Biased random walk with restart for link prediction with graph embedding method

2021 ◽  
Vol 570 ◽  
pp. 125783
Author(s):  
Yinzuo Zhou ◽  
Chencheng Wu ◽  
Lulu Tan
2020 ◽  
Vol 17 ◽  
Author(s):  
Guiyang Zhang ◽  
Pan Wang ◽  
You Li ◽  
Guohua Huang

Abstract: The biomedical network is becoming a fundamental tool to represent sophisticated bio-systems, while random walk models on it are becoming a sharp sword to address such challenging issues as gene function annotation, drug target identification, and disease biomarker recognition. Recently, numerous random walk models have been proposed and applied to biomedical networks. Due to good performances, the random walk is increasingly attracting more and more attention from multiple communities. In this survey, we firstly introduced various random walk models, with emphasis on the Pag-eRank and the random walk with restart. We then summarized applications of the RW on the biomedical networks from the graph learning point of view, which mainly included node classification, link prediction, cluster/community detection, and learning representation of the node. We discussed briefly its limitation and existing issues also


2021 ◽  
Vol 12 ◽  
Author(s):  
Jia Qu ◽  
Chun-Chun Wang ◽  
Shu-Bin Cai ◽  
Wen-Di Zhao ◽  
Xiao-Long Cheng ◽  
...  

Numerous experiments have proved that microRNAs (miRNAs) could be used as diagnostic biomarkers for many complex diseases. Thus, it is conceivable that predicting the unobserved associations between miRNAs and diseases is extremely significant for the medical field. Here, based on heterogeneous networks built on the information of known miRNA–disease associations, miRNA function similarity, disease semantic similarity, and Gaussian interaction profile kernel similarity for miRNAs and diseases, we developed a computing model of biased random walk with restart on multilayer heterogeneous networks for miRNA–disease association prediction (BRWRMHMDA) through enforcing degree-based biased random walk with restart (BRWR). Assessment results reflected that an AUC of 0.8310 was gained in local leave-one-out cross-validation (LOOCV), which proved the calculation algorithm’s good performance. Besides, we carried out BRWRMHMDA to prioritize candidate miRNAs for esophageal neoplasms based on HMDD v2.0. We further prioritize candidate miRNAs for breast neoplasms based on HMDD v1.0. The local LOOCV results and performance analysis of the case study all showed that the proposed model has good and stable performance.


Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.


IEEE Access ◽  
2021 ◽  
Vol 9 ◽  
pp. 1454-1464
Author(s):  
Wei Dou ◽  
Weiyu Zhang ◽  
Ziqiang Weng ◽  
Zhongxiu Xia
Keyword(s):  

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