Asmaa Abbas

Identifying high-quality and easily accessible annotated samples poses a notable challenge in medical image analysis. Transfer learning techniques, leveraging pre-training data, offer a flexible solution to this issue. However, the impact of fine-tuning diminishes when the dataset exhibits an irregular distribution between classes. This paper introduces a novel deep convolutional neural network, named Curriculum Learning and Progressive Self-supervised Training (CURVETE). CURVETE addresses challenges related to limited samples, enhances model generalisability, and improves overall classification performance. It achieves this by employing a curriculum learning strategy based on the granularity of sample decomposition during the training of generic unlabelled samples. Moreover, CURVETE address the challenge of irregular class distribution by incorporating a class decomposition approach in the downstream task. The proposed method undergoes evaluation on three distinct medical image datasets: brain tumour, digital knee x-ray, and Mini-DDSM datasets. We investigate the classification performance using a generic self-supervised sample decomposition approach with and without the curriculum learning component in training the pretext task. Experimental results demonstrate that the CURVETE model achieves superior performance on test sets with an accuracy of 96.60% on the brain tumour dataset, 75.60% on the digital knee x-ray dataset, and 93.35% on the Mini-DDSM dataset using the baseline ResNet-50. Furthermore, with the baseline DenseNet-121, it achieved accuracies of 95.77%, 80.36%, and 93.22% on the brain tumour, digital knee x-ray, and Mini-DDSM datasets, respectively, outperforming other training strategies.

Curriculum learning strategies have been proven to be effective in various applications and have gained significant interest in the field of machine learning. It has the ability to improve the final model's performance and accelerate the training process. However, in the medical imaging domain, data irregularities can make the recognition task more challenging and usually result in misclassification between the different classes in the dataset. Class-decomposition approaches have shown promising results in solving such a problem by learning the boundaries within the classes of the data set. In this paper, we present a novel convolutional neural network (CNN) training method based on the curriculum learning strategy and the class decomposition approach, which we call CLOG-CD, to improve the performance of medical image classification. We evaluated our method on four different imbalanced medical image datasets, such as Chest X-ray (CXR), brain tumour, digital knee X-ray, and histopathology colorectal cancer (CRC). CLOG-CD utilises the learnt weights from the decomposition granularity of the classes, and the training is accomplished from descending to ascending order (i.e., anti-curriculum technique). We also investigated the classification performance of our proposed method based on different acceleration factors and pace function curricula. We used two pre-trained networks, ResNet-50 and DenseNet-121, as the backbone for CLOG-CD. The results with ResNet-50 show that CLOG-CD has the ability to improve classification performance with an accuracy of 96.08% for the CXR dataset, 96.91% for the brain tumour dataset, 79.76% for the digital knee X-ray, and 99.17% for the CRC dataset, compared to other training strategies. In addition, with DenseNet-121, CLOG-CD has achieved 94.86%, 94.63%, 76.19%, and 99.45% for CXR, brain tumour, digital knee X-ray, and CRC datasets, respectively

Background: Escherichia albertii is a newly identified enteropathogen that affects humans and birds. It is a Gram-negative bacterium frequently mistaken for E. coli. Objective: To isolate E. albertii from chicken feces, products, and patients with diarrhea to assess its role in gastroenteritis and inflammatory bowel disease (IBD), also to assess antimicrobial susceptibility of this pathogen, and to identify it genetically by PCR. Methodology: 225 random samples from Assiut Governorate were tested, representing (100) chicken feces, (50) chicken products and (75) human feces from patients with gastroenteritis and IBD. The fecal samples were cultured on Hektoen enteric agar and xylose lysine deoxycholate plates. Biochemical identification of E-albertii was done by sulfur-indole motility (SIM), Simmonsʼ citrate, urease test, triple-sugar iron (TSI), lysine iron and indole test. Genotypic detection of E. albertii was done by PCR for eae and mdh genes. The isolates were tested for antimicrobial susceptibility. Results: The prevalence of E. albertii was 21.7% by culture, 18.6 % by biochemical tests and 12.8 % by PCR. E. albertii was identified by PCR in 20% of chicken feces and 9% of human feces. No E. albertii was identified in chicken products. Out of 29 isolates, 65.5 %, 51.7% were resistant to tetracycline, nalidixic acid, respectively, while lower resistance rates were observed to other antibiotics. Conclusion: E. albertii could be isolated from chicken and human feces, but not from chicken products. High resistance rate was observed for tetracycline, and nalidixic acid. E. albertii culture should be interpreted carefully and confirmed by PCR.

