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Article: Modality specific U-Net variants for biomedical image segmentation: a survey.

Punn, Narinder Singh / Agarwal, Sonali

2022 Volume 55, Issue 7, Page(s) 5845–5889

Abstract: With the advent of advancements in deep learning approaches, such as deep convolution neural network, residual neural network, adversarial network; U-Net architectures are most widely utilized in biomedical image segmentation to address the automation in ...

Abstract	With the advent of advancements in deep learning approaches, such as deep convolution neural network, residual neural network, adversarial network; U-Net architectures are most widely utilized in biomedical image segmentation to address the automation in identification and detection of the target regions or sub-regions. In recent studies, U-Net based approaches have illustrated state-of-the-art performance in different applications for the development of computer-aided diagnosis systems for early diagnosis and treatment of diseases such as brain tumor, lung cancer, alzheimer, breast cancer, etc., using various modalities. This article contributes in presenting the success of these approaches by describing the U-Net framework, followed by the comprehensive analysis of the U-Net variants by performing (1) inter-modality, and (2) intra-modality categorization to establish better insights into the associated challenges and solutions. Besides, this article also highlights the contribution of U-Net based frameworks in the ongoing pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also known as COVID-19. Finally, the strengths and similarities of these U-Net variants are analysed along with the challenges involved in biomedical image segmentation to uncover promising future research directions in this area.
Language	English
Publishing date	2022-03-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1479828-1
ISSN	1573-7462 ; 0269-2821
ISSN (online)	1573-7462
ISSN	0269-2821
DOI	10.1007/s10462-022-10152-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: CHS-Net: A Deep Learning Approach for Hierarchical Segmentation of COVID-19 via CT Images.

Punn, Narinder Singh / Agarwal, Sonali

Neural processing letters

2022 Volume 54, Issue 5, Page(s) 3771–3792

Abstract: The pandemic of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also known as COVID-19 has been spreading worldwide, causing rampant loss of lives. Medical imaging such as computed tomography (CT), X-ray, etc., plays a significant role ...

Abstract	The pandemic of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also known as COVID-19 has been spreading worldwide, causing rampant loss of lives. Medical imaging such as computed tomography (CT), X-ray, etc., plays a significant role in diagnosing the patients by presenting the visual representation of the functioning of the organs. However, for any radiologist analyzing such scans is a tedious and time-consuming task. The emerging deep learning technologies have displayed its strength in analyzing such scans to aid in the faster diagnosis of the diseases and viruses such as COVID-19. In the present article, an automated deep learning based model, COVID-19 hierarchical segmentation network (CHS-Net) is proposed that functions as a semantic hierarchical segmenter to identify the COVID-19 infected regions from lungs contour via CT medical imaging using two cascaded residual attention inception U-Net (RAIU-Net) models. RAIU-Net comprises of a residual inception U-Net model with spectral spatial and depth attention network (SSD) that is developed with the contraction and expansion phases of depthwise separable convolutions and hybrid pooling (max and spectral pooling) to efficiently encode and decode the semantic and varying resolution information. The CHS-Net is trained with the segmentation loss function that is the defined as the average of binary cross entropy loss and dice loss to penalize false negative and false positive predictions. The approach is compared with the recently proposed approaches and evaluated using the standard metrics like accuracy, precision, specificity, recall, dice coefficient and Jaccard similarity along with the visualized interpretation of the model prediction with GradCam++ and uncertainty maps. With extensive trials, it is observed that the proposed approach outperformed the recently proposed approaches and effectively segments the COVID-19 infected regions in the lungs.
Language	English
Publishing date	2022-03-16
Publishing country	Belgium
Document type	Journal Article
ZDB-ID	1478375-7
ISSN	1573-773X ; 1370-4621
ISSN (online)	1573-773X
ISSN	1370-4621
DOI	10.1007/s11063-022-10785-x
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Article ; Online: Liver fibrosis classification from ultrasound using machine learning: a systematic literature review.

Punn, Narinder Singh / Patel, Bhavik / Banerjee, Imon

Abdominal radiology (New York)

2023 Volume 49, Issue 1, Page(s) 69–80

Abstract: Purpose: Liver biopsy was considered the gold standard for diagnosing liver fibrosis; however, with advancements in medical technology and increasing awareness of potential complications, the reliance on liver biopsy has diminished. Ultrasound is ... ...

