As part of the drug repurposing process, it is imperative to predict the interactions between drugs and target proteins in an accurate and efficient manner. With the introduction of contrastive learning into drug-target prediction, the accuracy of drug repurposing will be further improved. However, a large part of DTI prediction methods based on deep learning either focus only on the structural features of proteins and drugs extracted using GNN or CNN, or focus only on their relational features extracted using heterogeneous graph neural networks on a DTI heterogeneous graph. Since the structural and relational features of proteins and drugs describe their attribute information from different perspectives, their combination can improve DTI prediction performance. We propose a relational similarity-based graph contrastive learning for DTI prediction (RSGCL-DTI), which combines the structural and relational features of drugs and proteins to enhance the accuracy of DTI predictions. In our proposed method, the inter-protein relational features and inter-drug relational features are extracted from the heterogeneous drug-protein interaction network through graph contrastive learning, respectively. The results demonstrate that combining the relational features obtained by graph contrastive learning with the structural ones extracted by D-MPNN and CNN enhances feature representation ability, thereby improving DTI prediction performance. Our proposed RSGCL-DTI outperforms eight SOTA baseline models on the four benchmark datasets, performs well on the imbalanced dataset, and also shows excellent generalization ability on unseen drug-protein pairs.

Drug-target interactions (DTIs) are a key part of drug development process and their accurate and efficient prediction can significantly boost development efficiency and reduce development time. Recent years have witnessed the rapid advancement of deep learning, resulting in an abundance of deep learning-based models for DTI prediction. However, most of these models used a single representation of drugs and proteins, making it difficult to comprehensively represent their characteristics. Multimodal data fusion can effectively compensate for the limitations of single-modal data. However, existing multimodal models for DTI prediction do not take into account both intra- and inter-modal interactions simultaneously, resulting in limited presentation capabilities of fused features and a reduction in DTI prediction accuracy. A hierarchical multimodal self-attention-based graph neural network for DTI prediction, called HMSA-DTI, is proposed to address multimodal feature fusion. Our proposed HMSA-DTI takes drug SMILES, drug molecular graphs, protein sequences and protein 2-mer sequences as inputs, and utilizes a hierarchical multimodal self-attention mechanism to achieve deep fusion of multimodal features of drugs and proteins, enabling the capture of intra- and inter-modal interactions between drugs and proteins. It is demonstrated that our proposed HMSA-DTI has significant advantages over other baseline methods on multiple evaluation metrics across five benchmark datasets.

BACKGROUND: The identification of drug side effects plays a critical role in drug repositioning and drug screening. While clinical experiments yield accurate and reliable information about drug-related side effects, they are costly and time-consuming. Computational models have emerged as a promising alternative to predict the frequency of drug-side effects. However, earlier research has primarily centered on extracting and utilizing representations of drugs, like molecular structure or interaction graphs, often neglecting the inherent biomedical semantics of drugs and side effects. RESULTS: To address the previously mentioned issue, we introduce a hybrid multi-modal fusion framework (HMMF) for predicting drug side effect frequencies. Considering the wealth of biological and chemical semantic information related to drugs and side effects, incorporating multi-modal information offers additional, complementary semantics. HMMF utilizes various encoders to understand molecular structures, biomedical textual representations, and attribute similarities of both drugs and side effects. It then models drug-side effect interactions using both coarse and fine-grained fusion strategies, effectively integrating these multi-modal features. CONCLUSIONS: HMMF exhibits the ability to successfully detect previously unrecognized potential side effects, demonstrating superior performance over existing state-of-the-art methods across various evaluation metrics, including root mean squared error and area under receiver operating characteristic curve, and shows remarkable performance in cold-start scenarios.

Accurate and effective drug-target interaction (DTI) prediction can greatly shorten the drug development lifecycle and reduce the cost of drug development. In the deep-learning-based paradigm for predicting DTI, robust drug and protein feature representations and their interaction features play a key role in improving the accuracy of DTI prediction. Additionally, the class imbalance problem and the overfitting problem in the drug-target dataset can also affect the prediction accuracy, and reducing the consumption of computational resources and speeding up the training process are also critical considerations. In this paper, we propose shared-weight-based MultiheadCrossAttention, a precise and concise attention mechanism that can establish the association between target and drug, making our models more accurate and faster. Then, we use the cross-attention mechanism to construct two models: MCANet and MCANet-B. In MCANet, the cross-attention mechanism is used to extract the interaction features between drugs and proteins for improving the feature representation ability of drugs and proteins, and the PolyLoss loss function is applied to alleviate the overfitting problem and the class imbalance problem in the drug-target dataset. In MCANet-B, the robustness of the model is improved by combining multiple MCANet models and prediction accuracy further increases. We train and evaluate our proposed methods on six public drug-target datasets and achieve state-of-the-art results. In comparison with other baselines, MCANet saves considerable computational resources while maintaining accuracy in the leading position; however, MCANet-B greatly improves prediction accuracy by combining multiple models while maintaining a balance between computational resource consumption and prediction accuracy.

Identifying gene regulatory networks (GRNs) at the resolution of single cells has long been a great challenge, and the advent of single-cell multi-omics data provides unprecedented opportunities to construct GRNs. Here, we propose a novel strategy to integrate omics datasets of single-cell ribonucleic acid sequencing and single-cell Assay for Transposase-Accessible Chromatin using sequencing, and using an unsupervised learning neural network to divide the samples with high copy number variation scores, which are used to infer the GRN in each gene block. Accuracy validation of proposed strategy shows that approximately 80% of transcription factors are directly associated with cancer, colorectal cancer, malignancy and disease by TRRUST; and most transcription factors are prone to produce multiple transcript variants and lead to tumorigenesis by RegNetwork database, respectively. The source code access are available at: https://github.com/Cuily-v/Colorectal_cancer.

With the rapid development of Internet of Things (IoT), massive sensor data are being generated by the sensors deployed everywhere at an unprecedented rate. As the number of Internet of Things devices is estimated to grow to 25 billion by 2021, when facing the explicit or implicit anomalies in the real-time sensor data collected from Internet of Things devices, it is necessary to develop an effective and efficient anomaly detection method for IoT devices. Recent advances in the edge computing have significant impacts on the solution of anomaly detection in IoT. In this study, an adaptive graph updating model is first presented, based on which a novel anomaly detection method for edge computing environment is then proposed. At the cloud center, the unknown patterns are classified by a deep leaning model, based on the classification results, the feature graphs are updated periodically, and the classification results are constantly transmitted to each edge node where a cache is employed to keep the newly emerging anomalies or normal patterns temporarily until the edge node receives a newly updated feature graph. Finally, a series of comparison experiments are conducted to demonstrate the effectiveness of the proposed anomaly detection method for edge computing. And the results show that the proposed method can detect the anomalies in the real-time sensor data efficiently and accurately. More than that, the proposed method performs well when there exist newly emerging patterns, no matter they are anomalous or normal.