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Finding association rules of cis-regulatory elements involved in alternative splicing 发现参与选择性剪接的顺式调控元件的关联规则
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233383
Jihye Kim, Sihui Zhao, S. Heber
{"title":"Finding association rules of cis-regulatory elements involved in alternative splicing","authors":"Jihye Kim, Sihui Zhao, S. Heber","doi":"10.1145/1233341.1233383","DOIUrl":"https://doi.org/10.1145/1233341.1233383","url":null,"abstract":"Alternative splicing (AS) is a major mechanism to generate protein diversity. A single gene might generate hundreds or even thousands of different proteins. Recently, powerful large-scale AS profiling microarrays have been developed, but computational methods which investigate the regulation of AS are still lagging behind. Researchers have focused on finding cis-regulatory motifs in pre-mRNA sequences. However, most studies are searching for single motifs, while many splicing events seem to be regulated by a combination of splicing factors.\u0000 In this paper, we use association rule mining to discover cis-regulatory motifs that are responsible for distinct alternative splicing patterns in 10 mouse tissues. The inferred association rules indicate that alternative splicing pattern in different tissues might be explained by different motif combinations. Many of our discovered cis-regulatory motif candidates coincide with known splicing factor binding sites.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"97 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126890078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Retrieving information in topic maps: the case of TM4L 检索主题图中的信息:TM4L的情况
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233358
Dandan Wang, D. Dicheva, Christo Dichev, Jerry Akouala
{"title":"Retrieving information in topic maps: the case of TM4L","authors":"Dandan Wang, D. Dicheva, Christo Dichev, Jerry Akouala","doi":"10.1145/1233341.1233358","DOIUrl":"https://doi.org/10.1145/1233341.1233358","url":null,"abstract":"Recent approaches to enhancing the quality of Web searches are based on associating metadata with the resources on the Web. Various metadata standardization initiatives have been created, including Dublin Core, and more recently the Semantic Web standards. Topic Maps are a Semantic Web technology for semantic annotation of resources, involving topics, their associations, and their occurrences. We have created TM4L, an environment for building, maintaining, and browsing Topic Mapbased, ontology-aware e-learning repositories. However, in large topic maps it is often more convenient for the users to search for needed information by querying the topic map as opposed to browsing it. In this paper we discuss the design and implementation of a Query plug-in for the TM4L Editor. We propose a generic Topic Map Query-By-Example framework based on the Tolog query language. The goal is to provide an efficient, user-friendly interface where the user can specify search queries by filling in predefined query templates and perform the specified queries on the topic map.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123803073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
Clarifications and extensions to tactical waypoint graph algorithms for video games 澄清和扩展战术航路点图形算法的电子游戏
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233398
Dustin White
{"title":"Clarifications and extensions to tactical waypoint graph algorithms for video games","authors":"Dustin White","doi":"10.1145/1233341.1233398","DOIUrl":"https://doi.org/10.1145/1233341.1233398","url":null,"abstract":"This paper explores pathfinding in a video game environment using a waypoint graph, a common way of representing locations in the environment. I take algorithms created by Lars Liden on finding strategic positions for agents within a waypoint graph and extend these algorithms. I demonstrate how the extended algorithms are able to effectively calculate tactical ambush positions and pinch points for any number of agents. The extended algorithms are also able to work in an environment where the agent does not have complete knowledge of the waypoint graph.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128130999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Design and implementation of a command processor for high level human-robot interaction system 高级人机交互系统命令处理器的设计与实现
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233379
M. Sarkar, Abisoye Mudasiru, N. Sarkar
{"title":"Design and implementation of a command processor for high level human-robot interaction system","authors":"M. Sarkar, Abisoye Mudasiru, N. Sarkar","doi":"10.1145/1233341.1233379","DOIUrl":"https://doi.org/10.1145/1233341.1233379","url":null,"abstract":"This paper presents an innovative semi-autonomous human-robot interaction concept for people with severe disability and discusses a proof-of-concept prototype system. The user communicates with the robot through electromyographic (EMG) signals. However, unlike most EMG controlled robotic operations, here the user can issue high-level commands to the robot. This would allow people with severe disability to access robots that can help them in activities of daily living. This paper describes a high-level command processor that translates high-level commands issued by a disabled user to perform certain activities of daily living (ADL), into a sequence of lower level commands that are executable by a robot. The command processor is implemented using TXL (Tree Transformation Language).","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"118 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131725299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analysis goal expression language 分析目标表达语言
