arXiv subjects

Amit Sethi

Publications and source records attributed to Amit Sethi.

103 records · Page 6Linked to original sources

arXiv2020

Visualization for Histopathology Images using Graph Convolutional Neural Networks

With the increase in the use of deep learning for computer-aided diagnosis in medical images, the criticism of the black-box nature of the deep learning models is also on the rise. The medical community needs interpretable models for both due diligence and advancing the understanding of disease and treatment mechanisms. In histology, in particular, while there is rich detail available at the cellular level and that of spatial relationships between cells, it is difficult to modify convolutional neural networks to point out the relevant visual features. We adopt an approach to model histology tissue as a graph of nuclei and develop a graph convolutional network framework based on attention mechanism and node occlusion for disease diagnosis. The proposed method highlights the relative contribution of each cell nucleus in the whole-slide image. Our visualization of such networks trained to distinguish between invasive and in-situ breast cancers, and Gleason 3 and 4 prostate cancers generate interpretable visual maps that correspond well with our understanding of the structures that are important to experts for their diagnosis.

eess.IV↗

arXiv2020

Functional Space Variational Inference for Uncertainty Estimation in Computer Aided Diagnosis

Deep neural networks have revolutionized medical image analysis and disease diagnosis. Despite their impressive performance, it is difficult to generate well-calibrated probabilistic outputs for such networks, which makes them uninterpretable black boxes. Bayesian neural networks provide a principled approach for modelling uncertainty and increasing patient safety, but they have a large computational overhead and provide limited improvement in calibration. In this work, by taking skin lesion classification as an example task, we show that by shifting Bayesian inference to the functional space we can craft meaningful priors that give better calibrated uncertainty estimates at a much lower computational cost.

cs.LG↗

arXiv2020

A Cyclical Deep Learning Based Framework For Simultaneous Inverse and Forward design of Nanophotonic Metasurfaces

The conventional approach to nanophotonic metasurface design and optimization for a targeted electromagnetic response involves exploring large geometry and material spaces, which is computationally costly, time consuming and a highly iterative process based on trial and error. Moreover, the non-uniqueness of structural designs and high non-linearity between electromagnetic response and design makes this problem challenging. To model this non-intuitive relationship between electromagnetic response and metasurface structural design as a probability distribution in the design space, we introduce a cyclical deep learning (DL) based framework for inverse design of nanophotonic metasurfaces. The proposed framework performs inverse design and optimization mechanism for the generation of meta-atoms and meta-molecules as metasurface units based on DL models and genetic algorithm. The framework includes consecutive DL models that emulate both numerical electromagnetic simulation and iterative processes of optimization, and generate optimized structural designs while simultaneously performing forward and inverse design tasks. A selection and evaluation of generated structural designs is performed by the genetic algorithm to construct a desired optical response and design space that mimics real world responses. Importantly, our cyclical generation framework also explores the space of new metasurface topologies. As an example application of utility of our proposed architecture, we demonstrate the inverse design of gap-plasmon based half-wave plate metasurface for user-defined optical response. Our proposed technique can be easily generalized for designing nanophtonic metasurfaces for a wide range of targeted optical response.

physics.optics↗

arXiv2020

Image-based phenotyping of diverse Rice (Oryza Sativa L.) Genotypes

Development of either drought-resistant or drought-tolerant varieties in rice (Oryza sativa L.), especially for high yield in the context of climate change, is a crucial task across the world. The need for high yielding rice varieties is a prime concern for developing nations like India, China, and other Asian-African countries where rice is a primary staple food. The present investigation is carried out for discriminating drought tolerant, and susceptible genotypes. A total of 150 genotypes were grown under controlled conditions to evaluate at High Throughput Plant Phenomics facility, Nanaji Deshmukh Plant Phenomics Centre, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi. A subset of 10 genotypes is taken out of 150 for the current investigation. To discriminate against the genotypes, we considered features such as the number of leaves per plant, the convex hull and convex hull area of a plant-convex hull formed by joining the tips of the leaves, the number of leaves per unit convex hull of a plant, canopy spread - vertical spread, and horizontal spread of a plant. We trained You Only Look Once (YOLO) deep learning algorithm for leaves tips detection and to estimate the number of leaves in a rice plant. With this proposed framework, we screened the genotypes based on selected traits. These genotypes were further grouped among different groupings of drought-tolerant and drought susceptible genotypes using the Ward method of clustering.

