A novel abnormality annotation database for COVID-19 affected frontal lung X-rays

Consistent clinical observations of characteristic findings of COVID-19 pneumonia on chest X-rays have attracted the research community to strive to provide a fast and reliable method for screening suspected patients. Several machine learning algorithms have been proposed to find the abnormalities in the lungs using chest X-rays specific to COVID-19 pneumonia and distinguish them from other etiologies of pneumonia. However, despite the enormous magnitude of the pandemic, there are very few instances of public databases of COVID-19 pneumonia, and to the best of our knowledge, there is no database with annotation of abnormalities on the chest X-rays of COVID-19 affected patients. Annotated databases of X-rays can be of significant value in the design and development of algorithms for disease prediction. Further, explainability analysis for the performance of existing or new deep learning algorithms will be enhanced significantly with access to ground-truth abnormality annotations. The proposed COVID Abnormality Annotation for X-Rays (CAAXR) database is built upon the BIMCV-COVID19+ database which is a large-scale dataset containing COVID-19+ chest X-rays. The primary contribution of this study is the annotation of the abnormalities in over 1700 frontal chest X-rays. Further, we define protocols for semantic segmentation as well as classification for robust evaluation of algorithms. We provide benchmark results on the defined protocols using popular deep learning models such as DenseNet, ResNet, MobileNet, and VGG for classification, and UNet, SegNet, and Mask-RCNN for semantic segmentation. The classwise accuracy, sensitivity, and AUC-ROC scores are reported for the classification models, and the IoU and DICE scores are reported for the segmentation models.

Multi-task driven explainable diagnosis of COVID-19 using chest X-ray images

With increasing number of COVID-19 cases globally, all the countries are ramping up the testing numbers. While the RT-PCR kits are available in sufficient quantity in several countries, others are facing challenges with limited availability of testing kits and processing centers in remote areas. This has motivated researchers to find alternate methods of testing which are reliable, easily accessible and faster. Chest X-Ray is one of the modalities that is gaining acceptance as a screening modality. Towards this direction, the paper has two primary contributions. Firstly, we present the COVID-19 Multi-Task Network (COMiT-Net) which is an automated end-to-end network for COVID-19 screening. The proposed network not only predicts whether the CXR has COVID-19 features present or not, it also performs semantic segmentation of the regions of interest to make the model explainable. Secondly, with the help of medical professionals, we manually annotate the lung regions and semantic segmentation of COVID19 symptoms in CXRs taken from the ChestXray-14, CheXpert, and a consolidated COVID-19 dataset. These annotations will be released to the research community. Experiments performed with more than 2500 frontal CXR images show that at 90% specificity, the proposed COMiT-Net yields 96.80% sensitivity.

Handling non-stationarity in E-nose design: a review

Purpose

The electronic nose is an array of chemical or gas sensors and associated with a pattern-recognition framework competent in identifying and classifying odorant or non-odorant and simple or complex gases. Despite more than 30 years of research, the robust e-nose device is still limited. Most of the challenges towards reliable e-nose devices are associated with the non-stationary environment and non-stationary sensor behaviour. Data distribution of sensor array response evolves with time, referred to as non-stationarity. The purpose of this paper is to provide a comprehensive introduction to challenges related to non-stationarity in e-nose design and to review the existing literature from an application, system and algorithm perspective to provide an integrated and practical view.

Design/methodology/approach

The authors discuss the non-stationary data in general and the challenges related to the non-stationarity environment in e-nose design or non-stationary sensor behaviour. The challenges are categorised and discussed with the perspective of learning with data obtained from the sensor systems. Later, the e-nose technology is reviewed with the system, application and algorithmic point of view to discuss the current status.

Findings

The discussed challenges in e-nose design will be beneficial for researchers, as well as practitioners as it presents a comprehensive view on multiple aspects of non-stationary learning, system, algorithms and applications for e-nose. The paper presents a review of the pattern-recognition techniques, public data sets that are commonly referred to as olfactory research. Generic techniques for learning in the non-stationary environment are also presented. The authors discuss the future direction of research and major open problems related to handling non-stationarity in e-nose design.

Originality/value

The authors first time review the existing literature related to learning with e-nose in a non-stationary environment and existing generic pattern-recognition algorithms for learning in the non-stationary environment to bridge the gap between these two. The authors also present details of publicly available sensor array data sets, which will benefit the upcoming researchers in this field. The authors further emphasise several open problems and future directions, which should be considered to provide efficient solutions that can handle non-stationarity to make e-nose the next everyday device.

Block Sparse Variational Bayes Regression Using Matrix Variate Distributions With Application to SSVEP Detection

Due to the nonsparse representation, the use of compressed sensing (CS) for physiological signals, such as a multichannel electroencephalogram (EEG), has been a challenge. We present a generalized Bayesian CS framework that is capable of handling representations that arise in the spatiotemporal setting. The proposed model utilizes the standard linear Gaussian observation model associated with the hierarchical modeling of data using the matrix-variate Gaussian scale mixture (GSM). It deploys various random and deterministic parameters to incorporate the knowledge of spatial and temporal correlation present in data. By varying distributions over random parameters, a family of generalized hyperbolic matrix variate distributions is derived. For estimation, we rely on variational Bayes (VB) for random parameters and expectation-maximization (EM) for deterministic parameters. Furthermore, the model is compared with recent developments in matrix-variate distribution-based modeling of data, and we briefly discuss its extension to finite mixtures of skewed distributions. Finally, the framework is applied to the steady-state visual evoked potential (SSVEP)-based EEG benchmark data set, and a comparative study is conducted to show its effectiveness for the frequency detection task. One of the crucial features of the proposed model is that it simultaneously processes multichannel signals with low computational cost and time, making it suitable for real-time systems, especially in a resource-constrained environment.

