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Background: Cancer survival prediction is vital in improving patients' prospects and recommending therapies. Understanding the molecular behavior of cancer can be enhanced through the integration of multi-omics data, including mRNA, miRNA, and DNA methylation data. In light of these multi-omics data, we proposed a graph attention network (GAT) model in this study to predict the survival of non-small cell lung cancer (NSCLC). Methods: The different omics data were obtained from The Cancer Genome Atlas (TCGA) and preprocessed and combined into a single dataset using the sample ID. We used the chi-square test to select the most significant features to be used in our model. We used the synthetic minority oversampling technique (SMOTE) to balance the dataset and the concordance index (C-index) to measure the performance of our model on different combinations of omics data. Results: Our model demonstrated superior performance, with the highest value of the C-index obtained when we used both mRNA and miRNA data. This demonstrates that the multi-omics approach could be effective in predicting survival. Further pathway analysis conducted with KEGG showed that our GAT model provided high weights to the features that are associated with the viral entry pathways, such as the Epstein–Barr virus and Influenza A pathways, which are involved in lung cancer development. From our findings, it can be observed that the proposed GAT model leads to a significantly improved prediction of survival by exploiting the strengths of multiple omics datasets and the findings from the enriched pathways. Our GAT model outperforms other state-of-the-art methods that are used for NSCLC prediction. Conclusions: In this study, we developed a new model for the survival prediction of NSCLC using the GAT based on multi-omics data. Our model showed outstanding predictive values, and the KEGG analysis of the selected significant features showed that they were implicated in pivotal biological processes underlying pathways such as Influenza A and the Epstein–Barr virus infection, which are linked to lung cancer progression. [ABSTRACT FROM AUTHOR]

The problem addressed in this study is the limitations of previous works that considered electrocardiogram (ECG) classification as a multiclass problem, despite many abnormalities being diagnosed simultaneously in real life, making it a multilabel classification problem. The aim of the study is to test the effectiveness of deep learning (DL)-based methods (Inception, MobileNet, LeNet, AlexNet, VGG16, and ResNet50) using three large 12-lead ECG datasets to overcome this limitation. The define-by-run technique is used to build the most efficient DL model using the tree-structured Parzen estimator (TPE) algorithm. Results show that the proposed methods achieve high accuracy and precision in classifying ECG abnormalities for large datasets, with the best results being 97.89% accuracy and 90.83% precision for the Ningbo dataset, classifying 42 classes for the Inception model; 96.53% accuracy and 85.67% precision for the PTB-XL dataset, classifying 24 classes for the Alex net model; and 95.02% accuracy and 70.71% precision for the Georgia dataset, classifying 23 classes for the Alex net model. The best results achieved for the optimum model that was proposed by the define-by-run technique were 97.33% accuracy and 97.71% precision for the Ningbo dataset, classifying 42 classes; 96.60% accuracy and 83.66% precision for the PTB-XL dataset, classifying 24 classes; and 94.32% accuracy and 66.97% precision for the Georgia dataset, classifying 23 classes. The proposed DL-based methods using the TPE algorithm provide accurate results for multilabel classification of ECG abnormalities, improving the diagnostic accuracy of heart conditions.

Medulloblastoma (MB) is a molecularly heterogeneous brain malignancy with large differences in clinical presentation. According to genomic studies, there are at least four distinct molecular subgroups of MB: sonic hedgehog (SHH), wingless/INT (WNT), Group 3, and Group 4. The treatment and outcomes depend on appropriate classification. It is difficult for the classification algorithms to identify these subgroups from an imbalanced MB genomic data set, where the distribution of samples among the MB subgroups may not be equal. To overcome this problem, we used singular value decomposition (SVD) and group lasso techniques to find DNA methylation probe features that maximize the separation between the different imbalanced MB subgroups. We used multinomial regression as a classification method to classify the four different molecular subgroups of MB using the reduced DNA methylation data. Coordinate descent is used to solve our loss function associated with the group lasso, which promotes sparsity. By using SVD, we were able to reduce the 321,174 probe features to just 200 features. Less than 40 features were successfully selected after applying the group lasso, which we then used as predictors for our classification models. Our proposed method achieved an average overall accuracy of 99% based on fivefold cross-validation technique. Our approach produces improved classification performance compared with the state-of-the-art methods for classifying MB molecular subgroups. [ABSTRACT FROM AUTHOR]

Palmprint identification has been conducted over the last two decades in many biometric systems. High-dimensional data with many uncorrelated and duplicated features remains difficult due to several computational complexity issues. This paper presents an interactive authentication approach based on deep learning and feature selection that supports Palmprint authentication. The proposed model has two stages of learning; the first stage is to transfer pre-trained VGG-16 of ImageNet to specific features based on the extraction model. The second stage involves the VGG-16 Palmprint feature extraction in the Siamese network to learn Palmprint similarity. The proposed model achieves robust and reliable end-to-end Palmprint authentication by extracting the convolutional features using VGG-16 Palmprint and the similarity of two input Palmprint using the Siamese network. The second stage uses the CASIA dataset to train and test the Siamese network. The suggested model outperforms comparable studies based on the deep learning approach achieving accuracy and EER of 91.8% and 0.082%, respectively, on the CASIA left-hand images and accuracy and EER of 91.7% and 0.084, respectively, on the CASIA right-hand images. [ABSTRACT FROM AUTHOR]

