectively learned and carried out in real-time by the proposed algorithm. In recent years, the convolutional neural network (CNN) has achieved great success in many computer vision tasks. Partially inspired by neuroscience, CNN shares many properties with the visual system of the brain. A prominent difference is that CNN is typically a feed-forward architecture while in the visual system recurrent connections are abundant. Inspired by this fact, we propose a recurrent CNN (RCNN) for object recognition by incorporating recurrent connections into each convolutional layer. Though the input is static, the activities of RCNN units evolve over time so that the activity of each unit is modulated by the activities of its neighboring units. This property enhances the ability of the model to integrate the context information, which is important for object recognition. Like other recurrent neural networks, unfolding the RCNN through time can result in an arbitrarily deep network with a fixed number of parameters. Furthermore, the unfolded network has multiple paths, which can facilitate the learning process. The model is tested on four benchmark object recognition datasets: CIFAR-10, CIFAR-100, MNIST and SVHN. With fewer trainable parameters, RCNN outperforms the state-of-the-art models on all of these datasets. Increasing the number of parameters leads to even better performance. These results demonstrate the advantage of the recurrent structure over purely feed-forward structure for object recognition. Recently, the convolutional neural network (CNN) has been successfully applied to the task of brain tumor segmentation. However, the effectiveness of a CNN-based method is limited by the small receptive field, and the segmentation results don’t perform well in the spatial contiguity. Therefore, many attempts have been made to strengthen the spatial contiguity of the network output. In this paper, we proposed an adversarial training approach to train the CNN network. A discriminator network is trained along with a generator network which produces the synthetic segmentation results. The discriminator network is encouraged to discriminate the synthetic labels from the ground truth labels. Adversarial adjustments provided by the discriminator network are fed back to the generator network to help reduce the differences between the synthetic labels and the ground truth labels and reinforce the spatial contiguity with high-order loss terms. The presented method is evaluated on the Brats2017 training dataset. The experiment results demonstrate that the presented method could enhance the spatial contiguity of the segmentation results and improve the segmentation accuracy. Convolutional neural networks (CNNs) have emerged as the most powerful technique for a range of different tasks in computer vision. Recent work suggested that CNN features are generic and can be used for classification tasks outside the exact domain for which the networks were trained. In this work we use the features from one such network, OverFeat, trained for object detection in natural images, for nodule detection in computed tomography scans. We use 865 scans from the publicly available LIDC data set, read by four thoracic radiologists. Nodule candidates are generated by a state-of-the-art nodule detection system. We extract 2D sagittal, coronal and axial patches for each nodule candidate and extract 4096 features from the penultimate layer of OverFeat and classify these with linear support vector machines. We show for various configurations that the off-the-shelf CNN features perform surprisingly well, but not as good as the dedicated detection system. When both approaches are combined, significantly better results are obtained than either approach alone. We conclude that CNN features have great potential to be used for detection tasks in volumetric medical data. Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models. Abstract In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we’ve found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster. Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods. Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods. A significant proportion of patients scanned in a clinical setting have follow-up scans. We show in this work that such longitudinal scans alone can be used as a form of “free” self-supervision for training a deep network. We demonstrate this self-supervised learning for the case of T2-weighted sagittal lumbar Magnetic Resonance Images (MRIs). A Siamese convolutional neural network (CNN) is trained using two losses: (i) a contrastive loss on whether the scan is of the same person (i.e. longitudinal) or not, together with (ii) a classification loss on predicting the level of vertebral bodies. The performance of this pre-trained network is then assessed on a grading classification task. We experiment on a dataset of 1016 subjects, 423 possessing follow-up scans, with the end goal of learning the disc degeneration radiological gradings attached to the intervertebral discs. We show that the performance of the pre-trained CNN on the supervised classification task is (i) superior to that of a network trained from scratch; and (ii) requires far fewer annotated training samples to reach an equivalent performance to that of the network trained from scratch. In recent years, Convolutional Neural Networks (CNNs) have shown remarkable performance in many computer vision tasks such as object recognition and detection. However, complex training issues, such as "catastrophic forgetting" and hyper-parameter tuning, make incremental learning in CNNs a difficult challenge. In this paper, we propose a hierarchical deep neural network, with CNNs at multiple levels, and a corresponding training method for lifelong learning. The network grows in a tree-like manner to accommodate the new classes of data without losing the ability to identify the previously trained classes. The proposed network was tested on CIFAR-10 and CIFAR-100 datasets, and compared against the method of fine tuning specific layers of a conventional CNN. We obtained comparable accuracies and achieved 40 and 20 reduction in training effort in CIFAR-10 and CIFAR 100 respectively. The network was able to organize the incoming classes of data into feature-driven super-classes. Our model improves upon existing hierarchical CNN models by adding the capability of self-growth and also yields important observations on feature selective classification. Convolutional neural network (CNN) depth is of crucial importance for image super-resolution (SR). However, we observe that deeper networks for image SR are more difficult to train. The low-resolution inputs and features contain abundant low-frequency information, which is treated equally across channels, hence hindering the representational ability of CNNs. To solve