Automatically Designing CNN Architectures for Medical Image Segmentation

Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.Comment: Accepted to Machine Learning in Medical Imaging (MLMI 2018

Impact of adversarial examples on deep learning models for biomedical image segmentation

Deep learning models, which are increasingly being used in the field of medical image analysis, come with a major security risk, namely, their vulnerability to adversarial examples. Adversarial examples are carefully crafted samples that force machine learning models to make mistakes during testing time. These malicious samples have been shown to be highly effective in misguiding classification tasks. However, research on the influence of adversarial examples on segmentation is significantly lacking. Given that a large portion of medical imaging problems are effectively segmentation problems, we analyze the impact of adversarial examples on deep learning-based image segmentation models. Specifically, we expose the vulnerability of these models to adversarial examples by proposing the Adaptive Segmentation Mask Attack (ASMA). This novel algorithm makes it possible to craft targeted adversarial examples that come with (1) high intersection-over-union rates between the target adversarial mask and the prediction and (2) with perturbation that is, for the most part, invisible to the bare eye. We lay out experimental and visual evidence by showing results obtained for the ISIC skin lesion segmentation challenge and the problem of glaucoma optic disc segmentation. An implementation of this algorithm and additional examples can be found at https://github.com/utkuozbulak/adaptive-segmentation-mask-attack

Brain Tumor Synthetic Segmentation in 3D Multimodal MRI Scans

The magnetic resonance (MR) analysis of brain tumors is widely used for diagnosis and examination of tumor subregions. The overlapping area among the intensity distribution of healthy, enhancing, non-enhancing, and edema regions makes the automatic segmentation a challenging task. Here, we show that a convolutional neural network trained on high-contrast images can transform the intensity distribution of brain lesions in its internal subregions. Specifically, a generative adversarial network (GAN) is extended to synthesize high-contrast images. A comparison of these synthetic images and real images of brain tumor tissue in MR scans showed significant segmentation improvement and decreased the number of real channels for segmentation. The synthetic images are used as a substitute for real channels and can bypass real modalities in the multimodal brain tumor segmentation framework. Segmentation results on BraTS 2019 dataset demonstrate that our proposed approach can efficiently segment the tumor areas. In the end, we predict patient survival time based on volumetric features of the tumor subregions as well as the age of each case through several regression models

3D-BEVIS: Bird's-Eye-View Instance Segmentation

Recent deep learning models achieve impressive results on 3D scene analysis tasks by operating directly on unstructured point clouds. A lot of progress was made in the field of object classification and semantic segmentation. However, the task of instance segmentation is less explored. In this work, we present 3D-BEVIS, a deep learning framework for 3D semantic instance segmentation on point clouds. Following the idea of previous proposal-free instance segmentation approaches, our model learns a feature embedding and groups the obtained feature space into semantic instances. Current point-based methods scale linearly with the number of points by processing local sub-parts of a scene individually. However, to perform instance segmentation by clustering, globally consistent features are required. Therefore, we propose to combine local point geometry with global context information from an intermediate bird's-eye view representation.Comment: camera-ready version for GCPR '1

Massively Parallel Video Networks

We introduce a class of causal video understanding models that aims to improve efficiency of video processing by maximising throughput, minimising latency, and reducing the number of clock cycles. Leveraging operation pipelining and multi-rate clocks, these models perform a minimal amount of computation (e.g. as few as four convolutional layers) for each frame per timestep to produce an output. The models are still very deep, with dozens of such operations being performed but in a pipelined fashion that enables depth-parallel computation. We illustrate the proposed principles by applying them to existing image architectures and analyse their behaviour on two video tasks: action recognition and human keypoint localisation. The results show that a significant degree of parallelism, and implicitly speedup, can be achieved with little loss in performance.Comment: Fixed typos in densenet model definition in appendi

Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation

Image segmentation is a fundamental problem in biomedical image analysis. Recent advances in deep learning have achieved promising results on many biomedical image segmentation benchmarks. However, due to large variations in biomedical images (different modalities, image settings, objects, noise, etc), to utilize deep learning on a new application, it usually needs a new set of training data. This can incur a great deal of annotation effort and cost, because only biomedical experts can annotate effectively, and often there are too many instances in images (e.g., cells) to annotate. In this paper, we aim to address the following question: With limited effort (e.g., time) for annotation, what instances should be annotated in order to attain the best performance? We present a deep active learning framework that combines fully convolutional network (FCN) and active learning to significantly reduce annotation effort by making judicious suggestions on the most effective annotation areas. We utilize uncertainty and similarity information provided by FCN and formulate a generalized version of the maximum set cover problem to determine the most representative and uncertain areas for annotation. Extensive experiments using the 2015 MICCAI Gland Challenge dataset and a lymph node ultrasound image segmentation dataset show that, using annotation suggestions by our method, state-of-the-art segmentation performance can be achieved by using only 50% of training data.Comment: Accepted at MICCAI 201

Deep Neural Network with l2-norm Unit for Brain Lesions Detection

Automated brain lesions detection is an important and very challenging clinical diagnostic task because the lesions have different sizes, shapes, contrasts, and locations. Deep Learning recently has shown promising progress in many application fields, which motivates us to apply this technology for such important problem. In this paper, we propose a novel and end-to-end trainable approach for brain lesions classification and detection by using deep Convolutional Neural Network (CNN). In order to investigate the applicability, we applied our approach on several brain diseases including high and low-grade glioma tumor, ischemic stroke, Alzheimer diseases, by which the brain Magnetic Resonance Images (MRI) have been applied as an input for the analysis. We proposed a new operating unit which receives features from several projections of a subset units of the bottom layer and computes a normalized l2-norm for next layer. We evaluated the proposed approach on two different CNN architectures and number of popular benchmark datasets. The experimental results demonstrate the superior ability of the proposed approach.Comment: Accepted for presentation in ICONIP-201

Semi-Supervised Deep Learning for Fully Convolutional Networks

Deep learning usually requires large amounts of labeled training data, but annotating data is costly and tedious. The framework of semi-supervised learning provides the means to use both labeled data and arbitrary amounts of unlabeled data for training. Recently, semi-supervised deep learning has been intensively studied for standard CNN architectures. However, Fully Convolutional Networks (FCNs) set the state-of-the-art for many image segmentation tasks. To the best of our knowledge, there is no existing semi-supervised learning method for such FCNs yet. We lift the concept of auxiliary manifold embedding for semi-supervised learning to FCNs with the help of Random Feature Embedding. In our experiments on the challenging task of MS Lesion Segmentation, we leverage the proposed framework for the purpose of domain adaptation and report substantial improvements over the baseline model.Comment: 9 pages, 6 figure

Recycle-GAN: Unsupervised Video Retargeting

We introduce a data-driven approach for unsupervised video retargeting that translates content from one domain to another while preserving the style native to a domain, i.e., if contents of John Oliver's speech were to be transferred to Stephen Colbert, then the generated content/speech should be in Stephen Colbert's style. Our approach combines both spatial and temporal information along with adversarial losses for content translation and style preservation. In this work, we first study the advantages of using spatiotemporal constraints over spatial constraints for effective retargeting. We then demonstrate the proposed approach for the problems where information in both space and time matters such as face-to-face translation, flower-to-flower, wind and cloud synthesis, sunrise and sunset.Comment: ECCV 2018; Please refer to project webpage for videos - http://www.cs.cmu.edu/~aayushb/Recycle-GA

Building Disease Detection Algorithms with Very Small Numbers of Positive Samples

Although deep learning can provide promising results in medical image analysis, the lack of very large annotated datasets confines its full potential. Furthermore, limited positive samples also create unbalanced datasets which limit the true positive rates of trained models. As unbalanced datasets are mostly unavoidable, it is greatly beneficial if we can extract useful knowledge from negative samples to improve classification accuracy on limited positive samples. To this end, we propose a new strategy for building medical image analysis pipelines that target disease detection. We train a discriminative segmentation model only on normal images to provide a source of knowledge to be transferred to a disease detection classifier. We show that using the feature maps of a trained segmentation network, deviations from normal anatomy can be learned by a two-class classification network on an extremely unbalanced training dataset with as little as one positive for 17 negative samples. We demonstrate that even though the segmentation network is only trained on normal cardiac computed tomography images, the resulting feature maps can be used to detect pericardial effusion and cardiac septal defects with two-class convolutional classification networks