Classical and Deep Learning Paradigms for Detection and Validation of Key Genes of Risky Outcomes of HCV

Using deep DenseNet with cyclical learning rate to classify leukocytes for leukemia identification

Background

The examination, counting, and classification of white blood cells (WBCs), also known as leukocytes, are essential processes in the diagnosis of many disorders, including leukemia, a kind of blood cancer characterized by the uncontrolled proliferation of carcinogenic leukocytes in the marrow of the bone. Blood smears can be chemically or microscopically studied to better understand hematological diseases and blood disorders. Detecting, identifying, and categorizing the many blood cell types are essential for disease diagnosis and therapy planning. A theoretical and practical issue. However, methods based on deep learning (DL) have greatly helped blood cell classification.

Materials and Methods

Images of blood cells in a microscopic smear were collected from GitHub, a public source that uses the MIT license. An end-to-end computer-aided diagnosis (CAD) system for leukocytes has been created and implemented as part of this study. The introduced system comprises image preprocessing and enhancement, image segmentation, feature extraction and selection, and WBC classification. By combining the DenseNet-161 and the cyclical learning rate (CLR), we contribute an approach that speeds up hyperparameter optimization. We also offer the one-cycle technique to rapidly optimize all hyperparameters of DL models to boost training performance.

Results

The dataset has been split into two sets: approximately 80% of the data (9,966 images) for the training set and 20% (2,487 images) for the validation set. The validation set has 623, 620, 620, and 624 eosinophil, lymphocyte, monocyte, and neutrophil images, whereas the training set has 2,497, 2,483, 2,487, and 2,499, respectively. The suggested method has 100% accuracy on the training set of images and 99.8% accuracy on the testing set.

Conclusion

Using a combination of the recently developed pretrained convolutional neural network (CNN), DenseNet, and the one fit cycle policy, this study describes a technique of training for the classification of WBCs for leukemia detection. The proposed method is more accurate compared to the state of the art.

Combining docking, molecular dynamics simulations, AD-MET pharmacokinetics properties, and MMGBSA calculations to create specialized protocols for running effective virtual screening campaigns on the autoimmune disorder and SARS-CoV-2 main protease

The development of novel medicines to treat autoimmune diseases and SARS-CoV-2 main protease (Mpro), a virus that can cause both acute and chronic illnesses, is an ongoing necessity for the global community. The primary objective of this research is to use CoMFA methods to evaluate the quantitative structure-activity relationship (QSAR) of a select group of chemicals concerning autoimmune illnesses. By performing a molecular docking analysis, we may verify previously observed tendencies and gain insight into how receptors and ligands interact. The results of the 3D QSAR models are quite satisfactory and give significant statistical results: Q_loo∧2 = 0.5548, Q_lto∧2 = 0.5278, R∧2 = 0.9990, F-test = 3,101.141, SDEC = 0.017 for the CoMFA FFDSEL, and Q_loo∧2 = 0.7033, Q_lto∧2 = 0.6827, Q_lmo∧2 = 0.6305, R∧2 = 0.9984, F-test = 1994.0374, SDEC = 0.0216 for CoMFA UVEPLS. The success of these two models in exceeding the external validation criteria used and adhering to the Tropsha and Glorbaikh criteria's upper and lower bounds can be noted. We report the docking simulation of the compounds as an inhibitor of the SARS-CoV-2 Mpro and an autoimmune disorder in this context. For a few chosen autoimmune disorder receptors (protein tyrosine phosphatase, nonreceptor type 22 (lymphoid) isoform 1 (PTPN22), type 1 diabetes, rheumatoid arthritis, and SARS-CoV-2 Mpro, the optimal binding characteristics of the compounds were described. According to their potential for effectiveness, the studied compounds were ranked, and those that demonstrated higher molecular docking scores than the reference drugs were suggested as potential new drug candidates for the treatment of autoimmune disease and SARS-CoV-2 Mpro. Additionally, the results of analyses of drug similarity, ADME (Absorption, Distribution, Metabolism, and Excretion), and toxicity were used to screen the best-docked compounds in which compound 4 scaled through. Finally, molecular dynamics (MD) simulation was used to verify compound 4's stability in the complex with the chosen autoimmune diseases and SARS-CoV-2 Mpro protein. This compound showed a steady trajectory and molecular characteristics with a predictable pattern of interactions. These findings suggest that compound 4 may hold potential as a therapy for autoimmune diseases and SARS-CoV-2 Mpro.

