Shams Nafisa Ali

Bio: Shams Nafisa Ali is an academic researcher from Bangladesh University of Engineering and Technology. The author has contributed to research in topics: Computer science & Feature (computer vision). The author has an hindex of 3, co-authored 12 publications receiving 29 citations.

CardioXNet: A Novel Lightweight Deep Learning Framework for Cardiovascular Disease Classification Using Heart Sound Recordings

Abstract: The alarmingly high mortality rate and increasing global prevalence of cardiovascular diseases (CVDs) signify the crucial need for early detection schemes. Phonocardiogram (PCG) signals have been historically applied in this domain owing to its simplicity and cost-effectiveness. In this article, we propose CardioXNet, a novel lightweight end-to-end CRNN architecture for automatic detection of five classes of cardiac auscultation namely normal, aortic stenosis, mitral stenosis, mitral regurgitation and mitral valve prolapse using raw PCG signal. The process has been automated by the involvement of two learning phases namely, representation learning and sequence residual learning. Three parallel CNN pathways have been implemented in the representation learning phase to learn the coarse and fine-grained features from the PCG and to explore the salient features from variable receptive fields involving 2D-CNN based squeeze-expansion. Thus, in the representation learning phase, the network extracts efficient time-invariant features and converges with great rapidity. In the sequential residual learning phase, because of the bidirectional-LSTMs and the skip connection, the network can proficiently extract temporal features without performing any feature extraction on the signal. The obtained results demonstrate that the proposed end-to-end architecture yields outstanding performance in all the evaluation metrics compared to the previous state-of-the-art methods with up to 99.60% accuracy, 99.56% precision, 99.52% recall and 99.68% F1- score on an average while being computationally comparable. This model outperforms any previous works using the same database by a considerable margin. Moreover, the proposed model was tested on PhysioNet/CinC 2016 challenge dataset achieving an accuracy of 86.57%. Finally the model was evaluated on a merged dataset of Github PCG dataset and PhysioNet dataset achieving excellent accuracy of 88.09%. The high accuracy metrics on both primary and secondary dataset combined with a significantly low number of parameters and end-to-end prediction approach makes the proposed network especially suitable for point of care CVD screening in low resource setups using memory constraint mobile devices.

A Lightweight CNN Model for Detecting Respiratory Diseases From Lung Auscultation Sounds Using EMD-CWT-Based Hybrid Scalogram

Abstract: Listening to lung sounds through auscultation is vital in examining the respiratory system for abnormalities. Automated analysis of lung auscultation sounds can be beneficial to the health systems in low-resource settings where there is a lack of skilled physicians. In this work, we propose a lightweight convolutional neural network (CNN) architecture to classify respiratory diseases from individual breath cycles using hybrid scalogram-based features of lung sounds. The proposed feature-set utilizes the empirical mode decomposition (EMD) and the continuous wavelet transform (CWT). The performance of the proposed scheme is studied using a patient independent train-validation-test set from the publicly available ICBHI 2017 lung sound dataset. Employing the proposed framework, weighted accuracy scores of 98.92% for three-class chronic classification and 98.70% for six-class pathological classification are achieved, which outperform well-known and much larger VGG16 in terms of accuracy by absolute margins of 1.10% and 1.11%, respectively. The proposed CNN model also outperforms other contemporary lightweight models while being computationally comparable.

