Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,th...Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,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 probability.To address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity.The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure.Secondly,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with restart.Finally,when the biased random walk with restart process reaches steady state,the protein importance score is obtained.In order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI networks.The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance.Especially,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%,respectively.Therefore,BRWR is effective and reasonable.展开更多
Circular RNAs(circRNAs) play important roles in various biological processes, as essential non-coding RNAs that have effects on transcriptional and posttranscriptional gene expression regulation. Recently, many studie...Circular RNAs(circRNAs) play important roles in various biological processes, as essential non-coding RNAs that have effects on transcriptional and posttranscriptional gene expression regulation. Recently, many studies have shown that circRNAs can be regarded as micro RNA(miRNA) sponges, which are known to be associated with certain diseases. Therefore efficient computation methods are needed to explore miRNAcircRNA interactions, but only very few computational methods for predicting the associations between miRNAs and circRNAs exist. In this study, we adopt an improved random walk computational method, named KRWRMC, to express complicated associations between miRNAs and circRNAs. Our major contributions can be summed up in two points. First, in the conventional Random Walk Restart Heterogeneous(RWRH) algorithm, the computational method simply converts the circRNA/miRNA similarity network into the transition probability matrix;in contrast,we take the influence of the neighbor of the node in the network into account, which can suggest or stress some potential associations. Second, our proposed KRWRMC is the first computational model to calculate large numbers of miRNA-circRNA associations, which can be regarded as biomarkers to diagnose certain diseases and can thus help us to better understand complicated diseases. The reliability of KRWRMC has been verified by Leave One Out Cross Validation(LOOCV) and 10-fold cross validation, the results of which indicate that this method achieves excellent performance in predicting potential miRNA-circRNA associations.展开更多
查询推荐是一种帮助搜索引擎更好的理解用户检索需求的方法.基于查询的上下文片段训练词汇和查询之间的语义关系,同时结合查询和URL的点击图以及查询中的序列行为构建Term Query URL异构信息网络,采用重启动随机游走（Random Walk withR...查询推荐是一种帮助搜索引擎更好的理解用户检索需求的方法.基于查询的上下文片段训练词汇和查询之间的语义关系,同时结合查询和URL的点击图以及查询中的序列行为构建Term Query URL异构信息网络,采用重启动随机游走（Random Walk withRestart,RWR）进行查询推荐.综合利用语义信息和日志信息,提高了稀疏查询的推荐效果.基于概率语言模型构造查询的词汇向量,可以为新的查询进行查询推荐.在大规模商业搜索引擎查询日志上的实验表明本文方法相比传统的查询推荐方法性能提升约为3％～10％.展开更多
为充分利用文本内容的上下文信息,结合图模型及查询向量的构建方法,提出一种融合查询内容信息的个性化引文推荐方法。通过三种论文信息构建三层图模型,并在不同层上设置不同参数,调整节点向不同层次的跳转概率;利用word2vec技术构建的...为充分利用文本内容的上下文信息,结合图模型及查询向量的构建方法,提出一种融合查询内容信息的个性化引文推荐方法。通过三种论文信息构建三层图模型,并在不同层上设置不同参数,调整节点向不同层次的跳转概率;利用word2vec技术构建的查询向量,可以有效利用文本上下文内容信息,使相似的文章在距离上更加接近,进而对候选文章进行评分预测与论文推荐。在association of computational linguistics anthology network数据集上进行计算分析,相同查询下与原有的方法相比在recall@ N 上平均提高约7%,在NDCG@ N 上平均提高约11%。实验结果表明该方法可以使引文推荐的质量得到有效的提升,能够获得较好的推荐效果。展开更多
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11861045 and 62162040)。
文摘Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,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 probability.To address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity.The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure.Secondly,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with restart.Finally,when the biased random walk with restart process reaches steady state,the protein importance score is obtained.In order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI networks.The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance.Especially,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%,respectively.Therefore,BRWR is effective and reasonable.
基金supported by the National Natural Science Foundation of China (No. 61672334)the Fundamental Research Funds for the Central Universities (No. GK201901010)
文摘Circular RNAs(circRNAs) play important roles in various biological processes, as essential non-coding RNAs that have effects on transcriptional and posttranscriptional gene expression regulation. Recently, many studies have shown that circRNAs can be regarded as micro RNA(miRNA) sponges, which are known to be associated with certain diseases. Therefore efficient computation methods are needed to explore miRNAcircRNA interactions, but only very few computational methods for predicting the associations between miRNAs and circRNAs exist. In this study, we adopt an improved random walk computational method, named KRWRMC, to express complicated associations between miRNAs and circRNAs. Our major contributions can be summed up in two points. First, in the conventional Random Walk Restart Heterogeneous(RWRH) algorithm, the computational method simply converts the circRNA/miRNA similarity network into the transition probability matrix;in contrast,we take the influence of the neighbor of the node in the network into account, which can suggest or stress some potential associations. Second, our proposed KRWRMC is the first computational model to calculate large numbers of miRNA-circRNA associations, which can be regarded as biomarkers to diagnose certain diseases and can thus help us to better understand complicated diseases. The reliability of KRWRMC has been verified by Leave One Out Cross Validation(LOOCV) and 10-fold cross validation, the results of which indicate that this method achieves excellent performance in predicting potential miRNA-circRNA associations.
文摘查询推荐是一种帮助搜索引擎更好的理解用户检索需求的方法.基于查询的上下文片段训练词汇和查询之间的语义关系,同时结合查询和URL的点击图以及查询中的序列行为构建Term Query URL异构信息网络,采用重启动随机游走（Random Walk withRestart,RWR）进行查询推荐.综合利用语义信息和日志信息,提高了稀疏查询的推荐效果.基于概率语言模型构造查询的词汇向量,可以为新的查询进行查询推荐.在大规模商业搜索引擎查询日志上的实验表明本文方法相比传统的查询推荐方法性能提升约为3％～10％.
文摘为充分利用文本内容的上下文信息,结合图模型及查询向量的构建方法,提出一种融合查询内容信息的个性化引文推荐方法。通过三种论文信息构建三层图模型,并在不同层上设置不同参数,调整节点向不同层次的跳转概率;利用word2vec技术构建的查询向量,可以有效利用文本上下文内容信息,使相似的文章在距离上更加接近,进而对候选文章进行评分预测与论文推荐。在association of computational linguistics anthology network数据集上进行计算分析,相同查询下与原有的方法相比在recall@ N 上平均提高约7%,在NDCG@ N 上平均提高约11%。实验结果表明该方法可以使引文推荐的质量得到有效的提升,能够获得较好的推荐效果。
