Efficient and Generic Interactive Segmentation Framework to Correct Mispredictions during Clinical Evaluation of Medical Images

Semantic segmentation of medical images is an essential first step in computer-aided diagnosis systems for many applications. However, given many disparate imaging modalities and inherent variations in the patient data, it is difficult to consistently achieve high accuracy using modern deep neural networks (DNNs). This has led researchers to propose interactive image segmentation techniques where a medical expert can interactively correct the output of a DNN to the desired accuracy. However, these techniques often need separate training data with the associated human interactions, and do not generalize to various diseases, and types of medical images. In this paper, we suggest a novel conditional inference technique for DNNs which takes the intervention by a medical expert as test time constraints and performs inference conditioned upon these constraints. Our technique is generic can be used for medical images from any modality. Unlike other methods, our approach can correct multiple structures simultaneously and add structures missed at initial segmentation. We report an improvement of 13.3, 12.5, 17.8, 10.2, and 12.4 times in user annotation time than full human annotation for the nucleus, multiple cells, liver and tumor, organ, and brain segmentation respectively. We report a time saving of 2.8, 3.0, 1.9, 4.4, and 8.6 fold compared to other interactive segmentation techniques. Our method can be useful to clinicians for diagnosis and post-surgical follow-up with minimal intervention from the medical expert. The source-code and the detailed results are available here [1].

Contextual Diversity for Active Learning

Requirement of large annotated datasets restrict the use of deep convolutional neural networks (CNNs) for many practical applications. The problem can be mitigated by using active learning (AL) techniques which, under a given annotation budget, allow to select a subset of data that yields maximum accuracy upon fine tuning. State of the art AL approaches typically rely on measures of visual diversity or prediction uncertainty, which are unable to effectively capture the variations in spatial context. On the other hand, modern CNN architectures make heavy use of spatial context for achieving highly accurate predictions. Since the context is difficult to evaluate in the absence of ground-truth labels, we introduce the notion of contextual diversity that captures the confusion associated with spatially co-occurring classes. Contextual Diversity (CD) hinges on a crucial observation that the probability vector predicted by a CNN for a region of interest typically contains information from a larger receptive field. Exploiting this observation, we use the proposed CD measure within two AL frameworks: (1) a core-set based strategy and (2) a reinforcement learning based policy, for active frame selection. Our extensive empirical evaluation establish state of the art results for active learning on benchmark datasets of Semantic Segmentation, Object Detection and Image Classification. Our ablation studies show clear advantages of using contextual diversity for active learning. The source code and additional results are available at https://github.com/sharat29ag/CDAL.

CovidAID: COVID-19 Detection Using Chest X-Ray

The exponential increase in COVID-19 patients is overwhelming healthcare systems across the world. With limited testing kits, it is impossible for every patient with respiratory illness to be tested using conventional techniques (RT-PCR). The tests also have long turn-around time, and limited sensitivity. Detecting possible COVID-19 infections on Chest X-Ray may help quarantine high risk patients while test results are awaited. X-Ray machines are already available in most healthcare systems, and with most modern X-Ray systems already digitized, there is no transportation time involved for the samples either. In this work we propose the use of chest X-Ray to prioritize the selection of patients for further RT-PCR testing. This may be useful in an inpatient setting where the present systems are struggling to decide whether to keep the patient in the ward along with other patients or isolate them in COVID-19 areas. It would also help in identifying patients with high likelihood of COVID with a false negative RT-PCR who would need repeat testing. Further, we propose the use of modern AI techniques to detect the COVID-19 patients using X-Ray images in an automated manner, particularly in settings where radiologists are not available, and help make the proposed testing technology scalable. We present CovidAID: COVID-19 AI Detector, a novel deep neural network based model to triage patients for appropriate testing. On the publicly available covid-chestxray-dataset [2], our model gives 90.5% accuracy with 100% sensitivity (recall) for the COVID-19 infection. We significantly improve upon the results of Covid-Net [10] on the same dataset.

Diversity in Fashion Recommendation using Semantic Parsing

Developing recommendation system for fashion images is challenging due to the inherent ambiguity associated with what criterion a user is looking at. Suggesting multiple images where each output image is similar to the query image on the basis of a different feature or part is one way to mitigate the problem. Existing works for fashion recommendation have used Siamese or Triplet network to learn features between a similar pair and a similar-dissimilar triplet respectively. However, these methods do not provide basic information such as, how two clothing images are similar, or which parts present in the two images make them similar. In this paper, we propose to recommend images by explicitly learning and exploiting part based similarity. We propose a novel approach of learning discriminative features from weakly-supervised data by using visual attention over the parts and a texture encoding network. We show that the learned features surpass the state-of-the-art in retrieval task on DeepFashion dataset. We then use the proposed model to recommend fashion images having an explicit variation with respect to similarity of any of the parts.

Making Third Person Techniques Recognize First-Person Actions in Egocentric Videos

We focus on first-person action recognition from egocentric videos. Unlike third person domain, researchers have divided first-person actions into two categories: involving hand-object interactions and the ones without, and developed separate techniques for the two action categories. Further, it has been argued that traditional cues used for third person action recognition do not suffice, and egocentric specific features, such as head motion and handled objects have been used for such actions. Unlike the state-of-the-art approaches, we show that a regular two stream Convolutional Neural Network (CNN) with Long Short-Term Memory (LSTM) architecture, having separate streams for objects and motion, can generalize to all categories of first-person actions. The proposed approach unifies the feature learned by all action categories, making the proposed architecture much more practical. In an important observation, we note that the size of the objects visible in the egocentric videos is much smaller. We show that the performance of the proposed model improves after cropping and resizing frames to make the size of objects comparable to the size of ImageNet's objects. Our experiments on the standard datasets: GTEA, EGTEA Gaze+, HUJI, ADL, UTE, and Kitchen, proves that our model significantly outperforms various state-of-the-art techniques.

