What has happened in machine learning lately, and what does it mean for the future of medical image analysis? Machine learning has witnessed a tremendous amount of attention over the last few years. The current boom started around 2009 when so-called deep artificial neural networks began outperforming other established models on a number of important benchmarks. Deep neural networks are now the state-of-the-art machine learning models across a variety of areas, from image analysis to natural language processing, and widely deployed in academia and industry. These developments have a huge potential for medical imaging technology, medical data analysis, medical diagnostics and healthcare in general, slowly being realized. We provide a short overview of recent advances and some associated challenges in machine learning applied to medical image processing and image analysis. As this has become a very broad and fast expanding field we will not survey the entire landscape of applications, but put particular focus on deep learning in MRI. 
Our aim is threefold: (i) give a brief introduction to deep learning with pointers to core references; (ii) indicate how deep learning has been applied to the entire MRI processing chain, from acquisition to image retrieval, from segmentation to disease prediction; (iii) provide a starting point for people interested in experimenting and perhaps contributing to the field of machine learning for medical imaging by pointing out good educational resources, state-of-the-art open-source code, and interesting sources of data and problems related medical imaging.

An overview of deep learning in medical imaging focusing on MRI

What has happened in machine learning lately, and what does it mean for the future of medical image analysis? Machine learning has witnessed a tremendous amount of attention over the last few years. The current boom started around 2009 when so-called deep artificial neural networks began outperforming other established models on a number of important benchmarks. Deep neural networks are now the state-of-the-art machine learning models across a variety of areas, from image analysis to natural language processing, and widely deployed in academia and industry. These developments have a huge potential for medical imaging technology, medical data analysis, medical diagnostics and healthcare in general, slowly being realized. We provide a short overview of recent advances and some associated challenges in machine learning applied to medical image processing and image analysis. As this has become a very broad and fast expanding field we will not survey the entire landscape of applications, but put particular focus on deep learning in MRI. Our aim is threefold: (i) give a brief introduction to deep learning with pointers to core references; (ii) indicate how deep learning has been applied to the entire MRI processing chain, from acquisition to image retrieval, from segmentation to disease prediction; (iii) provide a starting point for people interested in experimenting and perhaps contributing to the field of deep learning for medical imaging by pointing out good educational resources, state-of-the-art open-source code, and interesting sources of data and problems related medical imaging.

Blood vessel segmentation algorithms — Review of methods, datasets and evaluation metrics

The science of solving clinical problems by analyzing images generated in clinical practice is known as medical image analysis. The aim is to extract information in an effective and efficient manner for improved clinical diagnosis. The recent advances in the field of biomedical engineering has made medical image analysis one of the top research and development area. One of the reason for this advancement is the application of machine learning techniques for the analysis of medical images. Deep learning is successfully used as a tool for machine learning, where a neural network is capable of automatically learning features. This is in contrast to those methods where traditionally hand crafted features are used. The selection and calculation of these features is a challenging task. Among deep learning techniques, deep convolutional networks are actively used for the purpose of medical image analysis. This include application areas such as segmentation, abnormality detection, disease classification, computer aided diagnosis and retrieval. In this study, a comprehensive review of the current state-of-the-art in medical image analysis using deep convolutional networks is presented. The challenges and potential of these techniques are also highlighted.

Medical Image Analysis using Convolutional Neural Networks: A Review

The Hausdorff Distance (HD) is widely used in evaluating medical image segmentation methods. However, the existing segmentation methods do not attempt to reduce HD directly. In this paper, we present novel loss functions for training convolutional neural network (CNN)-based segmentation methods with the goal of reducing HD directly. We propose three methods to estimate HD from the segmentation probability map produced by a CNN. One method makes use of the distance transform of the segmentation boundary. Another method is based on applying morphological erosion on the difference between the true and estimated segmentation maps. The third method works by applying circular/spherical convolution kernels of different radii on the segmentation probability maps. Based on these three methods for estimating HD, we suggest three loss functions that can be used for training to reduce HD. We use these loss functions to train CNNs for segmentation of the prostate, liver, and pancreas in ultrasound, magnetic resonance, and computed tomography images and compare the results with commonly-used loss functions. Our results show that the proposed loss functions can lead to approximately 18–45% reduction in HD without degrading other segmentation performance criteria such as the Dice similarity coefficient. The proposed loss functions can be used for training medical image segmentation methods in order to reduce the large segmentation errors.