cs.CV↗

arXiv2020

Uncertainty Estimation in Cancer Survival Prediction

Survival models are used in various fields, such as the development of cancer treatment protocols. Although many statistical and machine learning models have been proposed to achieve accurate survival predictions, little attention has been paid to obtain well-calibrated uncertainty estimates associated with each prediction. The currently popular models are opaque and untrustworthy in that they often express high confidence even on those test cases that are not similar to the training samples, and even when their predictions are wrong. We propose a Bayesian framework for survival models that not only gives more accurate survival predictions but also quantifies the survival uncertainty better. Our approach is a novel combination of variational inference for uncertainty estimation, neural multi-task logistic regression for estimating nonlinear and time-varying risk models, and an additional sparsity-inducing prior to work with high dimensional data.

cs.LG↗

arXiv2020

Breast Cancer Histopathology Image Classification and Localization using Multiple Instance Learning

Breast cancer has the highest mortality among cancers in women. Computer-aided pathology to analyze microscopic histopathology images for diagnosis with an increasing number of breast cancer patients can bring the cost and delays of diagnosis down. Deep learning in histopathology has attracted attention over the last decade of achieving state-of-the-art performance in classification and localization tasks. The convolutional neural network, a deep learning framework, provides remarkable results in tissue images analysis, but lacks in providing interpretation and reasoning behind the decisions. We aim to provide a better interpretation of classification results by providing localization on microscopic histopathology images. We frame the image classification problem as weakly supervised multiple instance learning problem where an image is collection of patches i.e. instances. Attention-based multiple instance learning (A-MIL) learns attention on the patches from the image to localize the malignant and normal regions in an image and use them to classify the image. We present classification and localization results on two publicly available BreakHIS and BACH dataset. The classification and visualization results are compared with other recent techniques. The proposed method achieves better localization results without compromising classification accuracy.

cs.CV↗

arXiv2019

Pixel-wise Segmentation of Right Ventricle of Heart

One of the first steps in the diagnosis of most cardiac diseases, such as pulmonary hypertension, coronary heart disease is the segmentation of ventricles from cardiac magnetic resonance (MRI) images. Manual segmentation of the right ventricle requires diligence and time, while its automated segmentation is challenging due to shape variations and illdefined borders. We propose a deep learning based method for the accurate segmentation of right ventricle, which does not require post-processing and yet it achieves the state-of-the-art performance of 0.86 Dice coefficient and 6.73 mm Hausdorff distance on RVSC-MICCAI 2012 dataset. We use a novel adaptive cost function to counter extreme class-imbalance in the dataset. We present a comprehensive comparative study of loss functions, architectures, and ensembling techniques to build a principled approach for biomedical segmentation tasks.

eess.IV↗

arXiv2019

Histographs: Graphs in Histopathology

Spatial arrangement of cells of various types, such as tumor infiltrating lymphocytes and the advancing edge of a tumor, are important features for detecting and characterizing cancers. However, convolutional neural networks (CNNs) do not explicitly extract intricate features of the spatial arrangements of the cells from histopathology images. In this work, we propose to classify cancers using graph convolutional networks (GCNs) by modeling a tissue section as a multi-attributed spatial graph of its constituent cells. Cells are detected using their nuclei in H&E stained tissue image, and each cell's appearance is captured as a multi-attributed high-dimensional vertex feature. The spatial relations between neighboring cells are captured as edge features based on their distances in a graph. We demonstrate the utility of this approach by obtaining classification accuracy that is competitive with CNNs, specifically, Inception-v3, on two tasks-cancerous versus non-cancerous and in situ versus invasive-on the BACH breast cancer dataset.