Abstract	Purpose: Liver biopsy was considered the gold standard for diagnosing liver fibrosis; however, with advancements in medical technology and increasing awareness of potential complications, the reliance on liver biopsy has diminished. Ultrasound is gaining popularity due to its wider availability and cost-effectiveness. This study examined the machine learning / deep learning (ML/DL) models for non-invasive liver fibrosis classification from ultrasound. Methods: Following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) protocol, we searched five academic databases using the query. We defined population, intervention, comparison, outcomes, and study design (PICOS) framework for the inclusion. Furthermore, Joana Briggs Institute (JBI) checklist for analytical cross-sectional studies is used for quality assessment. Results: Among the 188 screened studies, 17 studies are selected. The methods are categorized as off-the-shelf (OTS), attention, generative, and ensemble classifiers. Most studies used OTS classifiers that combined pre-trained ML/DL methods with radiomics features to determine fibrosis staging. Although machine learning shows potential for fibrosis classification, there are limited external comparisons of interventions and prospective clinical trials, which limits their applicability. Conclusion: With the recent success of ML/DL toward biomedical image analysis, automated solutions using ultrasound are developed for predicting liver diseases. However, their applicability is bounded by the limited and imbalanced retrospective studies having high heterogeneity. This challenge could be addressed by generating a standard protocol for study design by selecting appropriate population, interventions, outcomes, and comparison.
MeSH term(s)	Humans ; Prospective Studies ; Retrospective Studies ; Cross-Sectional Studies ; Liver Cirrhosis/diagnostic imaging ; Liver Cirrhosis/pathology ; Machine Learning
Language	English
Publishing date	2023-11-10
Publishing country	United States
Document type	Systematic Review ; Journal Article ; Review
ZDB-ID	2839786-1
ISSN	2366-0058 ; 2366-004X
ISSN (online)	2366-0058
ISSN	2366-004X
DOI	10.1007/s00261-023-04081-y
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Article ; Online: Automated diagnosis of COVID-19 with limited posteroanterior chest X-ray images using fine-tuned deep neural networks.

Punn, Narinder Singh / Agarwal, Sonali

Applied intelligence (Dordrecht, Netherlands)

2020 Volume 51, Issue 5, Page(s) 2689–2702

Abstract: The novel coronavirus 2019 (COVID-19) is a respiratory syndrome that resembles pneumonia. The current diagnostic procedure of COVID-19 follows reverse-transcriptase polymerase chain reaction (RT-PCR) based approach which however is less sensitive to ... ...

Abstract	The novel coronavirus 2019 (COVID-19) is a respiratory syndrome that resembles pneumonia. The current diagnostic procedure of COVID-19 follows reverse-transcriptase polymerase chain reaction (RT-PCR) based approach which however is less sensitive to identify the virus at the initial stage. Hence, a more robust and alternate diagnosis technique is desirable. Recently, with the release of publicly available datasets of corona positive patients comprising of computed tomography (CT) and chest X-ray (CXR) imaging; scientists, researchers and healthcare experts are contributing for faster and automated diagnosis of COVID-19 by identifying pulmonary infections using deep learning approaches to achieve better cure and treatment. These datasets have limited samples concerned with the positive COVID-19 cases, which raise the challenge for unbiased learning. Following from this context, this article presents the random oversampling and weighted class loss function approach for unbiased fine-tuned learning (transfer learning) in various state-of-the-art deep learning approaches such as baseline ResNet, Inception-v3, Inception ResNet-v2, DenseNet169, and NASNetLarge to perform binary classification (as normal and COVID-19 cases) and also multi-class classification (as COVID-19, pneumonia, and normal case) of posteroanterior CXR images. Accuracy, precision, recall, loss, and area under the curve (AUC) are utilized to evaluate the performance of the models. Considering the experimental results, the performance of each model is scenario dependent; however, NASNetLarge displayed better scores in contrast to other architectures, which is further compared with other recently proposed approaches. This article also added the visual explanation to illustrate the basis of model classification and perception of COVID-19 in CXR images.
Language	English
Publishing date	2020-10-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1479519-X
ISSN	1573-7497 ; 0924-669X
ISSN (online)	1573-7497
ISSN	0924-669X
DOI	10.1007/s10489-020-01900-3
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Article: Automated diagnosis of COVID-19 with limited posteroanterior chest X-ray images using fine-tuned deep neural networks

