Samiul Based Shuvo

Shams Nafisa Ali, Afia Zahin, Samiul Based Shuvo et al.

Cardiac auscultation, an integral tool in diagnosing cardiovascular diseases (CVDs), often relies on the subjective interpretation of clinicians, presenting a limitation in consistency and accuracy. Addressing this, we introduce the BUET Multi-disease Heart Sound (BMD-HS) dataset - a comprehensive and meticulously curated collection of heart sound recordings. This dataset, encompassing 864 recordings across five distinct classes of common heart sounds, represents a broad spectrum of valvular heart diseases, with a focus on diagnostically challenging cases. The standout feature of the BMD-HS dataset is its innovative multi-label annotation system, which captures a diverse range of diseases and unique disease states. This system significantly enhances the dataset's utility for developing advanced machine learning models in automated heart sound classification and diagnosis. By bridging the gap between traditional auscultation practices and contemporary data-driven diagnostic methods, the BMD-HS dataset is poised to revolutionize CVD diagnosis and management, providing an invaluable resource for the advancement of cardiac health research. The dataset is publicly available at this link: https://github.com/mHealthBuet/BMD-HS-Dataset.

Samiul Based Shuvo, Tasnia Binte Mamun

Lung cancer is a leading cause of cancer-related deaths worldwide, and early detection is crucial for improving patient outcomes. Nevertheless, early diagnosis of cancer is a major challenge, particularly in low-resource settings where access to medical resources and trained radiologists is limited. The objective of this study is to propose an automated end-to-end deep learning-based framework for the early detection and classification of lung nodules, specifically for low-resource settings. The proposed framework consists of three stages: lung segmentation using a modified 3D U-Net named 3D Res-U-Net, nodule detection using YOLO-v5, and classification with a Vision Transformer-based architecture. We evaluated the proposed framework on a publicly available dataset, LUNA16. The proposed framework's performance was measured using the respective domain's evaluation matrices. The proposed framework achieved a 98.82% lung segmentation dice score while detecting the lung nodule with 0.76 mAP@50 from the segmented lung, at a low false-positive rate. The performance of both networks of the proposed framework was compared with other studies and found to outperform them regarding segmentation and detection accuracy. Additionally, our proposed Vision transformer network obtained an accuracy of 93.57%, which is 1.21% higher than the state-of-the-art networks. Our proposed end-to-end deep learning-based framework can effectively segment lungs, and detect and classify lung nodules, specifically in low-resource settings with limited access to radiologists. The proposed framework outperforms existing studies regarding all the respective evaluation metrics. The proposed framework can potentially improve the accuracy and efficiency of lung cancer screening in low-resource settings, ultimately leading to better patient outcomes.

Ridoy Chandra Shil, Ragib Abid, Tasnia Binte Mamun et al.

Background and Objective: Colorectal cancer prevention relies on early detection of polyps during colonoscopy. Existing public datasets, such as CVC-ClinicDB and Kvasir-SEG, provide valuable benchmarks but are limited by small sample sizes, curated image selection, or lack of real-world artifacts. There remains a need for datasets that capture the complexity of clinical practice, particularly in resource-constrained settings. Methods: We introduce a dataset, BUET Polyp Dataset (BPD), of colonoscopy images collected using Olympus 170 and Pentax i-Scan series endoscopes under routine clinical conditions. The dataset contains images with corresponding expert-annotated binary masks, reflecting diverse challenges such as motion blur, specular highlights, stool artifacts, blood, and low-light frames. Annotations were manually reviewed by clinical experts to ensure quality. To demonstrate baseline performance, we provide benchmark results for classification using VGG16, ResNet50, and InceptionV3, and for segmentation using UNet variants with VGG16, ResNet34, and InceptionV4 backbones. Results: The dataset comprises 1,288 images with polyps from 164 patients with corresponding ground-truth masks and 1,657 polyp-free images from 31 patients. Benchmarking experiments achieved up to 90.8% accuracy for binary classification (VGG16) and a maximum Dice score of 0.64 with InceptionV4-UNet for segmentation. Performance was lower compared to curated datasets, reflecting the real-world difficulty of images with artifacts and variable quality.

