Internet-scale open source software （OSS） pro- duction in various communities generates abundant reusable resources for software developers. However, finding the de- sired and mature software with keyword queries fr...Internet-scale open source software （OSS） pro- duction in various communities generates abundant reusable resources for software developers. However, finding the de- sired and mature software with keyword queries from a considerable number of candidates, especially for the fresher, is a significant challenge because current search services often fail to understand the semantics of user queries. In this paper, we construct a software term database （STDB） by analyzing tagging data in Stack Overflow and propose a correlationbased software search （CBSS） approach that performs correlation retrieval based on the term relevance obtained from STDB. In addition, we design a novel ranking method to optimize the initial retrieval result. We explore four research questions in four experiments, respectively, to evaluate the effectiveness of the STDB and investigate the performance of the CBSS. The experiment results show that the proposed CBSS can effectively respond to keyword-based software searches and significantly outperforms other existing search services at finding mature software.展开更多
Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathw...Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehen- sive understanding of the molecular mechanisms underlying complex diseases. Extensive studies uti- lizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available path- way-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are dis- cussed. This review will provide a useful guide to dissect complex diseases.展开更多
基金The research was supported by the National Natural Science Foundation of China （Grant Nos. 61432020, 61303064, 61472430, 61502512） and National Grand R＆D Plan （2016YFB 1000805）.
文摘Internet-scale open source software （OSS） pro- duction in various communities generates abundant reusable resources for software developers. However, finding the de- sired and mature software with keyword queries from a considerable number of candidates, especially for the fresher, is a significant challenge because current search services often fail to understand the semantics of user queries. In this paper, we construct a software term database （STDB） by analyzing tagging data in Stack Overflow and propose a correlationbased software search （CBSS） approach that performs correlation retrieval based on the term relevance obtained from STDB. In addition, we design a novel ranking method to optimize the initial retrieval result. We explore four research questions in four experiments, respectively, to evaluate the effectiveness of the STDB and investigate the performance of the CBSS. The experiment results show that the proposed CBSS can effectively respond to keyword-based software searches and significantly outperforms other existing search services at finding mature software.
基金supported in part by the National Natural Science Foundation of China (Grant Nos. 31071166 and 81373085)Natural Science Foundation of Guangdong Province (Grant No. 8251008901000007)+2 种基金Science and Technology Planning Project of Guangdong Province (Grant No. 2009A030301004)Dongguan City Science and Technology Project (Grant No. 2011108101015)the Guangdong Medical College Funds (Grant Nos. JB1214, XG1001, XZ1105 and STIF201122)
文摘Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehen- sive understanding of the molecular mechanisms underlying complex diseases. Extensive studies uti- lizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available path- way-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are dis- cussed. This review will provide a useful guide to dissect complex diseases.
