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Register a new userDeep Algorithm Unrolling for Biomedical Imaging
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Yuelong Li
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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In this chapter, we review biomedical applications and breakthroughs via leveraging algorithm unrolling, an important technique that bridges between traditional iterative algorithms and modern deep learning techniques. To provide context, we start by tracing the origin of algorithm unrolling and providing a comprehensive tutorial on how to unroll iterative algorithms into deep networks. We then extensively cover algorithm unrolling in a wide variety of biomedical imaging modalities and delve into several representative recent works in detail. Indeed, there is a rich history of iterative algorithms for biomedical image synthesis, which makes the field ripe for unrolling techniques. In addition, we put algorithm unrolling into a broad perspective, in order to understand why it is particularly effective and discuss recent trends. Finally, we conclude the chapter by discussing open challenges, and suggesting future research directions.
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Graph signal processing is a ubiquitous task in many applications such as sensor, social, transportation and brain networks, point cloud processing, and graph neural networks. Graph signals are often corrupted through sensing processes, and need to be restored for the above applications. In this paper, we propose two graph signal restoration methods based on deep algorithm unrolling (DAU). First, we present a graph signal denoiser by unrolling iterations of the alternating direction method of multiplier (ADMM). We then propose a general restoration method for linear degradation by unrolling iterations of Plug-and-Play ADMM (PnP-ADMM). In the second method, the unrolled ADMM-based denoiser is incorporated as a submodule. Therefore, our restoration method has a nested DAU structure. Thanks to DAU, parameters in the proposed denoising/restoration methods are trainable in an end-to-end manner. Since the proposed restoration methods are based on iterations of a (convex) optimization algorithm, the method is interpretable and keeps the number of parameters small because we only need to tune graph-independent regularization parameters. We solve two main problems in existing graph signal restoration methods: 1) limited performance of convex optimization algorithms due to fixed parameters which are often determined manually. 2) large number of parameters of graph neural networks that result in difficulty of training. Several experiments for graph signal denoising and interpolation are performed on synthetic and real-world data. The proposed methods show performance improvements to several existing methods in terms of root mean squared error in both tasks.
Massive access is a critical design challenge of Internet of Things (IoT) networks. In this paper, we consider the grant-free uplink transmission of an IoT network with a multiple-antenna base station (BS) and a large number of single-antenna IoT devices. Taking into account the sporadic nature of IoT devices, we formulate the joint activity detection and channel estimation (JADCE) problem as a group-sparse matrix estimation problem. This problem can be solved by applying the existing compressed sensing techniques, which however either suffer from high computational complexities or lack of algorithm robustness. To this end, we propose a novel algorithm unrolling framework based on the deep neural network to simultaneously achieve low computational complexity and high robustness for solving the JADCE problem. Specifically, we map the original iterative shrinkage thresholding algorithm (ISTA) into an unrolled recurrent neural network (RNN), thereby improving the convergence rate and computational efficiency through end-to-end training. Moreover, the proposed algorithm unrolling approach inherits the structure and domain knowledge of the ISTA, thereby maintaining the algorithm robustness, which can handle non-Gaussian preamble sequence matrix in massive access. With rigorous theoretical analysis, we further simplify the unrolled network structure by reducing the redundant training parameters. Furthermore, we prove that the simplified unrolled deep neural network structures enjoy a linear convergence rate. Extensive simulations based on various preamble signatures show that the proposed unrolled networks outperform the existing methods in terms of the convergence rate, robustness and estimation accuracy.
Recovering an underlying image from under-sampled measurements, Compressive Sensing Imaging (CSI) is a challenging problem and has many practical applications. Recently, deep neural networks have been applied to this problem with promising results, owing to its implicitly learned prior to alleviate the ill-poseness of CSI. However, existing neural network approaches require separate models for each imaging parameter like sampling ratios, leading to training difficulties and overfitting to specific settings. In this paper, we present a dynamic proximal unrolling network (dubbed DPUNet), which can handle a variety of measurement matrices via one single model without retraining. Specifically, DPUNet can exploit both embedded physical model via gradient descent and imposing image prior with learned dynamic proximal mapping leading to joint reconstruction. A key component of DPUNet is a dynamic proximal mapping module, whose parameters can be dynamically adjusted at inference stage and make it adapt to any given imaging setting. Experimental results demonstrate that the proposed DPUNet can effectively handle multiple CSI modalities under varying sampling ratios and noise levels with only one model, and outperform the state-of-the-art approaches.
Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.
The success of deep learning has been witnessed as a promising technique for computer-aided biomedical image analysis, due to end-to-end learning framework and availability of large-scale labelled samples. However, in many cases of biomedical image analysis, deep learning techniques suffer from the small sample learning (SSL) dilemma caused mainly by lack of annotations. To be more practical for biomedical image analysis, in this paper we survey the key SSL techniques that help relieve the suffering of deep learning by combining with the development of related techniques in computer vision applications. In order to accelerate the clinical usage of biomedical image analysis based on deep learning techniques, we intentionally expand this survey to include the explanation methods for deep models that are important to clinical decision making. We survey the key SSL techniques by dividing them into five categories: (1) explanation techniques, (2) weakly supervised learning techniques, (3) transfer learning techniques, (4) active learning techniques, and (5) miscellaneous techniques involving data augmentation, domain knowledge, traditional shallow methods and attention mechanism. These key techniques are expected to effectively support the application of deep learning in clinical biomedical image analysis, and furtherly improve the analysis performance, especially when large-scale annotated samples are not available. We bulid demos at https://github.com/PengyiZhang/MIADeepSSL.
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