arXiv subjects

Abhijit Guha Roy

Publications and source records attributed to Abhijit Guha Roy.

28 records · Page 2Linked to original sources

arXiv2018

InfiNet: Fully Convolutional Networks for Infant Brain MRI Segmentation

We present a novel, parameter-efficient and practical fully convolutional neural network architecture, termed InfiNet, aimed at voxel-wise semantic segmentation of infant brain MRI images at iso-intense stage, which can be easily extended for other segmentation tasks involving multi-modalities. InfiNet consists of double encoder arms for T1 and T2 input scans that feed into a joint-decoder arm that terminates in the classification layer. The novelty of InfiNet lies in the manner in which the decoder upsamples lower resolution input feature map(s) from multiple encoder arms. Specifically, the pooled indices computed in the max-pooling layers of each of the encoder blocks are related to the corresponding decoder block to perform non-linear learning-free upsampling. The sparse maps are concatenated with intermediate encoder representations (skip connections) and convolved with trainable filters to produce dense feature maps. InfiNet is trained end-to-end to optimize for the Generalized Dice Loss, which is well-suited for high class imbalance. InfiNet achieves the whole-volume segmentation in under 50 seconds and we demonstrate competitive performance against multiple state-of-the art deep architectures and their multi-modal variants.

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arXiv2018

Recalibrating Fully Convolutional Networks with Spatial and Channel 'Squeeze & Excitation' Blocks

In a wide range of semantic segmentation tasks, fully convolutional neural networks (F-CNNs) have been successfully leveraged to achieve state-of-the-art performance. Architectural innovations of F-CNNs have mainly been on improving spatial encoding or network connectivity to aid gradient flow. In this article, we aim towards an alternate direction of recalibrating the learned feature maps adaptively; boosting meaningful features while suppressing weak ones. The recalibration is achieved by simple computational blocks that can be easily integrated in F-CNNs architectures. We draw our inspiration from the recently proposed 'squeeze & excitation' (SE) modules for channel recalibration for image classification. Towards this end, we introduce three variants of SE modules for segmentation, (i) squeezing spatially and exciting channel-wise, (ii) squeezing channel-wise and exciting spatially and (iii) joint spatial and channel 'squeeze & excitation'. We effectively incorporate the proposed SE blocks in three state-of-the-art F-CNNs and demonstrate a consistent improvement of segmentation accuracy on three challenging benchmark datasets. Importantly, SE blocks only lead to a minimal increase in model complexity of about 1.5%, while the Dice score increases by 4-9% in the case of U-Net. Hence, we believe that SE blocks can be an integral part of future F-CNN architectures.

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arXiv2018

SynNet: Structure-Preserving Fully Convolutional Networks for Medical Image Synthesis

Cross modal image syntheses is gaining significant interests for its ability to estimate target images of a different modality from a given set of source images,like estimating MR to MR, MR to CT, CT to PET etc, without the need for an actual acquisition.Though they show potential for applications in radiation therapy planning,image super resolution, atlas construction, image segmentation etc.The synthesis results are not as accurate as the actual acquisition.In this paper,we address the problem of multi modal image synthesis by proposing a fully convolutional deep learning architecture called the SynNet.We extend the proposed architecture for various input output configurations. And finally, we propose a structure preserving custom loss function for cross-modal image synthesis.We validate the proposed SynNet and its extended framework on BRATS dataset with comparisons against three state-of-the art methods.And the results of the proposed custom loss function is validated against the traditional loss function used by the state-of-the-art methods for cross modal image synthesis.

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arXiv2018

Concurrent Spatial and Channel Squeeze & Excitation in Fully Convolutional Networks

Fully convolutional neural networks (F-CNNs) have set the state-of-the-art in image segmentation for a plethora of applications. Architectural innovations within F-CNNs have mainly focused on improving spatial encoding or network connectivity to aid gradient flow. In this paper, we explore an alternate direction of recalibrating the feature maps adaptively, to boost meaningful features, while suppressing weak ones. We draw inspiration from the recently proposed squeeze & excitation (SE) module for channel recalibration of feature maps for image classification. Towards this end, we introduce three variants of SE modules for image segmentation, (i) squeezing spatially and exciting channel-wise (cSE), (ii) squeezing channel-wise and exciting spatially (sSE) and (iii) concurrent spatial and channel squeeze & excitation (scSE). We effectively incorporate these SE modules within three different state-of-the-art F-CNNs (DenseNet, SD-Net, U-Net) and observe consistent improvement of performance across all architectures, while minimally effecting model complexity. Evaluations are performed on two challenging applications: whole brain segmentation on MRI scans (Multi-Atlas Labelling Challenge Dataset) and organ segmentation on whole body contrast enhanced CT scans (Visceral Dataset).