eess.IV↗

arXiv2019

Fast GPU-Enabled Color Normalization for Digital Pathology

Normalizing unwanted color variations due to differences in staining processes and scanner responses has been shown to aid machine learning in computational pathology. Of the several popular techniques for color normalization, structure preserving color normalization (SPCN) is well-motivated, convincingly tested, and published with its code base. However, SPCN makes occasional errors in color basis estimation leading to artifacts such as swapping the color basis vectors between stains or giving a colored tinge to the background with no tissue. We made several algorithmic improvements to remove these artifacts. Additionally, the original SPCN code is not readily usable on gigapixel whole slide images (WSIs) due to long run times, use of proprietary software platform and libraries, and its inability to automatically handle WSIs. We completely rewrote the software such that it can automatically handle images of any size in popular WSI formats. Our software utilizes GPU-acceleration and open-source libraries that are becoming ubiquitous with the advent of deep learning. We also made several other small improvements and achieved a multifold overall speedup on gigapixel images. Our algorithm and software is usable right out-of-the-box by the computational pathology community.

cs.CV↗

arXiv2018

Some New Layer Architectures for Graph CNN

While convolutional neural networks (CNNs) have recently made great strides in supervised classification of data structured on a grid (e.g. images composed of pixel grids), in several interesting datasets, the relations between features can be better represented as a general graph instead of a regular grid. Although recent algorithms that adapt CNNs to graphs have shown promising results, they mostly neglect learning explicit operations for edge features while focusing on vertex features alone. We propose new formulations for convolutional, pooling, and fully connected layers for neural networks that make more comprehensive use of the information available in multi-dimensional graphs. Using these layers led to an improvement in classification accuracy over the state-of-the-art methods on benchmark graph datasets.

cs.LG↗

arXiv2018

Classification of Breast Cancer Histology using Deep Learning

Breast Cancer is a major cause of death worldwide among women. Hematoxylin and Eosin (H&E) stained breast tissue samples from biopsies are observed under microscopes for the primary diagnosis of breast cancer. In this paper, we propose a deep learning-based method for classification of H&E stained breast tissue images released for BACH challenge 2018 by fine-tuning Inception-v3 convolutional neural network (CNN) proposed by Szegedy et al. These images are to be classified into four classes namely, i) normal tissue, ii) benign tumor, iii) in-situ carcinoma and iv) invasive carcinoma. Our strategy is to extract patches based on nuclei density instead of random or grid sampling, along with rejection of patches that are not rich in nuclei (non-epithelial) regions for training and testing. Every patch (nuclei-dense region) in an image is classified in one of the four above mentioned categories. The class of the entire image is determined using majority voting over the nuclear classes. We obtained an average four class accuracy of 85% and an average two class (non-cancer vs. carcinoma) accuracy of 93%, which improves upon a previous benchmark by Araujo et al.

cs.CV↗

arXiv2018

A Learnable Distortion Correction Module for Modulation Recognition

Modulation recognition is a challenging task while performing spectrum sensing in a cognitive radio setup. Recently, the use of deep convolutional neural networks (CNNs) has shown to achieve state-of-the-art accuracy for modulation recognition \cite{survey}. However, a wireless channel distorts the signal and CNNs are not explicitly designed to undo these artifacts. To improve the performance of CNN-based recognition schemes we propose a signal distortion correction module (CM) and show that this CM+CNN scheme achieves accuracy better than the existing schemes. The proposed CM is also based on a neural network that estimates the random carrier frequency and phase offset introduced by the channel and feeds it to a part that undoes this distortion right before CNN-based modulation recognition. Its output is differentiable with respect to its weights, which allows it to be trained end-to-end with the modulation recognition CNN based on the received signal. For supervision, only the modulation scheme label is used and the knowledge of true frequency or phase offset is not required.

eess.SP↗

arXiv2016

Deep Learning-Based Image Kernel for Inductive Transfer

We propose a method to classify images from target classes with a small number of training examples based on transfer learning from non-target classes. Without using any more information than class labels for samples from non-target classes, we train a Siamese net to estimate the probability of two images to belong to the same class. With some post-processing, output of the Siamese net can be used to form a gram matrix of a Mercer kernel. Coupled with a support vector machine (SVM), such a kernel gave reasonable classification accuracy on target classes without any fine-tuning. When the Siamese net was only partially fine-tuned using a small number of samples from the target classes, the resulting classifier outperformed the state-of-the-art and other alternatives. We share class separation capabilities and insights into the learning process of such a kernel on MNIST, Dogs vs. Cats, and CIFAR-10 datasets.

cs.CV↗