Exploiting Test Time Evidence to Improve Predictions of Deep Neural Networks

Many prediction tasks, especially in computer vision, are often inherently ambiguous. For example, the output of semantic segmentation may depend on the scale one is looking at, and image saliency or video summarization is often user or context dependent. Arguably, in such scenarios, exploiting instance specific evidence, such as scale or user context, can help resolve the underlying ambiguity leading to the improved predictions. While existing literature has considered incorporating such evidence in classical models such as probabilistic graphical models (PGMs), there is limited (or no) prior work looking at this problem in the context of deep neural network (DNN) models. In this paper, we present a generic multi task learning (MTL) based framework which handles the evidence as the output of one or more secondary tasks, while modeling the original problem as the primary task of interest. Our training phase is identical to the one used by standard MTL architectures. During prediction, we back-propagate the loss on secondary task(s) such that network weights are re-adjusted to match the evidence. An early stopping or two norm based regularizer ensures weights do not deviate significantly from the ones learned originally. Implementation in two specific scenarios (a) predicting semantic segmentation given the image level tags (b) predicting instance level segmentation given the text description of the image, clearly demonstrates the effectiveness of our proposed approach.

U-SegNet: Fully Convolutional Neural Network based Automated Brain tissue segmentation Tool

Automated brain tissue segmentation into white matter (WM), gray matter (GM), and cerebro-spinal fluid (CSF) from magnetic resonance images (MRI) is helpful in the diagnosis of neuro-disorders such as epilepsy, Alzheimer's, multiple sclerosis, etc. However, thin GM structures at the periphery of cortex and smooth transitions on tissue boundaries such as between GM and WM, or WM and CSF pose difficulty in building a reliable segmentation tool. This paper proposes a Fully Convolutional Neural Network (FCN) tool, that is a hybrid of two widely used deep learning segmentation architectures SegNet and U-Net, for improved brain tissue segmentation. We propose a skip connection inspired from U-Net, in the SegNet architetcure, to incorporate fine multiscale information for better tissue boundary identification. We show that the proposed U-SegNet architecture, improves segmentation performance, as measured by average dice ratio, to 89.74% on the widely used IBSR dataset consisting of T-1 weighted MRI volumes of 18 subjects.

A Joint 3D-2D based Method for Free Space Detection on Roads

In this paper, we address the problem of road segmentation and free space detection in the context of autonomous driving. Traditional methods either use 3-dimensional (3D) cues such as point clouds obtained from LIDAR, RADAR or stereo cameras or 2-dimensional (2D) cues such as lane markings, road boundaries and object detection. Typical 3D point clouds do not have enough resolution to detect fine differences in heights such as between road and pavement. Image based 2D cues fail when encountering uneven road textures such as due to shadows, potholes, lane markings or road restoration. We propose a novel free road space detection technique combining both 2D and 3D cues. In particular, we use CNN based road segmentation from 2D images and plane/box fitting on sparse depth data obtained from SLAM as priors to formulate an energy minimization using conditional random field (CRF), for road pixels classification. While the CNN learns the road texture and is unaffected by depth boundaries, the 3D information helps in overcoming texture based classification failures. Finally, we use the obtained road segmentation with the 3D depth data from monocular SLAM to detect the free space for the navigation purposes. Our experiments on KITTI odometry dataset, Camvid dataset, as well as videos captured by us, validate the superiority of the proposed approach over the state of the art.

Batch based Monocular SLAM for Egocentric Videos

Simultaneous Localization and Mapping (SLAM) from a monocular camera has been a well researched area. However, estimating camera pose and 3d geometry reliably for egocentric videos still remain a challenge. Some of the common causes of failures are dominant 3D rotations and low parallax between successive frames, resulting in unreliable pose and 3d estimates. For forward moving cameras, with no opportunities for loop closures, the drift leads to eventual failures for traditional feature based and direct SLAM techniques. We propose a novel batch mode structure from motion based technique for robust SLAM in such scenarios. In contrast to most of the existing techniques, we process frames in short batches, wherein we exploit short loop closures arising out of to-and-fro motion of wearer's head, and stabilize the egomotion estimates by 2D batch mode techniques such as motion averaging on pairwise epipolar results. Once pose estimates are obtained reliably over a batch, we refine the 3d estimate by triangulation and batch mode Bundle Adjustment (BA). Finally, we merge the batches using 3D correspondences and carry out a BA refinement post merging. We present both qualitative and quantitative comparison of our method on various public first and third person video datasets, to establish the robustness and accuracy of our algorithm over the state of the art.

Computing Egomotion with Local Loop Closures for Egocentric Videos

Finding the camera pose is an important step in many egocentric video applications. It has been widely reported that, state of the art SLAM algorithms fail on egocentric videos. In this paper, we propose a robust method for camera pose estimation, designed specifically for egocentric videos. In an egocentric video, the camera views the same scene point multiple times as the wearer's head sweeps back and forth. We use this specific motion profile to perform short loop closures aligned with wearer's footsteps. For egocentric videos, depth estimation is usually noisy. In an important departure, we use 2D computations for rotation averaging which do not rely upon depth estimates. The two modification results in much more stable algorithm as is evident from our experiments on various egocentric video datasets for different egocentric applications. The proposed algorithm resolves a long standing problem in egocentric vision and unlocks new usage scenarios for future applications.