Objective: Since its outbreak, the rapid spread of COrona VIrus Disease 2019 (COVID-19) across the globe has pushed the health care system in many countries to the verge of collapse. Therefore, it is imperative to correctly identify COVID-19 positive patients and isolate them as soon as possible to contain the spread of the disease and reduce the ongoing burden on the healthcare system. The primary COVID-19 screening test, RT-PCR although accurate and reliable, has a long turn-around time. In the recent past, several researchers have demonstrated the use of Deep Learning (DL) methods on chest radiography (such as X-ray and CT) for COVID-19 detection. However, existing CNN based DL methods fail to capture the global context due to their inherent image-specific inductive bias. Methods: Motivated by this, in this work, we propose the use of vision transformers (instead of convolutional networks) for COVID-19 screening using the X-ray and CT images. We employ a multi-stage transfer learning technique to address the issue of data scarcity. Furthermore, we show that the features learned by our transformer networks are explainable. Results: We demonstrate that our method not only quantitatively outperforms the recent benchmarks but also focuses on meaningful regions in the images for detection (as confirmed by Radiologists), aiding not only in accurate diagnosis of COVID-19 but also in localization of the infected area. The code for our implementation can be found here - https://github.com/arnabkmondal/xViTCOS. Conclusion: The proposed method will help in timely identification of COVID-19 and efficient utilization of limited resources. 

xViTCOS: Explainable Vision Transformer Based COVID-19 Screening Using Radiography

The steady spread of the 2019 Coronavirus disease has brought about human and economic losses, imposing a new lifestyle across the world. On this point, medical imaging tests such as computed tomography (CT) and X-ray have demonstrated a sound screening potential. Deep learning methodologies have evidenced superior image analysis capabilities with respect to prior handcrafted counterparts. In this paper, we propose a novel deep learning framework for Coronavirus detection using CT and X-ray images. In particular, a Vision Transformer architecture is adopted as a backbone in the proposed network, in which a Siamese encoder is utilized. The latter is composed of two branches: one for processing the original image and another for processing an augmented view of the original image. The input images are divided into patches and fed through the encoder. The proposed framework is evaluated on public CT and X-ray datasets. The proposed system confirms its superiority over state-of-the-art methods on CT and X-ray data in terms of accuracy, precision, recall, specificity, and F1 score. Furthermore, the proposed system also exhibits good robustness when a small portion of training data is allocated. 

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COVID-19 Detection in CT/X-ray Imagery Using Vision Transformers

Pneumonia is a prevalent severe respiratory infection that affects the distal and alveoli airways. Across the globe, it is a serious public health issue that has caused high mortality rate of children below five years old and the aged citizens who must have had previous chronic-related ailment. Pneumonia can be caused by a wide range of microorganisms, including virus, fungus, bacteria, which varies greatly across the globe. The spread of the ailment has gained computer-aided diagnosis (CAD) attention. This paper presents a multi-channel-based image processing scheme to automatically extract features and identify pneumonia from chest X-ray images. The proposed approach intends to address the problem of low quality and identify pneumonia in CXR images. Three channels of CXR images, namely, the Local Binary Pattern (LBP), Contrast Enhanced Canny Edge Detection (CECED), and Contrast Limited Adaptive Histogram Equalization (CLAHE) CXR images are processed by deep neural networks. CXR-related features of LBP images are extracted using shallow CNN, features of the CLAHE CXR images are extracted by pre-trained inception-V3, whereas the features of CECED CXR images are extracted using pre-trained MobileNet-V3. The final feature weights of the three channels are concatenated and softmax classification is utilized to determine the final identification result. The proposed network can accurately classify pneumonia according to the experimental result. The proposed method tested on publicly available dataset reports accuracy of 98.3%, sensitivity of 98.9%, and specificity of 99.2%. Compared with the single models and the state-of-the-art models, our proposed network achieves comparable performance.

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Multi-Channel Based Image Processing Scheme for Pneumonia Identification

According to research, classifiers and detectors are less accurate when images are blurry, have low contrast, or have other flaws which raise questions about the machine learning model’s ability to recognize items effectively. The chest X-ray image has proven to be the preferred image modality for medical imaging as it contains more information about a patient. Its interpretation is quite difficult, nevertheless. The goal of this research is to construct a reliable deep-learning model capable of producing high classification accuracy on chest x-ray images for lung diseases. To enable a thorough study of the chest X-ray image, the suggested framework first derived richer features using an ensemble technique, then a global second-order pooling is applied to further derive higher global features of the images. Furthermore, the images are then separated into patches and position embedding before analyzing the patches individually via a vision transformer approach. The proposed model yielded 96.01% sensitivity, 96.20% precision, and 98.00% accuracy for the COVID-19 Radiography Dataset while achieving 97.84% accuracy, 96.76% sensitivity and 96.80% precision, for the Covid-ChestX-ray-15k dataset. The experimental findings reveal that the presented models outperform traditional deep learning models and other state-of-the-art approaches provided in the literature.