Samiul Based Shuvo, Tasnia Binte Mamun, U Rajendra Acharya

DNA-binding proteins (DBPs) are integral to gene regulation and cellular processes, making their accurate identification essential for understanding biological functions and disease mechanisms. Experimental methods for DBP identification are time-consuming and costly, driving the need for efficient computational prediction techniques. In this study, we propose a novel deep learning framework, ResCap-DBP, that combines a residual learning-based encoder with a one-dimensional Capsule Network (1D-CapsNet) to predict DBPs directly from raw protein sequences. Our architecture incorporates dilated convolutions within residual blocks to mitigate vanishing gradient issues and extract rich sequence features, while capsule layers with dynamic routing capture hierarchical and spatial relationships within the learned feature space. We conducted comprehensive ablation studies comparing global and local embeddings from ProteinBERT and conventional one-hot encoding. Results show that ProteinBERT embeddings substantially outperform other representations on large datasets. Although one-hot encoding showed marginal advantages on smaller datasets, such as PDB186, it struggled to scale effectively. Extensive evaluations on four pairs of publicly available benchmark datasets demonstrate that our model consistently outperforms current state-of-the-art methods. It achieved AUC scores of 98.0% and 89.5% on PDB14189andPDB1075, respectively. On independent test sets PDB2272 and PDB186, the model attained top AUCs of 83.2% and 83.3%, while maintaining competitive performance on larger datasets such as PDB20000. Notably, the model maintains a well balanced sensitivity and specificity across datasets. These results demonstrate the efficacy and generalizability of integrating global protein representations with advanced deep learning architectures for reliable and scalable DBP prediction in diverse genomic contexts.

Samiul Based Shuvo, Taufiq Hasan

Automated analysis of lung sound auscultation is essential for monitoring respiratory health, especially in regions facing a shortage of skilled healthcare workers. While respiratory sound classification has been widely studied in adults, its ap plication in pediatric populations, particularly in children aged <6 years, remains an underexplored area. The developmental changes in pediatric lungs considerably alter the acoustic proper ties of respiratory sounds, necessitating specialized classification approaches tailored to this age group. To address this, we propose a multistage hybrid CNN-Transformer framework that combines CNN-extracted features with an attention-based architecture to classify pediatric respiratory diseases using scalogram images from both full recordings and individual breath events. Our model achieved an overall score of 0.9039 in binary event classifi cation and 0.8448 in multiclass event classification by employing class-wise focal loss to address data imbalance. At the recording level, the model attained scores of 0.720 for ternary and 0.571 for multiclass classification. These scores outperform the previous best models by 3.81% and 5.94%, respectively. This approach offers a promising solution for scalable pediatric respiratory disease diagnosis, especially in resource-limited settings.

Syed Samiul Alam, Samiul Based Shuvo, Shams Nafisa Ali et al.

Ocular Toxoplasmosis (OT), is a common eye infection caused by T. gondii that can cause vision problems. Diagnosis is typically done through a clinical examination and imaging, but these methods can be complicated and costly, requiring trained personnel. To address this issue, we have created a benchmark study that evaluates the effectiveness of existing pre-trained networks using transfer learning techniques to detect OT from fundus images. Furthermore, we have also analysed the performance of transfer-learning based segmentation networks to segment lesions in the images. This research seeks to provide a guide for future researchers looking to utilise DL techniques and develop a cheap, automated, easy-to-use, and accurate diagnostic method. We have performed in-depth analysis of different feature extraction techniques in order to find the most optimal one for OT classification and segmentation of lesions. For classification tasks, we have evaluated pre-trained models such as VGG16, MobileNetV2, InceptionV3, ResNet50, and DenseNet121 models. Among them, MobileNetV2 outperformed all other models in terms of Accuracy (Acc), Recall, and F1 Score outperforming the second-best model, InceptionV3 by 0.7% higher Acc. However, DenseNet121 achieved the best result in terms of Precision, which was 0.1% higher than MobileNetv2. For the segmentation task, this work has exploited U-Net architecture. In order to utilize transfer learning the encoder block of the traditional U-Net was replaced by MobileNetV2, InceptionV3, ResNet34, and VGG16 to evaluate different architectures moreover two different two different loss functions (Dice loss and Jaccard loss) were exploited in order to find the most optimal one. The MobileNetV2/U-Net outperformed ResNet34 by 0.5% and 2.1% in terms of Acc and Dice Score, respectively when Jaccard loss function is employed during the training.

Samiul Based Shuvo, Shams Nafisa Ali, Soham Irtiza Swapnil et al.

The alarmingly high mortality rate and increasing global prevalence of cardiovascular diseases 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 paper, 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. 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, with 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 the previous works using the same dataset by a considerable margin. 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 suitable for point of care CVD screening in low resource setups using memory constraint mobile devices.