Narinder Punn Singh / Sonali Agarwal

Abstract	The novel coronavirus 2019 (COVID-19) is a respiratory syndrome that resembles pneumonia. The current diagnostic procedure of COVID-19 follows reverse-transcriptase polymerase chain reaction (RT-PCR) based approach which however is less sensitive to identify the virus at the initial stage. Hence, a more robust and alternate diagnosis technique is desirable. Recently, with the release of publicly available datasets of corona positive patients comprising of computed tomography (CT) and chest X-ray (CXR) imaging; scientists, researchers and healthcare experts are contributing for faster and automated diagnosis of COVID-19 by identifying pulmonary infections using deep learning approaches to achieve better cure and treatment. These datasets have limited samples concerned with the positive COVID-19 cases, which raise the challenge for unbiased learning. Following from this context, this article presents the random oversampling and weighted class loss function approach for unbiased fine-tuned learning (transfer learning) in various state-of-the-art deep learning approaches such as baseline ResNet, Inception-v3, Inception ResNet-v2, DenseNet169, and NASNetLarge to perform binary classification (as normal and COVID-19 cases) and also multi-class classification (as COVID-19, pneumonia, and normal case) of posteroanterior CXR images. Accuracy, precision, recall, loss, and area under the curve (AUC) are utilized to evaluate the performance of the models. Considering the experimental results, the performance of each model is scenario dependent; however, NASNetLarge displayed better scores in contrast to other architectures. This article also added the visual explanation to illustrate the basis of model classification and perception of COVID-19 in CXR images.
Keywords	covid19
Publisher	arxiv
Document type	Article
Database	COVID19

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Book ; Online: Modality specific U-Net variants for biomedical image segmentation

Punn, Narinder Singh / Agarwal, Sonali

A survey

2021

Abstract	With the advent of advancements in deep learning approaches, such as deep convolution neural network, residual neural network, adversarial network; U-Net architectures are most widely utilized in biomedical image segmentation to address the automation in identification and detection of the target regions or sub-regions. In recent studies, U-Net based approaches have illustrated state-of-the-art performance in different applications for the development of computer-aided diagnosis systems for early diagnosis and treatment of diseases such as brain tumor, lung cancer, alzheimer, breast cancer, etc., using various modalities. This article contributes in presenting the success of these approaches by describing the U-Net framework, followed by the comprehensive analysis of the U-Net variants by performing 1) inter-modality, and 2) intra-modality categorization to establish better insights into the associated challenges and solutions. Besides, this article also highlights the contribution of U-Net based frameworks in the ongoing pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also known as COVID-19. Finally, the strengths and similarities of these U-Net variants are analysed along with the challenges involved in biomedical image segmentation to uncover promising future research directions in this area.
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition
Subject code	004
Publishing date	2021-07-09
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: RCA-IUnet

Punn, Narinder Singh / Agarwal, Sonali

A residual cross-spatial attention guided inception U-Net model for tumor segmentation in breast ultrasound imaging

2021

Abstract: The advancements in deep learning technologies have produced immense contribution to biomedical image analysis applications. With breast cancer being the common deadliest disease among women, early detection is the key means to improve survivability. ... ...

Abstract	The advancements in deep learning technologies have produced immense contribution to biomedical image analysis applications. With breast cancer being the common deadliest disease among women, early detection is the key means to improve survivability. Medical imaging like ultrasound presents an excellent visual representation of the functioning of the organs; however, for any radiologist analysing such scans is challenging and time consuming which delays the diagnosis process. Although various deep learning based approaches are proposed that achieved promising results, the present article introduces an efficient residual cross-spatial attention guided inception U-Net (RCA-IUnet) model with minimal training parameters for tumor segmentation using breast ultrasound imaging to further improve the segmentation performance of varying tumor sizes. The RCA-IUnet model follows U-Net topology with residual inception depth-wise separable convolution and hybrid pooling (max pooling and spectral pooling) layers. In addition, cross-spatial attention filters are added to suppress the irrelevant features and focus on the target structure. The segmentation performance of the proposed model is validated on two publicly available datasets using standard segmentation evaluation metrics, where it outperformed the other state-of-the-art segmentation models.
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition
Subject code	004
Publishing date	2021-08-05
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Automated diagnosis of COVID-19 with limited posteroanterior chest X-ray images using fine-tuned deep neural networks