Conditional Deep 3D-Convolutional Generative Adversarial Nets for RGB-D Generation

Generation of synthetic data is a challenging task. There are only a few significant works on RGB video generation and no pertinent works on RGB-D data generation. In the present work, we focus our attention on synthesizing RGB-D data which can further be used as dataset for various applications like object tracking, gesture recognition, and action recognition. This paper has put forward a proposal for a novel architecture that uses conditional deep 3D-convolutional generative adversarial networks to synthesize RGB-D data by exploiting 3D spatio-temporal convolutional framework. The proposed architecture can be used to generate virtually unlimited data. In this work, we have presented the architecture to generate RGB-D data conditioned on class labels. In the architecture, two parallel paths were used, one to generate RGB data and the second to synthesize depth map. The output from the two parallel paths is combined to generate RGB-D data. The proposed model is used for video generation at 30 fps (frames per second). The frame referred here is an RGB-D with the spatial resolution of 512 × 512.

"In-vitro Effects of Chlorpyrifos and Monocrotophos on the Activity of Acetylcholinesterase (AChE) in Different Tissues of Apple Snail Pila globosa (Swainson, 1822)"

The impact of two organophosphorus insecticides [Chlorpyrifos (CPF) and Monocrotophos (MCP)] on non-target wild natural gastropod, Pila globosa (apple snail) from the paddy fields was studied. The activity of acetylcholinesterase (AChE) was monitored on foot-muscle and hepatopancreas tissues of control and exposed snails. In the foot- muscle AChE inhibition progressed and reached 54.19% and 63.13% of the control, whereas, the AChE inhibition in the hepatopancreas reached 46.96% and 53.67% over control after 48 hours of exposure to 1.5 mL.L-1 and 2.5 mL.L-1 CPF respectively. After 48 hours of MCP exposure at 1.5 mL.L-1 and 2.5 mL.L-1 separately, the AChE inhibition of foot muscle was 49.07% and 57.59% respectively while in hepatopancreas it was 44.65% and 48.84% respectively. Our results show more inhibition of AChE activities on the foot-muscle than hepatopancreas in a concentration and time-dependent manner with greater severity by CPF in comparison to MCP. AChE inhibition increased with the increasing exposure time.

An Ontology Representation Language for Multimedia Event Applications

This paper presents formalization of a new Multimedia Web Ontology Language (E-MOWL) to handle events with media depictions. The temporal, spatial and entity aspects that are implicitly linked to an event are represented through this language to model the context of events. The already existing Multimedia Web Ontology Language (MOWL) can be leveraged for perceptual modelling of a domain, where the concepts manifest into media patterns in the multimedia document and helps in semantic processing of the contents. The language E-MOWL provides a rich method for representing knowledge corresponding to a specific domain wherein the context specifies the intended meaning of each element of the domain of discourse; an element in different context may correspond to different functional role. The context information associated with an event ties the audiovisual data with event related aspects. All these aspects when considered altogether provide the evidence and contribute towards recognizing an event from multimedia documents. The language also enables reasoning with the uncertainty associated with the events and is organized in the form of Bayesian Network (BN). The media items that are semantically relevant can be assimilated together on the basis of their association with events. We have demonstrated the efficacy of our approach by utilizing an ontology for the entertainment category in news domain to offer an application \textit{news aggregation} and event-based book recommendations.

A Novel Abnormality Annotation Database for COVID-19 Affected Frontal Lung X-rays.. [DOI: 10.1101/2021.01.07.21249323]

Purpose

To advance the usage of CXRs as a viable solution for efficient COVID-19 diagnostics by providing large-scale annotations of the abnormalities in frontal CXRs in BIMCV-COVID19+ database, and to provide a robust evaluation mechanism to facilitate its usage.

Materials and Methods

We provide the abnormality annotations in frontal CXRs by creating bounding boxes. The frontal CXRs are a part of the existing BIMCV-COVID19+ database. We also define four different protocols for robust evaluation of semantic segmentation and classification algorithms. Finally, we benchmark the defined protocols and report the results using popular deep learning models as a part of this study.

Results

For semantic segmentation, Mask-RCNN performs the best among all the models with a DICE score of 0.43 ± 0.01. For classification, we observe that MobileNetv2 yields the best results for 2-class and 3-class classification. We also observe that deep models report a lower performance for classifying other classes apart from the COVID class.

Conclusion

By making the annotated data and protocols available to the scientific community, we aim to advance the usage of CXRs as a viable solution for efficient COVID-19 diagnostics. This large-scale data will be useful for ML algorithms and can be used for learning radiological patterns observed in COVID-19 patients. Further, the protocols will facilitate ML practitioners for unified large-scale evaluation of their algorithms.

Data Availability Statement

The data associated with this work is available here : Radiologists’ Annotations on COVID-19+ X-rays https://osf.io/b35xu/ via @OSFramework andhttp://covbase4all.igib.res.in/.