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Biased random walk with restart for essential proteins prediction

Chinese Physics B 2022年第11期31卷 638-648页

作者： Pengli Lu Yuntian Chen Teng Zhang Yonggang Liao School of Computer and Communication Lanzhou University of TechnologyLanzhou 730050China China Mobile Communications Group Gansu Co. Ltd.Lanzhou 730070China

Predicting essential proteins is crucial for discovering the process of cellular organization and *** propose biased random walk with restart algorithm for essential proteins prediction,called ***,the common process of practice walk often sets the probability of particles transferring to adjacent nodes to be equal,neglecting the influence of the similarity structure on the transition *** address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location *** particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network ***,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with ***,when the biased random walk with restart process reaches steady state,the protein importance score is *** order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI *** results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition ***,compared with the contrast methods,the improvements of BRWR in terms of the ACC results range in 1.4%–5.7%,1.3%–11.9%,2.4%–8.8%,and 0.8%–14.2%,***,BRWR is effective and reasonable.

关键词： PPI network essential proteins random walk with restart gene expression

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iBole： A Hybrid Multi-Layer Architecture for Doctor Recommendation in Medical Social Networks

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Journal of Computer Science & Technology 2015年第5期30卷 1073-1081页

作者：宫继兵王立立孙胜涛彭思维 School of Information Science and Engineering Yanshan University Qinhuangdao 066004 China The Key Laboratory for Computer Virtual Technology and System Integration of Hebei Province Yanshan University Qinhuangdao 066004 China

In this paper, we try to systematically study how to perform doctor recommendation in medical social net- works （MSNs）. Specifically, employing a real-world medical dataset as the source in our work, we propose iBole, a novel hybrid multi-layer architecture, to solve this problem. First, we mine doctor-patient relationships/ties via a time-constraint probability factor graph model （TPFG）. Second, we extract network features for ranking nodes. Finally, we propose RWR- Model, a doctor recommendation model via the random walk with restart method. Our real-world experiments validate the effectiveness of the proposed methods. Experimental results show that we obtain good accuracy in mining doctor-patient relationships from the network, and the doctor recommendation performance is better than that of the baseline algorithms： traditional Ranking SVM （RSVM） and the individual doctor recommendation model （IDR-Model）. The results of our RWR-Model are more reasonable and satisfactory than those of the baseline approaches.

关键词： doctor recommendation architecture random walk with restart doctor-patient tie mining time-constraintprobability factor graph model medical social network

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Trinity： walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations

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Journal of Computer Science & Technology 2016年第3期31卷 577-594页

作者： Ming-Xin Gan Lily Sun Rui Jiang Department of Management Science and Engineering Donlinks School of Economics and Management University of Science and Technology Beijing Beijing 100083 China Department of Statistics University of California Berkeley Berkeley CA 94720 U.S.A. School of Systems Engineering University of Reading Reading RG6 6UR U.K. Department of Automation Tsinghua University Beijing 100084 China

The rapid evolution of the Internet has been appealing for effective recommender systems to pinpoint useful information from online resources. Although historical rating data has been widely used as the most important information in recommendation methods, recent advancements have been demonstrating the improvement in recommendation performance with the incorporation of tag information. Furthermore, the availability of tag annotations has been well addressed by such fruitful online social tagging applications as CiteULike, MovieLens and BibSonomy, which allow users to express their preferences, upload resources and assign their own tags. Nevertheless, most existing tag-aware recommendation approaches model relationships among users, objects and tags using a tripartite graph, and hence overlook relationships within the same types of nodes. To overcome this limitation, we propose a novel approach, Trinity, to integrate historical data and tag information towards personalised recommendation. Trinity constructs a three-layered object-user-tag network that considers not only interconnections between different types of nodes but also relationships within the same types of nodes. Based on this heterogeneous network, Trinity adopts a random walk with restart model to assign the strength of associations to candidate objects, thereby providing a means of prioritizing the objects for a query user. We validate our approach via a series of large-scale 10-fold cross-validation experiments and evaluate its performance using three comprehensive criteria. Results show that our method outperforms several existing methods, including supervised random walk with restart, simulation of resource allocating processes, and traditional collaborative filtering.

关键词： recommender system tag-aware recommendation random walk with restart heterogeneous network socialtag

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ASpediaFI:Functional Interaction Analysis of Alternative Splicing Events

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 466-482页

作者： Kyubin Lee Doyeong Yu Daejin Hyung Soo Young Cho Charny Park Bioinformatics Branch Research InstituteNational Cancer CenterGoyang 10408Republic of Korea

Alternative splicing(AS)regulates biological processes governing phenotypes and *** AS(DAS)gene test methods have been developed to investigate important exonic expression from high-throughput ***,the DAS events extracted using statistical tests are insufficient to delineate relevant biological *** this study,we developed a novel application,Alternative Splicing Encyclopedia:Functional Interaction(ASpediaFI),to systemically identify DAS events and co-regulated genes and *** establishes a heterogeneous interaction network of genes and their feature nodes(i.e.,AS events and pathways)connected by coexpression or pathway gene set ***,ASpediaFI explores the interaction network using the random walk with restart algorithm and interrogates the proximity from a query gene ***,ASpediaFI extracts significant AS events,genes,and *** evaluate the performance of our method,we simulated RNA sequencing(RNA-seq)datasets to consider various conditions of sequencing depth and sample *** performance was compared with that of other ***,we analyzed three public datasets of cancer patients or cell lines to evaluate how well ASpediaFI detects biologically relevant *** exhibits strong performance in both simulated and public *** integrative approach reveals that DAS events that recognize a global co-expression network and relevant pathways determine the functional importance of spliced genes in the *** is publicly available at https://***/packages/ASpediaFI.

关键词： Alternative splicing RNA-seq Heterogeneous interaction network random walk with restart Gene set enrichment analysis

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