A Highly Efficient Biomolecular Network Representation Model for Predicting Drug-Disease Associations

2020 ◽  
pp. 271-279
Author(s):  
Han-Jing Jiang ◽  
Zhu-Hong You ◽  
Lun Hu ◽  
Zhen-Hao Guo ◽  
Bo-Ya Ji ◽  
...  
Keyword(s):  
Highly Efficient ◽  
Network Representation ◽  
Representation Model ◽  
Biomolecular Network ◽  
Disease Associations

scholarly journals An effective drug-disease associations prediction model based on graphic representation learning over multi-biomolecular network

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Hanjing Jiang ◽  
Yabing Huang
Keyword(s):  
High Performance ◽  
Large Scale ◽  
Representation Learning ◽  
Biological Data ◽  
Graph Representation ◽  
Data Set ◽  
Validation Experiment ◽  
Biomolecular Network ◽  
Disease Associations ◽  
Drug Reposition

Abstract Background Drug-disease associations (DDAs) can provide important information for exploring the potential efficacy of drugs. However, up to now, there are still few DDAs verified by experiments. Previous evidence indicates that the combination of information would be conducive to the discovery of new DDAs. How to integrate different biological data sources and identify the most effective drugs for a certain disease based on drug-disease coupled mechanisms is still a challenging problem. Results In this paper, we proposed a novel computation model for DDA predictions based on graph representation learning over multi-biomolecular network (GRLMN). More specifically, we firstly constructed a large-scale molecular association network (MAN) by integrating the associations among drugs, diseases, proteins, miRNAs, and lncRNAs. Then, a graph embedding model was used to learn vector representations for all drugs and diseases in MAN. Finally, the combined features were fed to a random forest (RF) model to predict new DDAs. The proposed model was evaluated on the SCMFDD-S data set using five-fold cross-validation. Experiment results showed that GRLMN model was very accurate with the area under the ROC curve (AUC) of 87.9%, which outperformed all previous works in terms of both accuracy and AUC in benchmark dataset. To further verify the high performance of GRLMN, we carried out two case studies for two common diseases. As a result, in the ranking of drugs that were predicted to be related to certain diseases (such as kidney disease and fever), 15 of the top 20 drugs have been experimentally confirmed. Conclusions The experimental results show that our model has good performance in the prediction of DDA. GRLMN is an effective prioritization tool for screening the reliable DDAs for follow-up studies concerning their participation in drug reposition.

scholarly journals Inferring the Disease-Associated miRNAs Based on Network Representation Learning and Convolutional Neural Networks

2019 ◽  
Vol 20 (15) ◽  
pp. 3648 ◽  
Author(s):  
Xuan ◽  
Sun ◽  
Wang ◽  
Zhang ◽  
Pan
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Prediction Models ◽  
Prediction Method ◽  
Feature Space ◽  
Representation Learning ◽  
Superior Performance ◽  
Network Representation ◽  
Disease Associations ◽  
Low Dimensional

Identification of disease-associated miRNAs (disease miRNAs) are critical for understanding etiology and pathogenesis. Most previous methods focus on integrating similarities and associating information contained in heterogeneous miRNA-disease networks. However, these methods establish only shallow prediction models that fail to capture complex relationships among miRNA similarities, disease similarities, and miRNA-disease associations. We propose a prediction method on the basis of network representation learning and convolutional neural networks to predict disease miRNAs, called CNNMDA. CNNMDA deeply integrates the similarity information of miRNAs and diseases, miRNA-disease associations, and representations of miRNAs and diseases in low-dimensional feature space. The new framework based on deep learning was built to learn the original and global representation of a miRNA-disease pair. First, diverse biological premises about miRNAs and diseases were combined to construct the embedding layer in the left part of the framework, from a biological perspective. Second, the various connection edges in the miRNA-disease network, such as similarity and association connections, were dependent on each other. Therefore, it was necessary to learn the low-dimensional representations of the miRNA and disease nodes based on the entire network. The right part of the framework learnt the low-dimensional representation of each miRNA and disease node based on non-negative matrix factorization, and these representations were used to establish the corresponding embedding layer. Finally, the left and right embedding layers went through convolutional modules to deeply learn the complex and non-linear relationships among the similarities and associations between miRNAs and diseases. Experimental results based on cross validation indicated that CNNMDA yields superior performance compared to several state-of-the-art methods. Furthermore, case studies on lung, breast, and pancreatic neoplasms demonstrated the powerful ability of CNNMDA to discover potential disease miRNAs.