Monkeypox Skin Lesion Detection Using Deep Learning Models: A Feasibility Study

Abstract: The recent monkeypox outbreak has become a public health concern due to its rapid spread in more than 40 countries outside Africa. Clinical diagnosis of monkeypox in an early stage is challenging due to its similarity with chickenpox and measles. In cases where the confirmatory Polymerase Chain Reaction (PCR) tests are not readily available, computer-assisted detection of monkeypox lesions could be beneficial for surveillance and rapid identification of suspected cases. Deep learning methods have been found effective in the automated detection of skin lesions, provided that sufficient training examples are available. However, as of now, such datasets are not available for the monkeypox disease. In the current study, we first develop the ``Monkeypox Skin Lesion Dataset (MSLD)"consisting skin lesion images of monkeypox, chickenpox, and measles. The images are mainly collected from websites, news portals, and publicly accessible case reports. Data augmentation is used to increase the sample size, and a 3-fold cross-validation experiment is set up. In the next step, several pre-trained deep learning models, namely, VGG-16, ResNet50, and InceptionV3 are employed to classify monkeypox and other diseases. An ensemble of the three models is also developed. ResNet50 achieves the best overall accuracy of $82.96(\pm4.57\%)$, while VGG16 and the ensemble system achieved accuracies of $81.48(\pm6.87\%)$ and $79.26(\pm1.05\%)$, respectively. A prototype web-application is also developed as an online monkeypox screening tool. While the initial results on this limited dataset are promising, a larger demographically diverse dataset is required to further enhance the generalizability of these models.

A Lightweight CNN Model for Detecting Respiratory Diseases from Lung Auscultation Sounds using EMD-CWT-based Hybrid Scalogram

Abstract: Listening to lung sounds through auscultation is vital in examining the respiratory system for abnormalities. Automated analysis of lung auscultation sounds can be beneficial to the health systems in low-resource settings where there is a lack of skilled physicians. In this work, we propose a lightweight convolutional neural network (CNN) architecture to classify respiratory diseases using hybrid scalogram-based features of lung sounds. The hybrid scalogram features utilize the empirical mode decomposition (EMD) and continuous wavelet transform (CWT). The proposed scheme's performance is studied using a patient independent train-validation set from the publicly available ICBHI 2017 lung sound dataset. Employing the proposed framework, weighted accuracy scores of 99.20% for ternary chronic classification and 99.05% for six-class pathological classification are achieved, which outperform well-known and much larger VGG16 in terms of accuracy by 0.52% and 1.77% respectively. The proposed CNN model also outperforms other contemporary lightweight models while being computationally comparable.

CovTANet: A Hybrid Tri-Level Attention-Based Network for Lesion Segmentation, Diagnosis, and Severity Prediction of COVID-19 Chest CT Scans

Abstract: Rapid and precise diagnosis of COVID-19 is one of the major challenges faced by the global community to control the spread of this overgrowing pandemic. In this article, a hybrid neural network is proposed, named CovTANet, to provide an end-to-end clinical diagnostic tool for early diagnosis, lesion segmentation, and severity prediction of COVID-19 utilizing chest computer tomography (CT) scans. A multiphase optimization strategy is introduced for solving the challenges of complicated diagnosis at a very early stage of infection, where an efficient lesion segmentation network is optimized initially, which is later integrated into a joint optimization framework for the diagnosis and severity prediction tasks providing feature enhancement of the infected regions. Moreover, for overcoming the challenges with diffused, blurred, and varying shaped edges of COVID lesions with novel and diverse characteristics, a novel segmentation network is introduced, namely tri-level attention-based segmentation network. This network has significantly reduced semantic gaps in subsequent encoding–decoding stages, with immense parallelization of multiscale features for faster convergence providing considerable performance improvement over traditional networks. Furthermore, a novel tri-level attention mechanism has been introduced, which is repeatedly utilized over the network, combining channel, spatial, and pixel attention schemes for faster and efficient generalization of contextual information embedded in the feature map through feature recalibration and enhancement operations. Outstanding performances have been achieved in all three tasks through extensive experimentation on a large publicly available dataset containing 1110 chest CT-volumes, which signifies the effectiveness of the proposed scheme at the current stage of the pandemic.