Detection and Classification of Histopathological Breast Images Using a Fusion of CNN Frameworks

Breast cancer is responsible for the deaths of thousands of women each year. The diagnosis of breast cancer (BC) frequently makes the use of several imaging techniques. On the other hand, incorrect identification might occasionally result in unnecessary therapy and diagnosis. Therefore, the accurate identification of breast cancer can save a significant number of patients from undergoing unnecessary surgery and biopsy procedures. As a result of recent developments in the field, the performance of deep learning systems used for medical image processing has showed significant benefits. Deep learning (DL) models have found widespread use for the aim of extracting important features from histopathologic BC images. This has helped to improve the classification performance and has assisted in the automation of the process. In recent times, both convolutional neural networks (CNNs) and hybrid models of deep learning-based approaches have demonstrated impressive performance. In this research, three different types of CNN models are proposed: a straightforward CNN model (1-CNN), a fusion CNN model (2-CNN), and a three CNN model (3-CNN). The findings of the experiment demonstrate that the techniques based on the 3-CNN algorithm performed the best in terms of accuracy (90.10%), recall (89.90%), precision (89.80%), and f1-Score (89.90%). In conclusion, the CNN-based approaches that have been developed are contrasted with more modern machine learning and deep learning models. The application of CNN-based methods has resulted in a significant increase in the accuracy of the BC classification.

Clinical Decision Support Framework for Segmentation and Classification of Brain Tumor MRIs Using a U-Net and DCNN Cascaded Learning Algorithm

Brain tumors (BTs) are an uncommon but fatal kind of cancer. Therefore, the development of computer-aided diagnosis (CAD) systems for classifying brain tumors in magnetic resonance imaging (MRI) has been the subject of many research papers so far. However, research in this sector is still in its early stage. The ultimate goal of this research is to develop a lightweight effective implementation of the U-Net deep network for use in performing exact real-time segmentation. Moreover, a simplified deep convolutional neural network (DCNN) architecture for the BT classification is presented for automatic feature extraction and classification of the segmented regions of interest (ROIs). Five convolutional layers, rectified linear unit, normalization, and max-pooling layers make up the DCNN's proposed simplified architecture. The introduced method was verified on multimodal brain tumor segmentation (BRATS 2015) datasets. Our experimental results on BRATS 2015 acquired Dice similarity coefficient (DSC) scores, sensitivity, and classification accuracy of 88.8%, 89.4%, and 88.6% for high-grade gliomas. When it comes to segmenting BRATS 2015 BT images, the performance of our proposed CAD framework is on par with existing state-of-the-art methods. However, the accuracy achieved in this study for the classification of BT images has improved upon the accuracy reported in prior studies. Image classification accuracy for BRATS 2015 BT has been improved from 88% to 88.6%.

A Hybrid Deep Transfer Learning of CNN-Based LR-PCA for Breast Lesion Diagnosis via Medical Breast Mammograms

One of the most promising research areas in the healthcare industry and the scientific community is focusing on the AI-based applications for real medical challenges such as the building of computer-aided diagnosis (CAD) systems for breast cancer. Transfer learning is one of the recent emerging AI-based techniques that allow rapid learning progress and improve medical imaging diagnosis performance. Although deep learning classification for breast cancer has been widely covered, certain obstacles still remain to investigate the independency among the extracted high-level deep features. This work tackles two challenges that still exist when designing effective CAD systems for breast lesion classification from mammograms. The first challenge is to enrich the input information of the deep learning models by generating pseudo-colored images instead of only using the input original grayscale images. To achieve this goal two different image preprocessing techniques are parallel used: contrast-limited adaptive histogram equalization (CLAHE) and Pixel-wise intensity adjustment. The original image is preserved in the first channel, while the other two channels receive the processed images, respectively. The generated three-channel pseudo-colored images are fed directly into the input layer of the backbone CNNs to generate more powerful high-level deep features. The second challenge is to overcome the multicollinearity problem that occurs among the high correlated deep features generated from deep learning models. A new hybrid processing technique based on Logistic Regression (LR) as well as Principal Components Analysis (PCA) is presented and called LR-PCA. Such a process helps to select the significant principal components (PCs) to further use them for the classification purpose. The proposed CAD system has been examined using two different public benchmark datasets which are INbreast and mini-MAIS. The proposed CAD system could achieve the highest performance accuracies of 98.60% and 98.80% using INbreast and mini-MAIS datasets, respectively. Such a CAD system seems to be useful and reliable for breast cancer diagnosis.