Analysis of Deep Complex-Valued Convolutional Neural Networks for MRI Reconstruction

Many real-world signal sources are complex-valued, having real and imaginary components. However, the vast majority of existing deep learning platforms and network architectures do not support the use of complex-valued data. MRI data is inherently complex-valued, so existing approaches discard the richer algebraic structure of the complex data. In this work, we investigate end-to-end complex-valued convolutional neural networks - specifically, for image reconstruction in lieu of two-channel real-valued networks. We apply this to magnetic resonance imaging reconstruction for the purpose of accelerating scan times and determine the performance of various promising complex-valued activation functions. We find that complex-valued CNNs with complex-valued convolutions provide superior reconstructions compared to real-valued convolutions with the same number of trainable parameters, over a variety of network architectures and datasets

Cell Detection in Microscopy Images with Deep Convolutional Neural Network and Compressed Sensing

The ability to automatically detect certain types of cells or cellular subunits in microscopy images is of significant interest to a wide range of biomedical research and clinical practices. Cell detection methods have evolved from employing hand-crafted features to deep learning-based techniques. The essential idea of these methods is that their cell classifiers or detectors are trained in the pixel space, where the locations of target cells are labeled. In this paper, we seek a different route and propose a convolutional neural network (CNN)-based cell detection method that uses encoding of the output pixel space. For the cell detection problem, the output space is the sparsely labeled pixel locations indicating cell centers. We employ random projections to encode the output space to a compressed vector of fixed dimension. Then, CNN regresses this compressed vector from the input pixels. Furthermore, it is possible to stably recover sparse cell locations on the output pixel space from the predicted compressed vector using $L_1$-norm optimization. In the past, output space encoding using compressed sensing (CS) has been used in conjunction with linear and non-linear predictors. To the best of our knowledge, this is the first successful use of CNN with CS-based output space encoding. We made substantial experiments on several benchmark datasets, where the proposed CNN + CS framework (referred to as CNNCS) achieved the highest or at least top-3 performance in terms of F1-score, compared with other state-of-the-art methods

Highly Scalable Image Reconstruction using Deep Neural Networks with Bandpass Filtering

To increase the flexibility and scalability of deep neural networks for image reconstruction, a framework is proposed based on bandpass filtering. For many applications, sensing measurements are performed indirectly. For example, in magnetic resonance imaging, data are sampled in the frequency domain. The introduction of bandpass filtering enables leveraging known imaging physics while ensuring that the final reconstruction is consistent with actual measurements to maintain reconstruction accuracy. We demonstrate this flexible architecture for reconstructing subsampled datasets of MRI scans. The resulting high subsampling rates increase the speed of MRI acquisitions and enable the visualization rapid hemodynamics.Comment: 9 pages, 10 figure

Deep Convolutional Compressed Sensing for LiDAR Depth Completion

In this paper we consider the problem of estimating a dense depth map from a set of sparse LiDAR points. We use techniques from compressed sensing and the recently developed Alternating Direction Neural Networks (ADNNs) to create a deep recurrent auto-encoder for this task. Our architecture internally performs an algorithm for extracting multi-level convolutional sparse codes from the input which are then used to make a prediction. Our results demonstrate that with only two layers and 1800 parameters we are able to out perform all previously published results, including deep networks with orders of magnitude more parameters

One-dimensional Deep Image Prior for Time Series Inverse Problems

We extend the Deep Image Prior (DIP) framework to one-dimensional signals. DIP is using a randomly initialized convolutional neural network (CNN) to solve linear inverse problems by optimizing over weights to fit the observed measurements. Our main finding is that properly tuned one-dimensional convolutional architectures provide an excellent Deep Image Prior for various types of temporal signals including audio, biological signals, and sensor measurements. We show that our network can be used in a variety of recovery tasks including missing value imputation, blind denoising, and compressed sensing from random Gaussian projections. The key challenge is how to avoid overfitting by carefully tuning early stopping, total variation, and weight decay regularization. Our method requires up to 4 times fewer measurements than Lasso and outperforms NLM-VAMP for random Gaussian measurements on audio signals, has similar imputation performance to a Kalman state-space model on a variety of data, and outperforms wavelet filtering in removing additive noise from air-quality sensor readings

A Deep Information Sharing Network for Multi-contrast Compressed Sensing MRI Reconstruction

