A feature extraction method based on noise reduction for circRNA-miRNA interaction prediction combining multi-structure features in the association networks.

MOTIVATION: A large number of studies have shown that circular RNA (circRNA) affects biological processes by competitively binding miRNA, providing a new perspective for the diagnosis, and treatment of human diseases. Therefore, exploring the potential circRNA-miRNA interactions (CMIs) is an important and urgent task at present. Although some computational methods have been tried, their performance is limited by the incompleteness of feature extraction in sparse networks and the low computational efficiency of lengthy data. RESULTS: In this paper, we proposed JSNDCMI, which combines the multi-structure feature extraction framework and Denoising Autoencoder (DAE) to meet the challenge of CMI prediction in sparse networks. In detail, JSNDCMI integrates functional similarity and local topological structure similarity in the CMI network through the multi-structure feature extraction framework, then forces the neural network to learn the robust representation of features through DAE and finally uses the Gradient Boosting Decision Tree classifier to predict the potential CMIs. JSNDCMI produces the best performance in the 5-fold cross-validation of all data sets. In the case study, seven of the top 10 CMIs with the highest score were verified in PubMed. AVAILABILITY: The data and source code can be found at https://github.com/1axin/JSNDCMI.

BEROLECMI: a novel prediction method to infer circRNA-miRNA interaction from the role definition of molecular attributes and biological networks.

Circular RNA (CircRNA)-microRNA (miRNA) interaction (CMI) is an important model for the regulation of biological processes by non-coding RNA (ncRNA), which provides a new perspective for the study of human complex diseases. However, the existing CMI prediction models mainly rely on the nearest neighbor structure in the biological network, ignoring the molecular network topology, so it is difficult to improve the prediction performance. In this paper, we proposed a new CMI prediction method, BEROLECMI, which uses molecular sequence attributes, molecular self-similarity, and biological network topology to define the specific role feature representation for molecules to infer the new CMI. BEROLECMI effectively makes up for the lack of network topology in the CMI prediction model and achieves the highest prediction performance in three commonly used data sets. In the case study, 14 of the 15 pairs of unknown CMIs were correctly predicted.

MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules.

According to the expression of miRNA in pathological processes, miRNAs can be divided into oncogenes or tumor suppressors. Prediction of the regulation relations between miRNAs and small molecules (SMs) becomes a vital goal for miRNA-target therapy. But traditional biological approaches are laborious and expensive. Thus, there is an urgent need to develop a computational model. In this study, we proposed a computational model to predict whether the regulatory relationship between miRNAs and SMs is up-regulated or down-regulated. Specifically, we first use the Large-scale Information Network Embedding (LINE) algorithm to construct the node features from the self-similarity networks, then use the General Attributed Multiplex Heterogeneous Network Embedding (GATNE) algorithm to extract the topological information from the attribute network, and finally utilize the Light Gradient Boosting Machine (LightGBM) algorithm to predict the regulatory relationship between miRNAs and SMs. In the fivefold cross-validation experiment, the average accuracies of the proposed model on the SM2miR dataset reached 79.59% and 80.37% for up-regulation pairs and down-regulation pairs, respectively. In addition, we compared our model with another published model. Moreover, in the case study for 5-FU, 7 of 10 candidate miRNAs are confirmed by related literature. Therefore, we believe that our model can promote the research of miRNA-targeted therapy.

RBNE-CMI: An Efficient Method for Predicting circRNA-miRNA Interactions via Multiattribute Incomplete Heterogeneous Network Embedding.

Circular RNA (circRNA)-microRNA (miRNA) interaction (CMI) plays crucial roles in cellular regulation, offering promising perspectives for disease diagnosis and therapy. Therefore, it is necessary to employ computational methods for the rapid and cost-effective prediction of potential circRNA-miRNA interactions. However, the existing methods are limited by incomplete data; therefore, it is difficult to model molecules with different attributes on a large scale, which greatly hinders the efficiency and performance of prediction. In this study, we propose an effective method for predicting circRNA-miRNA interactions, called RBNE-CMI, and introduce a framework that can embed incomplete multiattribute CMI heterogeneous networks. By combining the proposed method, we integrate different data sets in the CMI prediction field into one incomplete network for modeling, achieving superior performance in 5-fold cross-validation. Moreover, in the prediction task based on complete data, the proposed method still achieves better performance than the known model. In addition, in the case study, we successfully predicted 18 of the 20 potential cancer biomarkers. The data and source code can be found at https://github.com/1axin/RBNE-CMI.

DeepMPF: deep learning framework for predicting drug-target interactions based on multi-modal representation with meta-path semantic analysis.