Punn, Narinder Singh / Agarwal, Sonali

Appl Intell

Abstract	The novel coronavirus 2019 (COVID-19) is a respiratory syndrome that resembles pneumonia. The current diagnostic procedure of COVID-19 follows reverse-transcriptase polymerase chain reaction (RT-PCR) based approach which however is less sensitive to identify the virus at the initial stage. Hence, a more robust and alternate diagnosis technique is desirable. Recently, with the release of publicly available datasets of corona positive patients comprising of computed tomography (CT) and chest X-ray (CXR) imaging; scientists, researchers and healthcare experts are contributing for faster and automated diagnosis of COVID-19 by identifying pulmonary infections using deep learning approaches to achieve better cure and treatment. These datasets have limited samples concerned with the positive COVID-19 cases, which raise the challenge for unbiased learning. Following from this context, this article presents the random oversampling and weighted class loss function approach for unbiased fine-tuned learning (transfer learning) in various state-of-the-art deep learning approaches such as baseline ResNet, Inception-v3, Inception ResNet-v2, DenseNet169, and NASNetLarge to perform binary classification (as normal and COVID-19 cases) and also multi-class classification (as COVID-19, pneumonia, and normal case) of posteroanterior CXR images. Accuracy, precision, recall, loss, and area under the curve (AUC) are utilized to evaluate the performance of the models. Considering the experimental results, the performance of each model is scenario dependent; however, NASNetLarge displayed better scores in contrast to other architectures, which is further compared with other recently proposed approaches. This article also added the visual explanation to illustrate the basis of model classification and perception of COVID-19 in CXR images.
Keywords	covid19
Publisher	ArXiv; PMC
Document type	Article ; Online
DOI	10.1007/s10489-020-01900-3
Database	COVID19

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Book ; Online: CHS-Net

Punn, Narinder Singh / Agarwal, Sonali

A Deep learning approach for hierarchical segmentation of COVID-19 infected CT images

2020

Abstract: The pandemic of novel SARS-CoV-2 also known as COVID-19 has been spreading worldwide, causing rampant loss of lives. Medical imaging such as CT, X-ray, etc., plays a significant role in diagnosing the patients by presenting the visual representation of ... ...

Abstract	The pandemic of novel SARS-CoV-2 also known as COVID-19 has been spreading worldwide, causing rampant loss of lives. Medical imaging such as CT, X-ray, etc., plays a significant role in diagnosing the patients by presenting the visual representation of the functioning of the organs. However, for any radiologist analyzing such scans is a tedious and time-consuming task. The emerging deep learning technologies have displayed its strength in analyzing such scans to aid in the faster diagnosis of the diseases and viruses such as COVID-19. In the present article, an automated deep learning based model, COVID-19 hierarchical segmentation network (CHS-Net) is proposed that functions as a semantic hierarchical segmenter to identify the COVID-19 infected regions from lungs contour via CT medical imaging using two cascaded residual attention inception U-Net (RAIU-Net) models. RAIU-Net comprises of a residual inception U-Net model with spectral spatial and depth attention network (SSD) that is developed with the contraction and expansion phases of depthwise separable convolutions and hybrid pooling (max and spectral pooling) to efficiently encode and decode the semantic and varying resolution information. The CHS-Net is trained with the segmentation loss function that is the defined as the average of binary cross entropy loss and dice loss to penalize false negative and false positive predictions. The approach is compared with the recently proposed approaches and evaluated using the standard metrics like accuracy, precision, specificity, recall, dice coefficient and Jaccard similarity along with the visualized interpretation of the model prediction with GradCam++ and uncertainty maps. With extensive trials, it is observed that the proposed approach outperformed the recently proposed approaches and effectively segments the COVID-19 infected regions in the lungs.
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition
Subject code	006
Publishing date	2020-12-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Automated diagnosis of COVID-19 with limited posteroanterior chest X-ray images using fine-tuned deep neural networks

Punn, Narinder Singh / Agarwal, Sonali

2020

Abstract	The novel coronavirus 2019 (COVID-19) is a respiratory syndrome that resembles pneumonia. The current diagnostic procedure of COVID-19 follows reverse-transcriptase polymerase chain reaction (RT-PCR) based approach which however is less sensitive to identify the virus at the initial stage. Hence, a more robust and alternate diagnosis technique is desirable. Recently, with the release of publicly available datasets of corona positive patients comprising of computed tomography (CT) and chest X-ray (CXR) imaging; scientists, researchers and healthcare experts are contributing for faster and automated diagnosis of COVID-19 by identifying pulmonary infections using deep learning approaches to achieve better cure and treatment. These datasets have limited samples concerned with the positive COVID-19 cases, which raise the challenge for unbiased learning. Following from this context, this article presents the random oversampling and weighted class loss function approach for unbiased fine-tuned learning (transfer learning) in various state-of-the-art deep learning approaches such as baseline ResNet, Inception-v3, Inception ResNet-v2, DenseNet169, and NASNetLarge to perform binary classification (as normal and COVID-19 cases) and also multi-class classification (as COVID-19, pneumonia, and normal case) of posteroanterior CXR images. Accuracy, precision, recall, loss, and area under the curve (AUC) are utilized to evaluate the performance of the models. Considering the experimental results, the performance of each model is scenario dependent; however, NASNetLarge displayed better scores in contrast to other architectures, which is further compared with other recently proposed approaches. This article also added the visual explanation to illustrate the basis of model classification and perception of COVID-19 in CXR images.
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; covid19
Subject code	006
Publishing date	2020-04-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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