In multi-contrast magnetic resonance imaging (MRI), compressed sensing theory can accelerate imaging by sampling fewer measurements within each contrast. The conventional optimization-based models suffer several limitations: strict assumption of shared sparse support, time-consuming optimization and "shallow" models with difficulties in encoding the rich patterns hiding in massive MRI data. In this paper, we propose the first deep learning model for multi-contrast MRI reconstruction. We achieve information sharing through feature sharing units, which significantly reduces the number of parameters. The feature sharing unit is combined with a data fidelity unit to comprise an inference block. These inference blocks are cascaded with dense connections, which allows for information transmission across different depths of the network efficiently. Our extensive experiments on various multi-contrast MRI datasets show that proposed model outperforms both state-of-the-art single-contrast and multi-contrast MRI methods in accuracy and efficiency. We show the improved reconstruction quality can bring great benefits for the later medical image analysis stage. Furthermore, the robustness of the proposed model to the non-registration environment shows its potential in real MRI applications.Comment: 13 pages, 16 figures, 3 table

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

CRDN: Cascaded Residual Dense Networks for Dynamic MR Imaging with Edge-enhanced Loss Constraint

Dynamic magnetic resonance (MR) imaging has generated great research interest, as it can provide both spatial and temporal information for clinical diagnosis. However, slow imaging speed or long scanning time is still one of the challenges for dynamic MR imaging. Most existing methods reconstruct Dynamic MR images from incomplete k-space data under the guidance of compressed sensing (CS) or low rank theory, which suffer from long iterative reconstruction time. Recently, deep learning has shown great potential in accelerating dynamic MR. Our previous work proposed a dynamic MR imaging method with both k-space and spatial prior knowledge integrated via multi-supervised network training. Nevertheless, there was still a certain degree of smooth in the reconstructed images at high acceleration factors. In this work, we propose cascaded residual dense networks for dynamic MR imaging with edge-enhance loss constraint, dubbed as CRDN. Specifically, the cascaded residual dense networks fully exploit the hierarchical features from all the convolutional layers with both local and global feature fusion. We further utilize the total variation (TV) loss function, which has the edge enhancement properties, for training the networks

DeepIoT: Compressing Deep Neural Network Structures for Sensing Systems with a Compressor-Critic Framework

Recent advances in deep learning motivate the use of deep neutral networks in sensing applications, but their excessive resource needs on constrained embedded devices remain an important impediment. A recently explored solution space lies in compressing (approximating or simplifying) deep neural networks in some manner before use on the device. We propose a new compression solution, called DeepIoT, that makes two key contributions in that space. First, unlike current solutions geared for compressing specific types of neural networks, DeepIoT presents a unified approach that compresses all commonly used deep learning structures for sensing applications, including fully-connected, convolutional, and recurrent neural networks, as well as their combinations. Second, unlike solutions that either sparsify weight matrices or assume linear structure within weight matrices, DeepIoT compresses neural network structures into smaller dense matrices by finding the minimum number of non-redundant hidden elements, such as filters and dimensions required by each layer, while keeping the performance of sensing applications the same. Importantly, it does so using an approach that obtains a global view of parameter redundancies, which is shown to produce superior compression. We conduct experiments with five different sensing-related tasks on Intel Edison devices. DeepIoT outperforms all compared baseline algorithms with respect to execution time and energy consumption by a significant margin. It reduces the size of deep neural networks by 90% to 98.9%. It is thus able to shorten execution time by 71.4% to 94.5%, and decrease energy consumption by 72.2% to 95.7%. These improvements are achieved without loss of accuracy. The results underscore the potential of DeepIoT for advancing the exploitation of deep neural networks on resource-constrained embedded devices.Comment: Published in SenSys2017. Code is available on https://github.com/yscacaca/DeepIo

Compressed Sensing with Deep Image Prior and Learned Regularization

We propose a novel method for compressed sensing recovery using untrained deep generative models. Our method is based on the recently proposed Deep Image Prior (DIP), wherein the convolutional weights of the network are optimized to match the observed measurements. We show that this approach can be applied to solve any differentiable linear inverse problem, outperforming previous unlearned methods. Unlike various learned approaches based on generative models, our method does not require pre-training over large datasets. We further introduce a novel learned regularization technique, which incorporates prior information on the network weights. This reduces reconstruction error, especially for noisy measurements. Finally, we prove that, using the DIP optimization approach, moderately overparameterized single-layer networks can perfectly fit any signal despite the non-convex nature of the fitting problem. This theoretical result provides justification for early stopping