Non-Learning based Deep Parallel MRI Reconstruction (NLDpMRI)

Fast data acquisition in Magnetic Resonance Imaging (MRI) is vastly in demand and scan time directly depends on the number of acquired k-space samples. Recently, the deep learning-based MRI reconstruction techniques were suggested to accelerate MR image acquisition. The most common issues in any deep learning-based MRI reconstruction approaches are generalizability and transferability. For different MRI scanner configurations using these approaches, the network must be trained from scratch every time with new training dataset, acquired under new configurations, to be able to provide good reconstruction performance. Here, we propose a new generalized parallel imaging method based on deep neural networks called NLDpMRI to reduce any structured aliasing ambiguities related to the different k-space undersampling patterns for accelerated data acquisition. Two loss functions including non-regularized and regularized are proposed for parallel MRI reconstruction using deep network optimization and we reconstruct MR images by optimizing the proposed loss functions over the network parameters. Unlike any deep learning-based MRI reconstruction approaches, our method doesn't include any training step that the network learns from a large number of training samples and it only needs the single undersampled multi-coil k-space data for reconstruction. Also, the proposed method can handle k-space data with different undersampling patterns, and the different number of coils. Experimental results show that the proposed method outperforms the current state-of-the-art GRAPPA method and the deep learning-based variational network method

A systematic study of the class imbalance problem in convolutional neural networks

In this study, we systematically investigate the impact of class imbalance on classification performance of convolutional neural networks (CNNs) and compare frequently used methods to address the issue. Class imbalance is a common problem that has been comprehensively studied in classical machine learning, yet very limited systematic research is available in the context of deep learning. In our study, we use three benchmark datasets of increasing complexity, MNIST, CIFAR-10 and ImageNet, to investigate the effects of imbalance on classification and perform an extensive comparison of several methods to address the issue: oversampling, undersampling, two-phase training, and thresholding that compensates for prior class probabilities. Our main evaluation metric is area under the receiver operating characteristic curve (ROC AUC) adjusted to multi-class tasks since overall accuracy metric is associated with notable difficulties in the context of imbalanced data. Based on results from our experiments we conclude that (i) the effect of class imbalance on classification performance is detrimental; (ii) the method of addressing class imbalance that emerged as dominant in almost all analyzed scenarios was oversampling; (iii) oversampling should be applied to the level that completely eliminates the imbalance, whereas the optimal undersampling ratio depends on the extent of imbalance; (iv) as opposed to some classical machine learning models, oversampling does not cause overfitting of CNNs; (v) thresholding should be applied to compensate for prior class probabilities when overall number of properly classified cases is of interest

Deep Learning Enabled Real Time Speckle Recognition and Hyperspectral Imaging using a Multimode Fiber Array

We demonstrate the use of deep learning for fast spectral deconstruction of speckle patterns. The artificial neural network can be effectively trained using numerically constructed multispectral datasets taken from a measured spectral transmission matrix. Optimized neural networks trained on these datasets achieve reliable reconstruction of both discrete and continuous spectra from a monochromatic camera image. Deep learning is compared to analytical inversion methods as well as to a compressive sensing algorithm and shows favourable characteristics both in the oversampling and in the sparse undersampling (compressive) regimes. The deep learning approach offers significant advantages in robustness to drift or noise and in reconstruction speed. In a proof-of-principle demonstrator we achieve real time recovery of hyperspectral information using a multi-core, multi-mode fiber array as a random scattering medium.Comment: 12 pages, 6 figures + Appendix of 5 pages and 5 figure

Spatio-Temporal Deep Learning-Based Undersampling Artefact Reduction for 2D Radial Cine MRI with Limited Data

In this work we reduce undersampling artefacts in two-dimensional ($2D$) golden-angle radial cine cardiac MRI by applying a modified version of the U-net. We train the network on $2D$ spatio-temporal slices which are previously extracted from the image sequences. We compare our approach to two $2D$ and a $3D$ Deep Learning-based post processing methods and to three iterative reconstruction methods for dynamic cardiac MRI. Our method outperforms the $2D$ spatially trained U-net and the $2D$ spatio-temporal U-net. Compared to the $3D$ spatio-temporal U-net, our method delivers comparable results, but with shorter training times and less training data. Compared to the Compressed Sensing-based methods $kt$-FOCUSS and a total variation regularised reconstruction approach, our method improves image quality with respect to all reported metrics. Further, it achieves competitive results when compared to an iterative reconstruction method based on adaptive regularization with Dictionary Learning and total variation, while only requiring a small fraction of the computational time. A persistent homology analysis demonstrates that the data manifold of the spatio-temporal domain has a lower complexity than the spatial domain and therefore, the learning of a projection-like mapping is facilitated. Even when trained on only one single subject without data-augmentation, our approach yields results which are similar to the ones obtained on a large training dataset. This makes the method particularly suitable for training a network on limited training data. Finally, in contrast to the spatial $2D$ U-net, our proposed method is shown to be naturally robust with respect to image rotation in image space and almost achieves rotation-equivariance where neither data-augmentation nor a particular network design are required.Comment: To be published in IEEE Transactions on Medical Imagin