Reducing the Hausdorff Distance in Medical Image Segmentation With Convolutional Neural Networks

Medical image segmentation on GPUs – A comprehensive review

Heterogeneous computing, which combines devices with different architectures, is rising in popularity, and promises increased performance combined with reduced energy consumption. OpenCL has been proposed as a standard for programing such systems, and offers functional portability. It does, however, suffer from poor performance portability, code tuned for one device must be re-tuned to achieve good performance on another device. In this paper, we use machine learning-based auto-tuning to address this problem. Benchmarks are run on a random subset of the entire tuning parameter configuration space, and the results are used to build an artificial neural network based model. The model can then be used to find interesting parts of the parameter space for further search. We evaluate our method with different benchmarks, on several devices, including an Intel i7 3770 CPU, an Nvidia K40 GPU and an AMD Radeon HD 7970 GPU. Our model achieves a mean relative error as low as 6.1%, and is able to find configurations as little as 1.3% worse than the global minimum.

Machine Learning Based Auto-Tuning for Enhanced OpenCL Performance Portability

Heterogeneous computing, combining devices with different architectures such as CPUs and GPUs, is rising in popularity and promises increased performance combined with reduced energy consumption. OpenCL has been proposed as a standard for programming such systems and offers functional portability. However, it suffers from poor performance portability, because applications must be retuned for every new device. In this paper, we use machine learning‐based auto‐tuning to address this problem. Benchmarks are run on a random subset of the tuning parameter spaces, and the results are used to build a machine learning‐based performance model. The model can then be used to find interesting subspaces for further search. We evaluate our method using five image processing benchmarks, with tuning parameter space sizes up to 2.3 M, using different input sizes, on several devices, including an Intel i7 4771 (Haswell) CPU, an Nvidia Tesla K40 GPU, and an AMD Radeon HD 7970 GPU. We compare different machine learning algorithms for the performance model. Our model achieves a mean relative error as low as 3.8% and is able to find solutions on average only 0.29% slower than the best configuration in some cases, evaluating less than 1.1% of the search space. The source code of our framework is available at https://github.com/acelster/ML‐autotuning.

Machine learning-based auto-tuning for enhanced performance portability of OpenCL applications

For most applications, taking full advantage of the memory system is key to achieving good performance on GPUs. In this paper, we introduce register caching, a novel idea where registers of multiple threads are combined and used as a shared, last level, manually managed cache for the contributing threads. This method is enabled by the shuffle instruction recently introduced in Nvidia's Kepler GPU architecture, which allows threads in the same warp to exchange data directly, previously only possible by going through shared memory. We evaluate our proposal with a stencil computation benchmark, achieving speedups of up to 2.04, compared to using shared memory on a GTX680 GPU. Stencil computations form the core of many scientific applications, which can therefore benefit from our proposal. Furthermore, our method is not limited to stencil computations, but is applicable to any application with a predictable memory access pattern suitable for manual caching.

Register Caching for Stencil Computations on GPUs

As data sets continue to grow in size, visualization has become a vitally important tool for extracting meaningful knowledge. Scattered point data, which are unordered sets of point coordinates with associated measured values, arise in many contexts, such as scientific experiments, sensor networks, and numerical simulations. In this paper, we present a method for visualizing such scattered point data sets. Our method is based on volume ray casting, and distinguishes itself by operating directly on the unstructured samples, rather than resampling them to form voxels. We estimate the intensity of the volume at points along the rays by interpolation using nearby samples, taking advantage of an octree to facilitate efficient range search. The method has been implemented on multi-core CPUs, GPUs as well as multi-GPU systems.1 To test our method, actual X-ray diffraction data sets have been used, consisting of up to 240 million data points. We are able to generate images of good quality and achieve interactive frame rates in favorable cases. The GPU implementation (Nvidia Tesla K20) achieves speedups of 8-14 compared with our parallelized CPU version (4-core, hyperthreaded Intel i7 3770K).

Thomas L. Falch

Papers

Medical image segmentation on GPUs – A comprehensive review

Machine Learning Based Auto-Tuning for Enhanced OpenCL Performance Portability

Machine learning-based auto-tuning for enhanced performance portability of OpenCL applications

Register Caching for Stencil Computations on GPUs

GPU-Accelerated Visualization of Scattered Point Data