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Protein hydroxylation is one type of post-translational modifications (PTMs) playing critical roles in human diseases. It is known that protein sequence contains many uncharacterized residues of proline and lysine. The question that needs to be answered is: which residue can be hydroxylated, and which one cannot. The answer will not only help understand the mechanism of hydroxylation but can also benefit the development of new drugs. In this paper, we proposed a novel approach for predicting hydroxylation using a hybrid deep learning model integrating the convolutional neural network (CNN) and long short-term memory network (LSTM). We employed a pseudo amino acid composition (PseAAC) method to construct valid benchmark datasets based on a sliding window strategy and used the position-specific scoring matrix (PSSM) to represent samples as inputs to the deep learning model. In addition, we compared our method with popular predictors including CNN, iHyd-PseAAC, and iHyd-PseCp. The results for 5-fold cross-validations all demonstrated that our method significantly outperforms the other methods in prediction accuracy.

In recent years, with the application of Internet of Things (IoT) and cloud technology in smart industrialization, Industrial Internet of Things (IIoT) has become an emerging hot topic. The increasing amount of data and device numbers in IIoT poses significant challenges to its security issues, making anomaly detection particularly important. Existing methods for anomaly detection in the IIoT often fall short when dealing with data imbalance, and the huge amount of IIoT data makes feature selection challenging and computationally intensive. In this paper, we propose an optimal deep learning model for anomaly detection in IIoT. Firstly, by setting different thresholds of eXtreme Gradient Boosting (XGBoost) for feature selection, features with importance above the given threshold are retained, while those below are ignored. Different thresholds yield different numbers of features. This approach not only secures effective features but also reduces the feature dimensionality, thereby decreasing the consumption of computational resources. Secondly, an optimized loss function is designed to study its impact on model performance in terms of handling imbalanced data, highly similar categories, and model training. We select the optimal threshold and loss function, which are part of our optimal model, by comparing metrics such as accuracy, precision, recall, False Alarm Rate (FAR), Area Under the Receiver Operating Characteristic Curve (AUC-ROC), and Area Under the Precision–Recall Curve (AUC-PR) values. Finally, combining the optimal threshold and loss function, we propose a model named MIX_LSTM for anomaly detection in IIoT. Experiments are conducted using the UNSW-NB15 and NSL-KDD datasets. The proposed MIX_LSTM model can achieve 0.084 FAR, 0.984 AUC-ROC, and 0.988 AUC-PR values in the binary anomaly detection experiment on the UNSW-NB15 dataset. In the NSL-KDD dataset, it can achieve 0.028 FAR, 0.967 AUC-ROC, and 0.962 AUC-PR values. By comparing the evaluation indicators, the model shows good performance in detecting abnormal attacks in the Industrial Internet of Things compared with traditional deep learning models, machine learning models and existing technologies. [ABSTRACT FROM AUTHOR]

Data categorization is a top concern in medical data to predict and detect illnesses; thus, it is applied in modern healthcare informatics. In modern informatics, machine learning and deep learning models have enjoyed great attention for categorizing medical data and improving illness detection. However, the existing techniques, such as features with high dimensionality, computational complexity, and long-term execution duration, raise fundamental problems. This study presents a novel classification model employing metaheuristic methods to maximize efficient positives on Chronic Kidney Disease diagnosis. The medical data is initially massively pre-processed, where the data is purified with various mechanisms, including missing values resolution, data transformation, and the employment of normalization procedures. The focus of such processes is to leverage the handling of the missing values and prepare the data for deep analysis. We adopt the Binary Grey Wolf Optimization method, a reliable subset selection feature using metaheuristics. This operation is aimed at improving illness prediction accuracy. In the classification step, the model adopts the Extreme Learning Machine with hidden nodes through data optimization to predict the presence of CKD. The complete classifier evaluation employs established measures, including recall, specificity, kappa, F-score, and accuracy, in addition to the feature selection. Data related to the study show that the proposed approach records high levels of accuracy, which is better than the existing models. [ABSTRACT FROM AUTHOR]