BACKGROUND: Drug-target interaction (DTI) prediction has become a crucial prerequisite in drug design and drug discovery. However, the traditional biological experiment is time-consuming and expensive, as there are abundant complex interactions present in the large size of genomic and chemical spaces. For alleviating this phenomenon, plenty of computational methods are conducted to effectively complement biological experiments and narrow the search spaces into a preferred candidate domain. Whereas, most of the previous approaches cannot fully consider association behavior semantic information based on several schemas to represent complex the structure of heterogeneous biological networks. Additionally, the prediction of DTI based on single modalities cannot satisfy the demand for prediction accuracy. METHODS: We propose a multi-modal representation framework of 'DeepMPF' based on meta-path semantic analysis, which effectively utilizes heterogeneous information to predict DTI. Specifically, we first construct protein-drug-disease heterogeneous networks composed of three entities. Then the feature information is obtained under three views, containing sequence modality, heterogeneous structure modality and similarity modality. We proposed six representative schemas of meta-path to preserve the high-order nonlinear structure and catch hidden structural information of the heterogeneous network. Finally, DeepMPF generates highly representative comprehensive feature descriptors and calculates the probability of interaction through joint learning. RESULTS: To evaluate the predictive performance of DeepMPF, comparison experiments are conducted on four gold datasets. Our method can obtain competitive performance in all datasets. We also explore the influence of the different feature embedding dimensions, learning strategies and classification methods. Meaningfully, the drug repositioning experiments on COVID-19 and HIV demonstrate DeepMPF can be applied to solve problems in reality and help drug discovery. The further analysis of molecular docking experiments enhances the credibility of the drug candidates predicted by DeepMPF. CONCLUSIONS: All the results demonstrate the effectively predictive capability of DeepMPF for drug-target interactions. It can be utilized as a useful tool to prescreen the most potential drug candidates for the protein. The web server of the DeepMPF predictor is freely available at http://120.77.11.78/DeepMPF/ , which can help relevant researchers to further study.

KS-CMI: A circRNA-miRNA interaction prediction method based on the signed graph neural network and denoising autoencoder.

Circular RNA (circRNA) plays an important role in the diagnosis, treatment, and prognosis of human diseases. The discovery of potential circRNA-miRNA interactions (CMI) is of guiding significance for subsequent biological experiments. Limited by the small amount of experimentally supported data and high randomness, existing models are difficult to accomplish the CMI prediction task based on real cases. In this paper, we propose KS-CMI, a novel method for effectively accomplishing CMI prediction in real cases. KS-CMI enriches the 'behavior relationships' of molecules by constructing circRNA-miRNA-cancer (CMCI) networks and extracts the behavior relationship attribute of molecules based on balance theory. Next, the denoising autoencoder (DAE) is used to enhance the feature representation of molecules. Finally, the CatBoost classifier was used for prediction. KS-CMI achieved the most reliable prediction results in real cases and achieved competitive performance in all datasets in the CMI prediction.

DeepCMI: a graph-based model for accurate prediction of circRNA-miRNA interactions with multiple information.

Recently, the role of competing endogenous RNAs in regulating gene expression through the interaction of microRNAs has been closely associated with the expression of circular RNAs (circRNAs) in various biological processes such as reproduction and apoptosis. While the number of confirmed circRNA-miRNA interactions (CMIs) continues to increase, the conventional in vitro approaches for discovery are expensive, labor intensive, and time consuming. Therefore, there is an urgent need for effective prediction of potential CMIs through appropriate data modeling and prediction based on known information. In this study, we proposed a novel model, called DeepCMI, that utilizes multi-source information on circRNA/miRNA to predict potential CMIs. Comprehensive evaluations on the CMI-9905 and CMI-9589 datasets demonstrated that DeepCMI successfully infers potential CMIs. Specifically, DeepCMI achieved AUC values of 90.54% and 94.8% on the CMI-9905 and CMI-9589 datasets, respectively. These results suggest that DeepCMI is an effective model for predicting potential CMIs and has the potential to significantly reduce the need for downstream in vitro studies. To facilitate the use of our trained model and data, we have constructed a computational platform, which is available at http://120.77.11.78/DeepCMI/. The source code and datasets used in this work are available at https://github.com/LiYuechao1998/DeepCMI.

LPIH2V: LncRNA-protein interactions prediction using HIN2Vec based on heterogeneous networks model.

LncRNA-protein interaction plays an important role in the development and treatment of many human diseases. As the experimental approaches to determine lncRNA-protein interactions are expensive and time-consuming, considering that there are few calculation methods, therefore, it is urgent to develop efficient and accurate methods to predict lncRNA-protein interactions. In this work, a model for heterogeneous network embedding based on meta-path, namely LPIH2V, is proposed. The heterogeneous network is composed of lncRNA similarity networks, protein similarity networks, and known lncRNA-protein interaction networks. The behavioral features are extracted in a heterogeneous network using the HIN2Vec method of network embedding. The results showed that LPIH2V obtains an AUC of 0.97 and ACC of 0.95 in the 5-fold cross-validation test. The model successfully showed superiority and good generalization ability. Compared to other models, LPIH2V not only extracts attribute characteristics by similarity, but also acquires behavior properties by meta-path wandering in heterogeneous networks. LPIH2V would be beneficial in forecasting interactions between lncRNA and protein.

An efficient circRNA-miRNA interaction prediction model by combining biological text mining and wavelet diffusion-based sparse network structure embedding.

