arXiv subjects

Dwarikanath Mahapatra

Publications and source records attributed to Dwarikanath Mahapatra.

70 records · Page 4Linked to original sources

arXiv2020

Pathological Retinal Region Segmentation From OCT Images Using Geometric Relation Based Augmentation

Medical image segmentation is an important task for computer aided diagnosis. Pixelwise manual annotations of large datasets require high expertise and is time consuming. Conventional data augmentations have limited benefit by not fully representing the underlying distribution of the training set, thus affecting model robustness when tested on images captured from different sources. Prior work leverages synthetic images for data augmentation ignoring the interleaved geometric relationship between different anatomical labels. We propose improvements over previous GAN-based medical image synthesis methods by jointly encoding the intrinsic relationship of geometry and shape. Latent space variable sampling results in diverse generated images from a base image and improves robustness. Given those augmented images generated by our method, we train the segmentation network to enhance the segmentation performance of retinal optical coherence tomography (OCT) images. The proposed method outperforms state-of-the-art segmentation methods on the public RETOUCH dataset having images captured from different acquisition procedures. Ablation studies and visual analysis also demonstrate benefits of integrating geometry and diversity.

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arXiv2020

Generative Adversarial Networks And Domain Adaptation For Training Data Independent Image Registration

Medical image registration is an important task in automated analysis of multi-modal images and temporal data involving multiple patient visits. Conventional approaches, although useful for different image types, are time consuming. Of late, deep learning (DL) based image registration methods have been proposed that outperform traditional methods in terms of accuracy and time. However,DL based methods are heavily dependent on training data and do not generalize well when presented with images of different scanners or anatomies. We present a DL based approach that can perform medical image registration of one image type despite being trained with images of a different type. This is achieved by unsupervised domain adaptation in the registration process and allows for easier application to different datasets without extensive retraining.To achieve our objective we train a network that transforms the given input image pair to a latent feature space vector using autoencoders. The resultant encoded feature space is used to generate the registered images with the help of generative adversarial networks (GANs). This feature transformation ensures greater invariance to the input image type. Experiments on chest Xray, retinal and brain MR images show that our method, trained on one dataset gives better registration performance for other datasets, outperforming conventional methods that do not incorporate domain adaptation

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arXiv2020

Adversarial Pulmonary Pathology Translation for Pairwise Chest X-ray Data Augmentation

Recent works show that Generative Adversarial Networks (GANs) can be successfully applied to chest X-ray data augmentation for lung disease recognition. However, the implausible and distorted pathology features generated from the less than perfect generator may lead to wrong clinical decisions. Why not keep the original pathology region? We proposed a novel approach that allows our generative model to generate high quality plausible images that contain undistorted pathology areas. The main idea is to design a training scheme based on an image-to-image translation network to introduce variations of new lung features around the pathology ground-truth area. Moreover, our model is able to leverage both annotated disease images and unannotated healthy lung images for the purpose of generation. We demonstrate the effectiveness of our model on two tasks: (i) we invite certified radiologists to assess the quality of the generated synthetic images against real and other state-of-the-art generative models, and (ii) data augmentation to improve the performance of disease localisation.

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arXiv2019

Efficient Active Learning for Image Classification and Segmentation using a Sample Selection and Conditional Generative Adversarial Network

Training robust deep learning (DL) systems for medical image classification or segmentation is challenging due to limited images covering different disease types and severity. We propose an active learning (AL) framework to select most informative samples and add to the training data. We use conditional generative adversarial networks (cGANs) to generate realistic chest xray images with different disease characteristics by conditioning its generation on a real image sample. Informative samples to add to the training set are identified using a Bayesian neural network. Experiments show our proposed AL framework is able to achieve state of the art performance by using about 35% of the full dataset, thus saving significant time and effort over conventional methods.