CardioXNet: A Novel Lightweight Deep Learning Framework for Cardiovascular Disease Classification Using Heart Sound Recordings

Abstract: The alarmingly high mortality rate and increasing global prevalence of cardiovascular diseases (CVDs) signify the crucial need for early detection schemes. Phonocardiogram (PCG) signals have been historically applied in this domain owing to its simplicity and cost-effectiveness. In this article, we propose CardioXNet, a novel lightweight end-to-end CRNN architecture for automatic detection of five classes of cardiac auscultation namely normal, aortic stenosis, mitral stenosis, mitral regurgitation and mitral valve prolapse using raw PCG signal. The process has been automated by the involvement of two learning phases namely, representation learning and sequence residual learning. Three parallel CNN pathways have been implemented in the representation learning phase to learn the coarse and fine-grained features from the PCG and to explore the salient features from variable receptive fields involving 2D-CNN based squeeze-expansion. Thus, in the representation learning phase, the network extracts efficient time-invariant features and converges with great rapidity. In the sequential residual learning phase, because of the bidirectional-LSTMs and the skip connection, the network can proficiently extract temporal features without performing any feature extraction on the signal. The obtained results demonstrate that the proposed end-to-end architecture yields outstanding performance in all the evaluation metrics compared to the previous state-of-the-art methods with up to 99.60% accuracy, 99.56% precision, 99.52% recall and 99.68% F1- score on an average while being computationally comparable. This model outperforms any previous works using the same database by a considerable margin. Moreover, the proposed model was tested on PhysioNet/CinC 2016 challenge dataset achieving an accuracy of 86.57%. Finally the model was evaluated on a merged dataset of Github PCG dataset and PhysioNet dataset achieving excellent accuracy of 88.09%. The high accuracy metrics on both primary and secondary dataset combined with a significantly low number of parameters and end-to-end prediction approach makes the proposed network especially suitable for point of care CVD screening in low resource setups using memory constraint mobile devices.

Classification of Monkeypox Images Based on Transfer Learning and the Al-Biruni Earth Radius Optimization Algorithm

Abstract: The world is still trying to recover from the devastation caused by the wide spread of COVID-19, and now the monkeypox virus threatens becoming a worldwide pandemic. Although the monkeypox virus is not as lethal or infectious as COVID-19, numerous countries report new cases daily. Thus, it is not surprising that necessary precautions have not been taken, and it will not be surprising if another worldwide pandemic occurs. Machine learning has recently shown tremendous promise in image-based diagnosis, including cancer detection, tumor cell identification, and COVID-19 patient detection. Therefore, a similar application may be implemented to diagnose monkeypox as it invades the human skin. An image can be acquired and utilized to further diagnose the condition. In this paper, two algorithms are proposed for improving the classification accuracy of monkeypox images. The proposed algorithms are based on transfer learning for feature extraction and meta-heuristic optimization for feature selection and optimization of the parameters of a multi-layer neural network. The GoogleNet deep network is adopted for feature extraction, and the utilized meta-heuristic optimization algorithms are the Al-Biruni Earth radius algorithm, the sine cosine algorithm, and the particle swarm optimization algorithm. Based on these algorithms, a new binary hybrid algorithm is proposed for feature selection, along with a new hybrid algorithm for optimizing the parameters of the neural network. To evaluate the proposed algorithms, a publicly available dataset is employed. The assessment of the proposed optimization of feature selection for monkeypox classification was performed in terms of ten evaluation criteria. In addition, a set of statistical tests was conducted to measure the effectiveness, significance, and robustness of the proposed algorithms. The results achieved confirm the superiority and effectiveness of the proposed methods compared to other optimization methods. The average classification accuracy was 98.8%.

Joint Learning of 3D Lesion Segmentation and Classification for Explainable COVID-19 Diagnosis