these problems, we propose the very deep residual channel attention networks (RCAN). Specifically, we propose a residual in residual (RIR) structure to form very deep network, which consists of several residual groups with long skip connections. Each residual group contains some residual blocks with short skip connections. Meanwhile, RIR allows abundant low-frequency information to be bypassed through multiple skip connections, making the main network focus on learning high-frequency information. Furthermore, we propose a channel attention mechanism to adaptively rescale channel-wise features by considering interdependencies among channels. Extensive experiments show that our RCAN achieves better accuracy and visual improvements against state-of-the-art methods. Convolutional neural network (CNN) depth is of crucial importance for image super-resolution (SR). However, we observe that deeper networks for image SR are more difficult to train. The low-resolution inputs and features contain abundant low-frequency information, which is treated equally across channels, hence hindering the representational ability of CNNs. To solve these problems, we propose the very deep residual channel attention networks (RCAN). Specifically, we propose a residual in residual (RIR) structure to form very deep network, which consists of several residual groups with long skip connections. Each residual group contains some residual blocks with short skip connections. Meanwhile, RIR allows abundant low-frequency information to be bypassed through multiple skip connections, making the main network focus on learning high-frequency information. Furthermore, we propose a channel attention mechanism to adaptively rescale channel-wise features by considering interdependencies among channels. Extensive experiments show that our RCAN achieves better accuracy and visual improvements against state-of-the-art methods. This paper describes a novel text-to-speech (TTS) technique based on deep convolutional neural networks (CNN), without use of any recurrent units. Recurrent neural networks (RNN) have become a standard technique to model sequential data recently, and this technique has been used in some cutting-edge neural TTS techniques. However, training RNN components often requires a very powerful computer, or a very long time, typically several days or weeks. Recent other studies, on the other hand, have shown that CNN-based sequence synthesis can be much faster than RNN-based techniques, because of high parallelizability. The objective of this paper is to show that an alternative neural TTS based only on CNN alleviate these economic costs of training. In our experiment, the proposed Deep Convolutional TTS was sufficiently trained overnight (15 hours), using an ordinary gaming PC equipped with two GPUs, while the quality of the synthesized speech was almost acceptable. Deep neural networks such as Convolutional Networks (ConvNets) and Deep Belief Networks (DBNs) represent the state-of-the-art for many machine learning and computer vision classification problems. To overcome the large computational cost of deep networks, spiking deep networks have recently been proposed, given the specialized hardware now available for spiking neural networks (SNNs). However, this has come at the cost of performance losses due to the conversion from analog neural networks (ANNs) without a notion of time, to sparsely firing, event-driven SNNs. Here we analyze the effects of converting deep ANNs into SNNs with respect to the choice of parameters for spiking neurons such as firing rates and thresholds. We present a set of optimization techniques to minimize performance loss in the conversion process for ConvNets and fully connected deep networks. These techniques yield networks that outperform all previous SNNs on the MNIST database to date, and many networks here are close to maximum performance after only 20 ms of simulated time. The techniques include using rectified linear units (ReLUs) with zero bias during training, and using a new weight normalization method to help regulate firing rates. Our method for converting an ANN into an SNN enables low-latency classification with high accuracies already after the first output spike, and compared with previous SNN approaches it yields improved performance without increased training time. The presented analysis and optimization techniques boost the value of spiking deep networks as an attractive framework for neuromorphic computing platforms aimed at fast and efficient pattern recognition. Convolutional neural networks (CNN) are a special type of deep neural networks (DNN). They have so far been successfully applied to image super-resolution (SR) as well as other image restoration tasks. In this paper, we consider the problem of video super-resolution. We propose a CNN that is trained on both the spatial and the temporal dimensions of videos to enhance their spatial resolution. Consecutive frames are motion compensated and used as input to a CNN that provides super-resolved video frames as output. We investigate different options of combining the video frames within one CNN architecture. While large image databases are available to train deep neural networks, it is more challenging to create a large video database of sufficient quality to train neural nets for video restoration. We show that by using images to pretrain our model, a relatively small video database is sufficient for the training of our model to achieve and even improve upon the current state-of-the-art. We compare our proposed approach to current video as well as image SR algorithms. Non-recurrent deep convolutional neural networks (CNNs) are currently the best at modeling core object recognition, a behavior that is supported by the densely recurrent primate ventral stream, culminating in the inferior temporal (IT) cortex. If recurrence is critical to this behavior, then primates should outperform feedforward-only deep CNNs for images that require additional recurrent processing beyond the feedforward IT response. Here we first used behavioral methods to discover hundreds of these ‘challenge’ images. Second, using large-scale electrophysiology, we observed that behaviorally sufficient object identity solutions emerged 30 ms later in the IT cortex for challenge images compared with primate performance-matched ‘control’ images. Third, these behaviorally critical late-phase IT response patterns were poorly predicted by feedforward deep CNN activations. Notably, very-deep CNNs and shallower recurrent CNNs better predicted these late IT responses, suggesting that there is a functional equivalence between additional nonlinear transformations and recurrence. Beyond arguing that recurrent circuits are critical for rapid object identification, our results provide strong constraints for future recurrent model development.