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arXiv2018

Inherent Brain Segmentation Quality Control from Fully ConvNet Monte Carlo Sampling

We introduce inherent measures for effective quality control of brain segmentation based on a Bayesian fully convolutional neural network, using model uncertainty. Monte Carlo samples from the posterior distribution are efficiently generated using dropout at test time. Based on these samples, we introduce next to a voxel-wise uncertainty map also three metrics for structure-wise uncertainty. We then incorporate these structure-wise uncertainty in group analyses as a measure of confidence in the observation. Our results show that the metrics are highly correlated to segmentation accuracy and therefore present an inherent measure of segmentation quality. Furthermore, group analysis with uncertainty results in effect sizes closer to that of manual annotations. The introduced uncertainty metrics can not only be very useful in translation to clinical practice but also provide automated quality control and group analyses in processing large data repositories.

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arXiv2017

ReLayNet: Retinal Layer and Fluid Segmentation of Macular Optical Coherence Tomography using Fully Convolutional Network

Optical coherence tomography (OCT) is used for non-invasive diagnosis of diabetic macular edema assessing the retinal layers. In this paper, we propose a new fully convolutional deep architecture, termed ReLayNet, for end-to-end segmentation of retinal layers and fluid masses in eye OCT scans. ReLayNet uses a contracting path of convolutional blocks (encoders) to learn a hierarchy of contextual features, followed by an expansive path of convolutional blocks (decoders) for semantic segmentation. ReLayNet is trained to optimize a joint loss function comprising of weighted logistic regression and Dice overlap loss. The framework is validated on a publicly available benchmark dataset with comparisons against five state-of-the-art segmentation methods including two deep learning based approaches to substantiate its effectiveness.

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arXiv2017

Error Corrective Boosting for Learning Fully Convolutional Networks with Limited Data

Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models.

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arXiv2016

Deep Residual Hashing

Hashing aims at generating highly compact similarity preserving code words which are well suited for large-scale image retrieval tasks. Most existing hashing methods first encode the images as a vector of hand-crafted features followed by a separate binarization step to generate hash codes. This two-stage process may produce sub-optimal encoding. In this paper, for the first time, we propose a deep architecture for supervised hashing through residual learning, termed Deep Residual Hashing (DRH), for an end-to-end simultaneous representation learning and hash coding. The DRH model constitutes four key elements: (1) a sub-network with multiple stacked residual blocks; (2) hashing layer for binarization; (3) supervised retrieval loss function based on neighbourhood component analysis for similarity preserving embedding; and (4) hashing related losses and regularisation to control the quantization error and improve the quality of hash coding. We present results of extensive experiments on a large public chest x-ray image database with co-morbidities and discuss the outcome showing substantial improvements over the latest state-of-the art methods.

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arXiv2016

Deep Neural Ensemble for Retinal Vessel Segmentation in Fundus Images towards Achieving Label-free Angiography

Automated segmentation of retinal blood vessels in label-free fundus images entails a pivotal role in computed aided diagnosis of ophthalmic pathologies, viz., diabetic retinopathy, hypertensive disorders and cardiovascular diseases. The challenge remains active in medical image analysis research due to varied distribution of blood vessels, which manifest variations in their dimensions of physical appearance against a noisy background. In this paper we formulate the segmentation challenge as a classification task. Specifically, we employ unsupervised hierarchical feature learning using ensemble of two level of sparsely trained denoised stacked autoencoder. First level training with bootstrap samples ensures decoupling and second level ensemble formed by different network architectures ensures architectural revision. We show that ensemble training of auto-encoders fosters diversity in learning dictionary of visual kernels for vessel segmentation. SoftMax classifier is used for fine tuning each member auto-encoder and multiple strategies are explored for 2-level fusion of ensemble members. On DRIVE dataset, we achieve maximum average accuracy of 95.33\% with an impressively low standard deviation of 0.003 and Kappa agreement coefficient of 0.708 . Comparison with other major algorithms substantiates the high efficacy of our model.

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arXiv2016

DASA: Domain Adaptation in Stacked Autoencoders using Systematic Dropout

Domain adaptation deals with adapting behaviour of machine learning based systems trained using samples in source domain to their deployment in target domain where the statistics of samples in both domains are dissimilar. The task of directly training or adapting a learner in the target domain is challenged by lack of abundant labeled samples. In this paper we propose a technique for domain adaptation in stacked autoencoder (SAE) based deep neural networks (DNN) performed in two stages: (i) unsupervised weight adaptation using systematic dropouts in mini-batch training, (ii) supervised fine-tuning with limited number of labeled samples in target domain. We experimentally evaluate performance in the problem of retinal vessel segmentation where the SAE-DNN is trained using large number of labeled samples in the source domain (DRIVE dataset) and adapted using less number of labeled samples in target domain (STARE dataset). The performance of SAE-DNN measured using $logloss$ in source domain is $0.19$, without and with adaptation are $0.40$ and $0.18$, and $0.39$ when trained exclusively with limited samples in target domain. The area under ROC curve is observed respectively as $0.90$, $0.86$, $0.92$ and $0.87$. The high efficiency of vessel segmentation with DASA strongly substantiates our claim.

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