/pdf/automated-lung-related-pneumonia-and-covid-19-detection-1yr0klfe.pdf

Automated Lung-Related Pneumonia and COVID-19 Detection Based on Novel Feature Extraction Framework and Vision Transformer Approaches Using Chest X-ray Images

An efficient deep learning-based framework for tuberculosis detection using chest X-ray images.

Coronavirus disease 2019 (COVID-19) is one of the most destructive pandemic after millennium, forcing the world to tackle a health crisis Automated lung infections classification using chest X-ray (CXR) images could strengthen diagnostic capability when handling COVID-19 However, classifying COVID-19 from pneumonia cases using CXR image is a difficult task because of shared spatial characteristics, high feature variation and contrast diversity between cases Moreover, massive data collection is impractical for a newly emerged disease, which limited the performance of data thirsty deep learning models To address these challenges, Multiscale Attention Guided deep network with Soft Distance regularization ( MAG-SD ) is proposed to automatically classify COVID-19 from pneumonia CXR images In MAG-SD , MA-Net is used to produce prediction vector and attention from multiscale feature maps To improve the robustness of trained model and relieve the shortage of training data, attention guided augmentations along with a soft distance regularization are posed, which aims at generating meaningful augmentations and reduce noise Our multiscale attention model achieves better classification performance on our pneumonia CXR image dataset Plentiful experiments are proposed for MAG-SD which demonstrates its unique advantage in pneumonia classification over cutting-edge models The code is available at https://githubcom/JasonLeeGHub/MAG-SD 

/pdf/multiscale-attention-guided-network-for-covid-19-diagnosis-49dsgae9rv.pdf

Multiscale Attention Guided Network for COVID-19 Diagnosis Using Chest X-Ray Images

Segmentation of brain tumors and their subregions remains a challenging task due to their weak features and deformable shapes. In this paper, three patterns (cross-skip, skip-1 and skip-2) of distributed dense connections (DDCs) are proposed to enhance feature reuse and propagation of CNNs by constructing tunnels between key layers of the network. For better detecting and segmenting brain tumors from multi-modal 3D MR images, CNN-based models embedded with DDCs (DDU-Nets) are trained efficiently from pixel to pixel with a limited number of parameters. Postprocessing is then applied to refine the segmentation results by reducing the false-positive samples. The proposed method is evaluated on the BraTS 2019 dataset with results demonstrating the effectiveness of the DDU-Nets while requiring less computational cost.

DDU-Nets: Distributed Dense Model for 3D MRI Brain Tumor Segmentation

. Karyotyping is an important procedure to assess the possible existence of chromosomal abnormalities. However, because of the non-rigid nature, chromosomes are usually heavily curved in microscopic images and such deformed shapes hinder the chromosome analysis for cytogeneticists. In this paper, we present a self-attention guided framework to erase the curvature of chromosomes. The proposed framework extracts spatial information and local textures to preserve banding patterns in a regression module. With complementary information from the bent chromosome, a reﬁnement module is designed to further improve ﬁne details. In addition, we propose two dedicated geometric constraints to maintain the length and restore the distortion of chromosomes. To train our framework, we create a synthetic dataset where curved chromosomes are generated from the real-world straight chromosomes by grid-deformation. Quantitative and qualitative experiments are conducted on synthetic and real-world data. Experimental results show that our proposed method can eﬀectively straighten bent chromosomes while keeping banding details and length.

ChrSNet: Chromosome Straightening using Self-attention Guided Networks

Point-based cell recognition, which aims to localize and classify cells present in a pathology image, is a fundamental task in digital pathology image analysis. The recently developed point-to-point network (P2PNet) has achieved unprecedented cell recognition accuracy and efficiency compared to methods that rely on intermediate density map representations. However, P2PNet could not leverage multi-scale information since it can only decode a single feature map. Moreover, the distribution of predefined point proposals, which is determined by data properties, restricts the resolution of the feature map to decode, i.e., the encoder design. To lift these limitations, we propose a variant of P2PNet named deformable proposal-aware P2PNet (DPA-P2PNet) in this study. The proposed method uses coordinates of point proposals to directly extract multi-scale region-of-interest (ROI) features for feature enhancement. Such a design also opens up possibilities to exploit dynamic distributions of proposals. We further devise a deformation module to improve the proposal quality. Extensive experiments on four datasets with various staining styles demonstrate that DPA-P2PNet outperforms the state-of-the-art methods on point-based cell recognition, which reveals the high potentiality in assisting pathologist assessments.

Jingxiong Li

Papers

Multiscale Attention Guided Network for COVID-19 Diagnosis Using Chest X-Ray Images

DDU-Nets: Distributed Dense Model for 3D MRI Brain Tumor Segmentation

DDU-Nets: Distributed Dense Model for 3D MRI Brain Tumor Segmentation

ChrSNet: Chromosome Straightening using Self-attention Guided Networks

Deformable Proposal-Aware P2PNet: A Universal Network for Cell Recognition under Point Supervision