MOTIVATION: Accumulating clinical evidence shows that circular RNA (circRNA) plays an important regulatory role in the occurrence and development of human diseases, which is expected to provide a new perspective for the diagnosis and treatment of related diseases. Using computational methods can provide high probability preselection for wet experiments to save resources. However, due to the lack of neighborhood structure in sparse biological networks, the model based on network embedding and graph embedding is difficult to achieve ideal results. RESULTS: In this paper, we propose BioDGW-CMI, which combines biological text mining and wavelet diffusion-based sparse network structure embedding to predict circRNA-miRNA interaction (CMI). In detail, BioDGW-CMI first uses the Bidirectional Encoder Representations from Transformers (BERT) for biological text mining to mine hidden features in RNA sequences, then constructs a CMI network, obtains the topological structure embedding of nodes in the network through heat wavelet diffusion patterns. Next, the Denoising autoencoder organically combines the structural features and Gaussian kernel similarity, finally, the feature is sent to lightGBM for training and prediction. BioDGW-CMI achieves the highest prediction performance in all three datasets in the field of CMI prediction. In the case study, all the 8 pairs of CMI based on circ-ITCH were successfully predicted. AVAILABILITY: The data and source code can be found at https://github.com/1axin/BioDGW-CMI-model.

BioDKG-DDI: predicting drug-drug interactions based on drug knowledge graph fusing biochemical information.

The way of co-administration of drugs is a sensible strategy for treating complex diseases efficiently. Because of existing massive unknown interactions among drugs, predicting potential adverse drug-drug interactions (DDIs) accurately is promotive to prevent unanticipated interactions, which may cause significant harm to patients. Currently, numerous computational studies are focusing on potential DDIs prediction on account of traditional experiments in wet lab being time-consuming, labor-consuming, costly and inaccurate. These approaches performed well; however, many approaches did not consider multi-scale features and have the limitation that they cannot predict interactions among novel drugs. In this paper, we proposed a model of BioDKG-DDI, which integrates multi-feature with biochemical information to predict potential DDIs through an attention machine with superior performance. Molecular structure features, representation of drug global association using drug knowledge graph (DKG) and drug functional similarity features are fused by attention machine and predicted through deep neural network. A novel negative selecting method is proposed to certify the robustness and stability of our method. Then, three datasets with different sizes are used to test BioDKG-DDI. Furthermore, the comparison experiments and case studies can demonstrate the reliability of our method. Upon our finding, BioDKG-DDI is a robust, yet simple method and can be used as a benefic supplement to the experimental process.

SGCNCMI: A New Model Combining Multi-Modal Information to Predict circRNA-Related miRNAs, Diseases and Genes.

Computational prediction of miRNAs, diseases, and genes associated with circRNAs has important implications for circRNA research, as well as provides a reference for wet experiments to save costs and time. In this study, SGCNCMI, a computational model combining multimodal information and graph convolutional neural networks, combines node similarity to form node information and then predicts associated nodes using GCN with a distributive contribution mechanism. The model can be used not only to predict the molecular level of circRNA-miRNA interactions but also to predict circRNA-cancer and circRNA-gene associations. The AUCs of circRNA-miRNA, circRNA-disease, and circRNA-gene associations in the five-fold cross-validation experiment of SGCNCMI is 89.42%, 84.18%, and 82.44%, respectively. SGCNCMI is one of the few models in this field and achieved the best results. In addition, in our case study, six of the top ten relationship pairs with the highest prediction scores were verified in PubMed.

KGDCMI: A New Approach for Predicting circRNA-miRNA Interactions From Multi-Source Information Extraction and Deep Learning.

Emerging evidence has revealed that circular RNA (circRNA) is widely distributed in mammalian cells and functions as microRNA (miRNA) sponges involved in transcriptional and posttranscriptional regulation of gene expression. Recognizing the circRNA-miRNA interaction provides a new perspective for the detection and treatment of human complex diseases. Compared with the traditional biological experimental methods used to predict the association of molecules, which are limited to the small-scale and are time-consuming and laborious, computing models can provide a basis for biological experiments at low cost. Considering that the proposed calculation model is limited, it is necessary to develop an effective computational method to predict the circRNA-miRNA interaction. This study thus proposed a novel computing method, named KGDCMI, to predict the interactions between circRNA and miRNA based on multi-source information extraction and fusion. The KGDCMI obtains RNA attribute information from sequence and similarity, capturing the behavior information in RNA association through a graph-embedding algorithm. Then, the obtained feature vector is extracted further by principal component analysis and sent to the deep neural network for information fusion and prediction. At last, KGDCMI obtains the prediction accuracy (area under the curve [AUC] = 89.30% and area under the precision-recall curve [AUPR] = 87.67%). Meanwhile, with the same dataset, KGDCMI is 2.37% and 3.08%, respectively, higher than the only existing model, and we conducted three groups of comparative experiments, obtaining the best classification strategy, feature extraction parameters, and dimensions. In addition, in the performed case study, 7 of the top 10 interaction pairs were confirmed in PubMed. These results suggest that KGDCMI is a feasible and useful method to predict the circRNA-miRNA interaction and can act as a reliable candidate for related RNA biological experiments.