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arXiv2019

sZoom: A Framework for Automatic Zoom into High Resolution Surveillance Videos

Current cameras are capable of recording high resolution video. While viewing on a mobile device, a user can manually zoom into this high resolution video to get more detailed view of objects and activities. However, manual zooming is not suitable for surveillance and monitoring. It is tiring to continuously keep zooming into various regions of the video. Also, while viewing one region, the operator may miss activities in other regions. In this paper, we propose sZoom, a framework to automatically zoom into a high resolution surveillance video. The proposed framework selectively zooms into the sensitive regions of the video to present details of the scene, while still preserving the overall context required for situation assessment. A multi-variate Gaussian penalty is introduced to ensure full coverage of the scene. The method achieves near real-time performance through a number of timing optimizations. An extensive user study shows that, while watching a full HD video on a mobile device, the system enhances the security operator's efficiency in understanding the details of the scene by 99% on the average compared to a scaled version of the original high resolution video. The produced video achieved 46% higher ratings for usefulness in a surveillance task.

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arXiv2019

GAN Based Medical Image Registration

Conventional approaches to image registration consist of time consuming iterative methods. Most current deep learning (DL) based registration methods extract deep features to use in an iterative setting. We propose an end-to-end DL method for registering multimodal images. Our approach uses generative adversarial networks (GANs) that eliminates the need for time consuming iterative methods, and directly generates the registered image with the deformation field. Appropriate constraints in the GAN cost function produce accurately registered images in less than a second. Experiments demonstrate their accuracy for multimodal retinal and cardiac MR image registration.

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arXiv2019

AMD Severity Prediction And Explainability Using Image Registration And Deep Embedded Clustering

We propose a method to predict severity of age related macular degeneration (AMD) from input optical coherence tomography (OCT) images. Although there is no standard clinical severity scale for AMD, we leverage deep learning (DL) based image registration and clustering methods to identify diseased cases and predict their severity. Experiments demonstrate our approach's disease classification performance matches state of the art methods. The predicted disease severity performs well on previously unseen data. Registration output provides better explainability than class activation maps regarding label and severity decisions

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arXiv2019

Informative sample generation using class aware generative adversarial networks for classification of chest Xrays

Training robust deep learning (DL) systems for disease detection from medical images is challenging due to limited images covering different disease types and severity. The problem is especially acute, where there is a severe class imbalance. We propose an active learning (AL) framework to select most informative samples for training our model using a Bayesian neural network. Informative samples are then used within a novel class aware generative adversarial network (CAGAN) to generate realistic chest xray images for data augmentation by transferring characteristics from one class label to another. Experiments show our proposed AL framework is able to achieve state-of-the-art performance by using about $35\%$ of the full dataset, thus saving significant time and effort over conventional methods.

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arXiv2019

Training Data Independent Image Registration With GANs Using Transfer Learning And Segmentation Information

Registration is an important task in automated medical image analysis. Although deep learning (DL) based image registration methods out perform time consuming conventional approaches, they are heavily dependent on training data and do not generalize well for new images types. We present a DL based approach that can register an image pair which is different from the training images. This is achieved by training generative adversarial networks (GANs) in combination with segmentation information and transfer learning. Experiments on chest Xray and brain MR images show that our method gives better registration performance over conventional methods.

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arXiv2019

Progressive Generative Adversarial Networks for Medical Image Super resolution

Anatomical landmark segmentation and pathology localization are important steps in automated analysis of medical images. They are particularly challenging when the anatomy or pathology is small, as in retinal images and cardiac MRI, or when the image is of low quality due to device acquisition parameters as in magnetic resonance (MR) scanners. We propose an image super-resolution method using progressive generative adversarial networks (P-GAN) that can take as input a low-resolution image and generate a high resolution image of desired scaling factor. The super resolved images can be used for more accurate detection of landmarks and pathology. Our primary contribution is in proposing a multistage model where the output image quality of one stage is progressively improved in the next stage by using a triplet loss function. The triplet loss enables stepwise image quality improvement by using the output of the previous stage as the baseline. This facilitates generation of super resolved images of high scaling factor while maintaining good image quality. Experimental results for image super-resolution show that our proposed multistage P-GAN outperforms competing methods and baseline GAN.

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arXiv2019

Night Time Haze and Glow Removal using Deep Dilated Convolutional Network

In this paper, we address the single image haze removal problem in a nighttime scene. The night haze removal is a severely ill-posed problem especially due to the presence of various visible light sources with varying colors and non-uniform illumination. These light sources are of different shapes and introduce noticeable glow in night scenes. To address these effects we introduce a deep learning based DeGlow-DeHaze iterative architecture which accounts for varying color illumination and glows. First, our convolution neural network (CNN) based DeGlow model is able to remove the glow effect significantly and on top of it a separate DeHaze network is included to remove the haze effect. For our recurrent network training, the hazy images and the corresponding transmission maps are synthesized from the NYU depth datasets and consequently restored a high-quality haze-free image. The experimental results demonstrate that our hybrid CNN model outperforms other state-of-the-art methods in terms of computation speed and image quality. We also show the effectiveness of our model on a number of real images and compare our results with the existing night haze heuristic models.