scholarly journals iMDA-BN: Identification of miRNA-Disease Associations based on the Biological Network and Graph Embedding Algorithm

2020 ◽  
Author(s):  
Kai Zheng ◽  
Zhu-Hong You ◽  
Lei Wang
Keyword(s):  
High Throughput ◽  
Biological Networks ◽  
Domain Knowledge ◽  
Biological Network ◽  
Representation Learning ◽  
Biological Properties ◽  
Disease Association ◽  
Sequence Information ◽  
Network Representation ◽  
Disease Associations

AbstractBenefiting from advances in high-throughput experimental techniques, important regulatory roles of miRNAs, lncRNAs, and proteins, as well as biological property information, are gradually being complemented. As the key data support to promote biomedical research, domain knowledge such as intermolecular relationships that are increasingly revealed by molecular genome-wide analysis is often used to guide the discovery of potential associations. However, the method of performing network representation learning from the perspective of the global biological network is scarce. These methods cover a very limited type of molecular associations and are therefore not suitable for more comprehensive analysis of molecular network representation information. In this study, we propose a computational model based on the Biological network for predicting potential associations between miRNAs and diseases called iMDA-BN. The iMDA-BN has three significant advantages: I) It uses a new method to describe disease and miRNA characteristics which analyzes node representation information for disease and miRNA from the perspective of biological networks. II) It can predict unproven associations even if miRNAs and diseases do not appear in the biological network. III) Accurate description of miRNA characteristics from biological properties based on high-throughput sequence information. The iMDA-BN predictor achieves an AUC of 0.9145 and an accuracy of 84.49% on the miRNA-disease association baseline dataset, and it can also achieve an AUC of 0.8765 and an accuracy of 80.96% when predicting unknown diseases and miRNAs in the biological network. Compared to existing miRNA-disease association prediction methods, iMDA-BN has higher accuracy and the advantage of predicting unknown associations. In addition, 45, 49, and 49 of the top 50 miRNA-disease associations with the highest predicted scores were confirmed in the case studies, respectively.

scholarly journals Fairness in Network Representation by Latent Structural Heterogeneity in Observational Data

2020 ◽  
Vol 34 (04) ◽  
pp. 3809-3816
Author(s):  
Xin Du ◽  
Yulong Pei ◽  
Wouter Duivesteijn ◽  
Mykola Pechenizkiy
Keyword(s):  
Machine Learning ◽  
Observational Data ◽  
Representation Learning ◽  
Structural Heterogeneity ◽  
Heterogeneous Distribution ◽  
Network Representation ◽  
Representation Model ◽  
Real World Datasets ◽  
Synthetic Datasets ◽  
Low Dimensional

While recent advances in machine learning put many focuses on fairness of algorithmic decision making, topics about fairness of representation, especially fairness of network representation, are still underexplored. Network representation learning learns a function mapping nodes to low-dimensional vectors. Structural properties, e.g. communities and roles, are preserved in the latent embedding space. In this paper, we argue that latent structural heterogeneity in the observational data could bias the classical network representation model. The unknown heterogeneous distribution across subgroups raises new challenges for fairness in machine learning. Pre-defined groups with sensitive attributes cannot properly tackle the potential unfairness of network representation. We propose a method which can automatically discover subgroups which are unfairly treated by the network representation model. The fairness measure we propose can evaluate complex targets with multi-degree interactions. We conduct randomly controlled experiments on synthetic datasets and verify our methods on real-world datasets. Both quantitative and quantitative results show that our method is effective to recover the fairness of network representations. Our research draws insight on how structural heterogeneity across subgroups restricted by attributes would affect the fairness of network representation learning.

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