Abstract: Given the outbreak of COVID-19 pandemic and the shortage of medical resource, extensive deep learning models have been proposed for automatic COVID-19 diagnosis, based on 3D computed tomography (CT) scans. However, the existing models independently process the 3D lesion segmentation and disease classification, ignoring the inherent correlation between these two tasks. In this paper, we propose a joint deep learning model of 3D lesion segmentation and classification for diagnosing COVID-19, called DeepSC-COVID, as the first attempt in this direction. Specifically, we establish a large-scale CT database containing 1,805 3D CT scans with fine-grained lesion annotations, and reveal 4 findings about lesion difference between COVID-19 and community acquired pneumonia (CAP). Inspired by our findings, DeepSC-COVID is designed with 3 subnets: a cross-task feature subnet for feature extraction, a 3D lesion subnet for lesion segmentation, and a classification subnet for disease diagnosis. Besides, the task-aware loss is proposed for learning the task interaction across the 3D lesion and classification subnets. Different from all existing models for COVID-19 diagnosis, our model is interpretable with fine-grained 3D lesion distribution. Finally, extensive experimental results show that the joint learning framework in our model significantly improves the performance of 3D lesion segmentation and disease classification in both efficiency and efficacy.

Can Artificial Intelligence Detect Monkeypox from Digital Skin Images?

Abstract: An outbreak of Monkeypox has been reported in 75 countries so far, and it is spreading at a fast pace around the world. The clinical attributes of Monkeypox resemble those of Smallpox, while skin lesions and rashes of Monkeypox often resemble those of other poxes, for example, Chickenpox and Cowpox. These similarities make Monkeypox detection challenging for healthcare professionals by examining the visual appearance of lesions and rashes. Additionally, there is a knowledge gap among healthcare professionals due to the rarity of Monkeypox before the current outbreak. Motivated by the success of artificial intelligence (AI) in COVID-19 detection, the scientific community has shown an increasing interest in using AI in Monkeypox detection from digital skin images. However, the lack of Monkeypox skin image data has been the bottleneck of using AI in Monkeypox detection. Therefore, in this paper, we used a web-scrapping-based Monkeypox, Chickenpox, Smallpox, Cowpox, Measles, and healthy skin image dataset to study the feasibility of using state-of-the-art AI deep models on skin images for Monkeypox detection. Our study found that deep AI models have great potential in the detection of Monkeypox from digital skin images (precision of 85%). However, achieving a more robust detection power requires larger training samples to train those deep models.

Detection of COVID-19 in smartphone-based breathing recordings: A pre-screening deep learning tool

Abstract: This study was sought to investigate the feasibility of using smartphone-based breathing sounds within a deep learning framework to discriminate between COVID-19, including asymptomatic, and healthy subjects. A total of 480 breathing sounds (240 shallow and 240 deep) were obtained from a publicly available database named Coswara. These sounds were recorded by 120 COVID-19 and 120 healthy subjects via a smartphone microphone through a website application. A deep learning framework was proposed herein that relies on hand-crafted features extracted from the original recordings and from the mel-frequency cepstral coefficients (MFCC) as well as deep-activated features learned by a combination of convolutional neural network and bi-directional long short-term memory units (CNN-BiLSTM). The statistical analysis of patient profiles has shown a significant difference (p-value: 0.041) for ischemic heart disease between COVID-19 and healthy subjects. The Analysis of the normal distribution of the combined MFCC values showed that COVID-19 subjects tended to have a distribution that is skewed more towards the right side of the zero mean (shallow: 0.59±1.74, deep: 0.65±4.35, p-value: <0.001). In addition, the proposed deep learning approach had an overall discrimination accuracy of 94.58% and 92.08% using shallow and deep recordings, respectively. Furthermore, it detected COVID-19 subjects successfully with a maximum sensitivity of 94.21%, specificity of 94.96%, and area under the receiver operating characteristic (AUROC) curves of 0.90. Among the 120 COVID-19 participants, asymptomatic subjects (18 subjects) were successfully detected with 100.00% accuracy using shallow recordings and 88.89% using deep recordings. This study paves the way towards utilizing smartphone-based breathing sounds for the purpose of COVID-19 detection. The observations found in this study were promising to suggest deep learning and smartphone-based breathing sounds as an effective pre-screening tool for COVID-19 alongside the current reverse-transcription polymerase chain reaction (RT-PCR) assay. It can be considered as an early, rapid, easily distributed, time-efficient, and almost no-cost diagnosis technique complying with social distancing restrictions during COVID-19 pandemic.