Of the various tumour types, colorectal cancer and brain tumours are still considered among the most serious and deadly diseases in the world. Therefore, many researchers are interested in improving the accuracy and reliability of diagnostic medical machine learning models. In computer-aided diagnosis, self-supervised learning has been proven to be an effective solution when dealing with datasets with insufficient data annotations. However, medical image datasets often suffer from data irregularities, making the recognition task even more challenging. The class decomposition approach has provided a robust solution to such a challenging problem by simplifying the learning of class boundaries of a dataset. In this paper, we propose a robust self-supervised model, called XDecompo, to improve the transferability of features from the pretext task to the downstream task. XDecompo has been designed based on an affinity propagation-based class decomposition to effectively encourage learning of the class boundaries in the downstream task. XDecompo has an explainable component to highlight important pixels that contribute to classification and explain the effect of class decomposition on improving the speciality of extracted features. We also explore the generalisability of XDecompo in handling different medical datasets, such as histopathology for colorectal cancer and brain tumour images. The quantitative results demonstrate the robustness of XDecompo with high accuracy of 96.16% and 94.30% for CRC and brain tumour images, respectively. XDecompo has demonstrated its generalization capability and achieved high classification accuracy (both quantitatively and qualitatively) in different medical image datasets, compared with other models. Moreover, a post hoc explainable method has been used to validate the feature transferability, demonstrating highly accurate feature representations.

Due to the high availability of large-scale annotated image datasets, knowledge transfer from pretrained models showed outstanding performance in medical image classification. However, building a robust image classification model for datasets with data irregularity or imbalanced classes can be a very challenging task, especially in the medical imaging domain. In this article, we propose a novel deep convolutional neural network, which we called self-supervised super sample decomposition for transfer learning (4S-DT) model. The 4S-DT encourages a coarse-to-fine transfer learning from large-scale image recognition tasks to a specific chest X-ray image classification task using a generic self-supervised sample decomposition approach. Our main contribution is a novel self-supervised learning mechanism guided by a super sample decomposition of unlabeled chest X-ray images. 4S-DT helps in improving the robustness of knowledge transformation via a downstream learning strategy with a class-decomposition (CD) layer to simplify the local structure of the data. The 4S-DT can deal with any irregularities in the image dataset by investigating its class boundaries using a downstream CD mechanism. We used 50,000 unlabeled chest X-ray images to achieve our coarse-to-fine transfer learning with an application to COVID-19 detection, as an exemplar. The 4S-DT has achieved a high accuracy of 99.8% on the larger of the two datasets used in the experimental study and an accuracy of 97.54% on the smaller dataset, which was enriched by augmented images, out of which all real COVID-19 cases were detected.

Chest X-ray is the first imaging technique that plays an important role in the diagnosis of COVID-19 disease. Due to the high availability of large-scale annotated image datasets, great success has been achieved using convolutional neural networks (CNNs) for image recognition and classification. However, due to the limited availability of annotated medical images, the classification of medical images remains the biggest challenge in medical diagnosis. Thanks to transfer learning, an effective mechanism that can provide a promising solution by transferring knowledge from generic object recognition tasks to domain-specific tasks. In this paper, we validate and a deepCNN, called Decompose, Transfer, and Compose (DeTraC), for the classification of COVID-19 chest X-ray images.DeTraCcan deal with any irregularities in the image dataset by investigating its class boundaries using a class decomposition mechanism. The experimental results showed the capability ofDeTraCin the detection of COVID-19 cases from a comprehensive image dataset collected from several hospitals around the world. High accuracy of 93.1% (with a sensitivity of 100%) was achieved byDeTraCin the detection of COVID-19 X-ray images from normal, and severe acute respiratory syndrome cases.

Due to the high availability of large-scale annotated image datasets, paramount progress has been made in deep convolutional neural networks (CNNs) for image classification tasks. CNNs enable learning highly representative and hierarchical local image features directly from data. However, the availability of annotated data, especially in the medical imaging domain, remains the biggest challenge in the field. Transfer learning can provide a promising and effective solution by transferring knowledge from generic image recognition tasks to the medical image classification. However, due to irregularities in the dataset distribution, transfer learning usually fails to provide a robust solution. Class decomposition facilitates easier to learn class boundaries of a dataset, and consequently can deal with any irregularities in the data distribution. Motivated by this challenging problem, the paper presents Decompose, Transfer, and Compose (DeTraC) approach, a novel CNN architecture based on class decomposition to improve the performance of medical image classification using transfer learning and class decomposition approach. DeTraC enables learning at the subclass level that can be more separable with a prospect to faster convergence.We validated our proposed approach with three different cohorts of chest X-ray images, histological images of human colorectal cancer, and digital mammograms. We compared DeTraC with the state-of-the-art CNN models to demonstrate its high performance in terms of accuracy, sensitivity, and specificity.

Automated classification of tuberculosis in x-ray images is of an increasing interest to all researchers and physicians. Due to the high level of intensity inhomogeneity and variations, statistical machine-learning approaches usually fail to offer a generic solution to image classification. Convolution neural networks (CNNs) have demonstrated superior effectiveness in computer-aided diagnosis systems. Transfer learning can provide a powerful deep learning solutions to the limited availability of labelled images. In this paper we study the effect of knowledge transferred from a pre-trained ImageNet, in different ways via a pre-trained CNN model, to classify chest x-ray images as having manifestations of tuberculosis or as healthy. We evaluated and compared various models using the learning curve between training and validation set, and receiver operating characteristic (ROC) curve. Our experiments revealed that using fine-tuning technique outperformed both shallow-tuning and deep-tuning techniques and achieved 0.998 for the AUC, 0.999 for specificity, and 0.997 for sensitivity rate.