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arXiv2018

Joint Segmentation and Uncertainty Visualization of Retinal Layers in Optical Coherence Tomography Images using Bayesian Deep Learning

Optical coherence tomography (OCT) is commonly used to analyze retinal layers for assessment of ocular diseases. In this paper, we propose a method for retinal layer segmentation and quantification of uncertainty based on Bayesian deep learning. Our method not only performs end-to-end segmentation of retinal layers, but also gives the pixel wise uncertainty measure of the segmentation output. The generated uncertainty map can be used to identify erroneously segmented image regions which is useful in downstream analysis. We have validated our method on a dataset of 1487 images obtained from 15 subjects (OCT volumes) and compared it against the state-of-the-art segmentation algorithms that does not take uncertainty into account. The proposed uncertainty based segmentation method results in comparable or improved performance, and most importantly is more robust against noise.

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arXiv2018

Deep multiscale convolutional feature learning for weakly supervised localization of chest pathologies in X-ray images

Localization of chest pathologies in chest X-ray images is a challenging task because of their varying sizes and appearances. We propose a novel weakly supervised method to localize chest pathologies using class aware deep multiscale feature learning. Our method leverages intermediate feature maps from CNN layers at different stages of a deep network during the training of a classification model using image level annotations of pathologies. During the training phase, a set of \emph{layer relevance weights} are learned for each pathology class and the CNN is optimized to perform pathology classification by convex combination of feature maps from both shallow and deep layers using the learned weights. During the test phase, to localize the predicted pathology, the multiscale attention map is obtained by convex combination of class activation maps from each stage using the \emph{layer relevance weights} learned during the training phase. We have validated our method using 112000 X-ray images and compared with the state-of-the-art localization methods. We experimentally demonstrate that the proposed weakly supervised method can improve the localization performance of small pathologies such as nodule and mass while giving comparable performance for bigger pathologies e.g., Cardiomegaly

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arXiv2018

Chest X-rays Classification: A Multi-Label and Fine-Grained Problem

The widely used ChestX-ray14 dataset addresses an important medical image classification problem and has the following caveats: 1) many lung pathologies are visually similar, 2) a variant of diseases including lung cancer, tuberculosis, and pneumonia are present in a single scan, i.e. multiple labels and 3) The incidence of healthy images is much larger than diseased samples, creating imbalanced data. These properties are common in medical domain. Existing literature uses stateof- the-art DensetNet/Resnet models being transfer learned where output neurons of the networks are trained for individual diseases to cater for multiple diseases labels in each image. However, most of them don't consider relationship between multiple classes. In this work we have proposed a novel error function, Multi-label Softmax Loss (MSML), to specifically address the properties of multiple labels and imbalanced data. Moreover, we have designed deep network architecture based on fine-grained classification concept that incorporates MSML. We have evaluated our proposed method on various network backbones and showed consistent performance improvements of AUC-ROC scores on the ChestX-ray14 dataset. The proposed error function provides a new method to gain improved performance across wider medical datasets.

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arXiv2018

Consensus Based Medical Image Segmentation Using Semi-Supervised Learning And Graph Cuts

Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.

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arXiv2018

Retinal Vasculature Segmentation Using Local Saliency Maps and Generative Adversarial Networks For Image Super Resolution

We propose an image super resolution(ISR) method using generative adversarial networks (GANs) that takes a low resolution input fundus image and generates a high resolution super resolved (SR) image upto scaling factor of $16$. This facilitates more accurate automated image analysis, especially for small or blurred landmarks and pathologies. Local saliency maps, which define each pixel's importance, are used to define a novel saliency loss in the GAN cost function. Experimental results show the resulting SR images have perceptual quality very close to the original images and perform better than competing methods that do not weigh pixels according to their importance. When used for retinal vasculature segmentation, our SR images result in accuracy levels close to those obtained when using the original images.

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