The convolutional neural network (CNN) is one of the main algorithms that is applied to deep transfer learning for classifying two essential types of liver lesions; Hemangioma and hepatocellular carcinoma (HCC). Ultrasound images, which are commonly available and have low cost and low risk compared to computerized tomography (CT) scan images, will be used as input for the model. A total of 350 ultrasound images belonging to 59 patients are used. The number of images with HCC is 202 and 148, respectively. These images were collected from ultrasound cases.info (28 Hemangiomas patients and 11 HCC patients), the department of radiology, the University of Washington (7 HCC patients), the Atlas of ultrasound Germany (3 HCC patients), and Radiopedia and others (10 HCC patients). The ultrasound images are divided into 225, 52, and 73 for training, validation, and testing. A data augmentation technique is used to enhance the validation performance. We proposed an approach based on ensembles of the best-selected deep transfer models from the on-the-shelf models: VGG16, VGG19, DenseNet, Inception, InceptionResNet, ResNet, and EfficientNet. After tuning both the feature extraction and the classification layers, the best models are selected. Validation accuracy is used for model tuning and selection. The accuracy, sensitivity, specificity and AUROC are used to evaluate the performance. The experiments are concluded in five stages. The first stage aims to evaluate the base model performance by training the on-the-shelf models. The best accuracy obtained in the first stage is 83.5%. In the second stage, we augmented the data and retrained the on-the-shelf models with the augmented data. The best accuracy we obtained in the second stage was 86.3%. In the third stage, we tuned the feature extraction layers of the on-the-shelf models. The best accuracy obtained in the third stage is 89%. In the fourth stage, we finetuned the classification layer and obtained an accuracy of 93% as the best accuracy. In the fifth stage, we applied the ensemble approach using the best three-performing models and obtained an accuracy, specificity, sensitivity, and AUROC of 94%, 93.7%, 95.1%, and 0.944, respectively. [ABSTRACT FROM AUTHOR]

Plasmodium falciparum is a parasitic protozoan that can cause malaria, which is a deadly disease. Therefore, the accurate identification of malaria parasite mitochondrial proteins is essential for understanding their functions and identifying novel drug targets. For classifying protein sequences, several adaptive statistical techniques have been devised. Despite significant gains, prediction performance is still constrained by the lack of appropriate feature descriptors and learning strategies in current systems. Moreover, good ground truth data is important for Artificial Intelligence (AI)-based models but there is a lack of that data in the literature. Therefore, in this work, we propose a novel hybrid network that combines 1D Convolutional Neural Network (CNN) and Bidirectional Gated Recurrent Unit (BGRU) to classify the malaria parasite mitochondrial proteins. Furthermore, we curate a sequential data that are collected from National Center for Biotechnology Information (NCBI) and UniProtKB/Swiss-Prot proteins databanks to prepare a dataset that can be used by the research community for AI-based algorithms evaluation. We obtain 4204 cases after preprocessing of the collected data and denote this set of proteins as PF4204. Finally, we conduct an ablation study on several conventional and deep models using PF4204 and the benchmark PF2095 datasets. The proposed model 'CNN-BGRU' obtains the accuracy values of 0.9096 and 0.9857 on PF4204 and PF2095 datasets, respectively. In addition, the CNN-BGRU is compared with state-of-the-arts, where the results illustrate that it can extract robust features and identify proteins accurately. [ABSTRACT FROM AUTHOR]

It is important to determine early on which patients require ICU admissions in managing COVID-19 especially when medical resources are limited. Delay in ICU admissions is associated with negative outcomes such as mortality and cost. Therefore, early identification of patients with a high risk of respiratory failure can prevent complications, enhance risk stratification, and improve the outcomes of severely-ill hospitalized patients. In this paper, we develop a model that uses the characteristics and information collected at the time of patients' admissions and during their early period of hospitalization to accurately predict whether they will need ICU admissions. We use the data explained and organized in a window-based manner by the Sírio-Libanês hospital team (published on Kaggle). Preprocessing is applied, including imputation, cleaning, and feature selection. In the cleaning process, we remove zero-variance, redundant, and/or highly correlated (measured by the Pearson correlation coefficient) features. We use Extreme Gradient Boosting (XGBoost) with early stopping as a predictor in our developed model. We run the experiment in four stages starting from the features of Window 1 in Stage 1 and then incrementally add the features of Windows 2-4 in Stages 2-4 respectively. We achieveAUCs of 0.73, 0.92, 0.95, and 0.97 in those four stages. [ABSTRACT FROM AUTHOR]