Broad Neural Network for Change Detection in Aerial Images

A change detection system takes as input two images of a region captured at two different times, and predicts which pixels in the region have undergone change over the time period. Since pixel-based analysis can be erroneous due to noise, illumination difference and other factors, contextual information is usually used to determine the class of a pixel (changed or not). This contextual information is taken into account by considering a pixel of the difference image along with its neighborhood. With the help of ground truth information, the labeled patterns are generated. Finally, Broad Learning classifier is used to get prediction about the class of each pixel. Results show that Broad Learning can classify the data set with a significantly higher F-Score than that of Multilayer Perceptron. Performance comparison has also been made with other popular classifiers, namely Multilayer Perceptron and Random Forest.Comment: $\textbf{Accepted at}$: IEMGraph (International Conference on Emerging Technology in Modelling and Graphics) 2018 $$$$ $\textbf{Date of Conference}$: 6-7 September, 2018 $$$$ $\textbf{Location of Conference}$: Kolkatta, Indi

Introducing DeepBalance: Random Deep Belief Network Ensembles to Address Class Imbalance

Class imbalance problems manifest in domains such as financial fraud detection or network intrusion analysis, where the prevalence of one class is much higher than another. Typically, practitioners are more interested in predicting the minority class than the majority class as the minority class may carry a higher misclassification cost. However, classifier performance deteriorates in the face of class imbalance as oftentimes classifiers may predict every point as the majority class. Methods for dealing with class imbalance include cost-sensitive learning or resampling techniques. In this paper, we introduce DeepBalance, an ensemble of deep belief networks trained with balanced bootstraps and random feature selection. We demonstrate that our proposed method outperforms baseline resampling methods such as SMOTE and under- and over-sampling in metrics such as AUC and sensitivity when applied to a highly imbalanced financial transaction data. Additionally, we explore performance and training time implications of various model parameters. Furthermore, we show that our model is easily parallelizable, which can reduce training times. Finally, we present an implementation of DeepBalance in R

Adversarial and Perceptual Refinement for Compressed Sensing MRI Reconstruction

Deep learning approaches have shown promising performance for compressed sensing-based Magnetic Resonance Imaging. While deep neural networks trained with mean squared error (MSE) loss functions can achieve high peak signal to noise ratio, the reconstructed images are often blurry and lack sharp details, especially for higher undersampling rates. Recently, adversarial and perceptual loss functions have been shown to achieve more visually appealing results. However, it remains an open question how to (1) optimally combine these loss functions with the MSE loss function and (2) evaluate such a perceptual enhancement. In this work, we propose a hybrid method, in which a visual refinement component is learnt on top of an MSE loss-based reconstruction network. In addition, we introduce a semantic interpretability score, measuring the visibility of the region of interest in both ground truth and reconstructed images, which allows us to objectively quantify the usefulness of the image quality for image post-processing and analysis. Applied on a large cardiac MRI dataset simulated with 8-fold undersampling, we demonstrate significant improvements ($p<0.01$) over the state-of-the-art in both a human observer study and the semantic interpretability score.Comment: To be published at MICCAI 201

Deep Learning Methods for Parallel Magnetic Resonance Image Reconstruction

Following the success of deep learning in a wide range of applications, neural network-based machine learning techniques have received interest as a means of accelerating magnetic resonance imaging (MRI). A number of ideas inspired by deep learning techniques from computer vision and image processing have been successfully applied to non-linear image reconstruction in the spirit of compressed sensing for both low dose computed tomography and accelerated MRI. The additional integration of multi-coil information to recover missing k-space lines in the MRI reconstruction process, is still studied less frequently, even though it is the de-facto standard for currently used accelerated MR acquisitions. This manuscript provides an overview of the recent machine learning approaches that have been proposed specifically for improving parallel imaging. A general background introduction to parallel MRI is given that is structured around the classical view of image space and k-space based methods. Both linear and non-linear methods are covered, followed by a discussion of recent efforts to further improve parallel imaging using machine learning, and specifically using artificial neural networks. Image-domain based techniques that introduce improved regularizers are covered as well as k-space based methods, where the focus is on better interpolation strategies using neural networks. Issues and open problems are discussed as well as recent efforts for producing open datasets and benchmarks for the community.Comment: 14 pages, 7 figure

Clustering and Learning from Imbalanced Data

A learning classifier must outperform a trivial solution, in case of imbalanced data, this condition usually does not hold true. To overcome this problem, we propose a novel data level resampling method - Clustering Based Oversampling for improved learning from class imbalanced datasets. The essential idea behind the proposed method is to use the distance between a minority class sample and its respective cluster centroid to infer the number of new sample points to be generated for that minority class sample. The proposed algorithm has very less dependence on the technique used for finding cluster centroids and does not effect the majority class learning in any way. It also improves learning from imbalanced data by incorporating the distribution structure of minority class samples in generation of new data samples. The newly generated minority class data is handled in a way as to prevent outlier production and overfitting. Implementation analysis on different datasets using deep neural networks as the learning classifier shows the effectiveness of this method as compared to other synthetic data resampling techniques across several evaluation metrics.Comment: 9 pages, To Appear at NIPS 2018 Workshop

Devising Malware Characterstics using Transformers

With the increasing number of cybersecurity threats, it becomes more difficult for researchers to skim through the security reports for malware analysis. There is a need to be able to extract highly relevant sentences without having to read through the entire malware reports. In this paper, we are finding relevant malware behavior mentions from Advanced Persistent Threat Reports. This main contribution is an opening attempt to Transformer the approach for malware behavior analysis.Comment: 5 pages, 3 figures, 3 table