With the emergence of blockchain technology, the cryptocurrency market has experienced significant growth in recent years, simultaneously fostering environments conducive to cybercrimes such as phishing scams. Phishing scams on blockchain platforms like Ethereum have become a grave economic threat. Consequently, there is a pressing demand for effective detection mechanisms for these phishing activities to establish a secure financial transaction environment. However, existing methods typically utilize only the most recent transaction record when constructing features, resulting in the loss of vast amounts of transaction data and failing to adequately reflect the characteristics of nodes. Addressing this need, this study introduces a multiscale feature fusion approach integrated with a graph convolutional network model to detect phishing scams on Ethereum. A node basic feature set comprising 12 features is initially designed based on the Ethereum transaction dataset in the basic feature module. Subsequently, in the edge embedding representation module, all transaction times and amounts between two nodes are sorted, and a gate recurrent unit (GRU) neural network is employed to capture the temporal features within this transaction sequence, generating a fixed-length edge embedding representation from variable-length input. In the time trading feature module, attention weights are allocated to all embedding representations surrounding a node, aggregating the edge embedding representations and structural relationships into the node. Finally, combining basic and time trading features of the node, graph convolutional networks (GCNs), SAGEConv, and graph attention networks (GATs) are utilized to classify phishing nodes. The performance of these three graph convolution-based deep learning models is validated on a real Ethereum phishing scam dataset, demonstrating commendable efficiency. Among these, SAGEConv achieves an F1-score of 0.958, an AUC-ROC value of 0.956, and an AUC-PR value of 0.949, outperforming existing methods and baseline models. [ABSTRACT FROM AUTHOR]

Artificial intelligence plays an essential role in diagnosing lung cancer. Lung cancer is notoriously difficult to diagnose until it has progressed to a late stage, making it a leading cause of cancer-related mortality. Lung cancer is fatal if not treated early, making this a significant issue. Initial diagnosis of malignant nodules is often made using chest radiography (X-ray) and computed tomography (CT) scans; nevertheless, the possibility of benign nodules leads to wrong choices. In their first phases, benign and malignant nodules seem very similar. Additionally, radiologists have a hard time viewing and categorizing lung abnormalities. Lung cancer screenings performed by radiologists are often performed with the use of computer-aided diagnostic technologies. Computer scientists have presented many methods for identifying lung cancer in recent years. Low-quality images compromise the segmentation process, rendering traditional lung cancer prediction algorithms inaccurate. This article suggests a highly effective strategy for identifying and categorizing lung cancer. Noise in the pictures was reduced using a weighted filter, and the improved Gray Wolf Optimization method was performed before segmentation with watershed modification and dilation operations. We used InceptionNet-V3 to classify lung cancer into three groups, and it performed well compared to prior studies: 98.96% accuracy, 94.74% specificity, as well as 100% sensitivity. [ABSTRACT FROM AUTHOR]

Deep learning technology is changing the landscape of cybersecurity research, especially the study of large amounts of data. With the rapid growth in the number of malware, developing of an efficient and reliable method for classifying malware has become one of the research priorities. In this paper, a new method, BIR-CNN, is proposed to classify of Android malware. It combines convolution neural network (CNN) with batch normalization and inception-residual (BIR) network modules by using 347-dim network traffic features. CNN combines inception-residual modules with a convolution layer that can enhance the learning ability of the model. Batch Normalization can speed up the training process and avoid over-fitting of the model. Finally, experiments are conducted on the publicly available network traffic dataset CICAndMal2017 and compared with three traditional machine learning algorithms and CNN. The accuracy of BIR-CNN is 99.73% in binary classification (2-classifier). Moreover, the BIR-CNN can classify malware by its category (4-classifier) and malicious family (35-classifier), with a classification accuracy of 99.53% and 94.38%, respectively. The experimental results show that the proposed model is an effective method for Android malware classification, especially in malware category and family classifier. [ABSTRACT FROM AUTHOR]

• A directed graph neural network-based method was developed for scRNA-seq analysis. • The proposed method could not only obtain the connection properties of the directed graph, but also expand the receptive field of the convolution operation. • The proposed model could achieve promising performance in gene imputation and cell clustering prediction. Single-cell RNA sequencing (scRNA-seq) data scale surges with high-throughput sequencing technology development. However, although single-cell data analysis is a powerful tool, various issues have been reported, such as sequencing sparsity and complex differential patterns in gene expression. Statistical or traditional machine learning methods are inefficient, and the accuracy needs to be improved. The methods based on deep learning can not directly process non-Euclidean spatial data, such as cell diagrams. In this study, we have developed graph autoencoders and graph attention network for scRNA-seq analysis based on a directed graph neural network named scDGAE. Directed graph neural networks cannot only retain the connection properties of the directed graph but also expand the receptive field of the convolution operation. Cosine similarity, median L1 distance, and root-mean-squared error are used to measure the gene imputation performance of different methods with scDGAE. Furthermore, adjusted mutual information, normalized mutual information, completeness score, and Silhouette coefficient score are used to measure the cell clustering performance of different methods with scDGAE. Experiment results show that the scDGAE model achieves promising performance in gene imputation and cell clustering prediction on four scRNA-seq data sets with gold-standard cell labels. Furthermore, it is a robust framework that can be applied to general scRNA-Seq analyses. [ABSTRACT FROM AUTHOR]