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233352
B. Belkhouche, S. Dekhane
{"title":"Analysis goal expression language","authors":"B. Belkhouche, S. Dekhane","doi":"10.1145/1233341.1233352","DOIUrl":"https://doi.org/10.1145/1233341.1233352","url":null,"abstract":"This paper presents the abstract representation of Goal Expression Language (GEL). GEL is a very simple language used to specify analysis goals for an object-oriented design. This language is close to natural language and hence the learning factor is very low. GEL is part of a formal framework designed for the specification and analysis of objectoriented designs (FSAF). GEL can be used to express analysis goals for the static and dynamic behavior analysis of the design. This paper describes the basic components of GEL, how and where they can be used and also provides examples for demonstration. This abstract representation is the first step towards the formal semantics of GEL","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"94 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125238478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigating new approaches to data collection, management and analysis for network intrusion detection 研究网络入侵检测数据收集、管理和分析的新方法
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233392
E. Joseph Derrick, R. Tibbs, Larry Lee Reynolds
{"title":"Investigating new approaches to data collection, management and analysis for network intrusion detection","authors":"E. Joseph Derrick, R. Tibbs, Larry Lee Reynolds","doi":"10.1145/1233341.1233392","DOIUrl":"https://doi.org/10.1145/1233341.1233392","url":null,"abstract":"Primary facets of network intrusion detection systems include the collection, management, and analysis of intrusion data. In this paper, we provide an overview of an ongoing project at Radford University to investigate new and innovative approaches in these critical areas. In particular, we discuss using small, low cost embedded Linux devices as mobile, highly configurable, and collaborative sensors for the collection of the data. Since the data can be in massive quantities and its collection burdensome to the operational network, we also present the use of a wireless network for the transmission of the data to a separate server or management application for analysis, effectively offloading the data from and reducing the burden on the operational network. Finally, effective techniques for analysis need to be identified that will reduce false positive and false negative determinations of intrusions. We introduce our work in data mining techniques which seeks to improve accuracy in analysis.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132932685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 19
Change propagations in the maintenance of kernel-based software with a study on Linux 基于内核的软件维护中的变更传播——以Linux为例
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233356
Liguo Yu, S. Ramaswamy
{"title":"Change propagations in the maintenance of kernel-based software with a study on Linux","authors":"Liguo Yu, S. Ramaswamy","doi":"10.1145/1233341.1233356","DOIUrl":"https://doi.org/10.1145/1233341.1233356","url":null,"abstract":"As a software system evolves to accommodate new features and repair bugs, changes are needed. Software components are interdependent, changes made to one component can require changes to be propagated to other components. Change propagation brings potential challenges for software maintenance. In this paper, we divide change propagations into four categories in kernel-based software. Different categories of change propagation have different effects on kernel maintenance. We use product version history to mine change propagations rules and apply the categorization to Linux operating system. Our study provides a framework for measuring, evaluating, and predicting change propagations in kernel-based software, which includes most operating systems, database management systems, game systems, and software product lines.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124224412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Higher-order functional programming and wildcards in java java中的高阶函数式编程和通配符
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233350
Nattawut Sridranop, R. Stansifer
{"title":"Higher-order functional programming and wildcards in java","authors":"Nattawut Sridranop, R. Stansifer","doi":"10.1145/1233341.1233350","DOIUrl":"https://doi.org/10.1145/1233341.1233350","url":null,"abstract":"Despite the absence of first-class functions in Java, it is possible to program in the style of functional languages like ML or Haskell using the new capabilities in Java 1.5. We show how to use generic classes to program higher-order functions and how this interacts with object-oriented programming. We also show the necessity of the wildcard construct in Java and reveal several pitfalls. We conclude that the constructs in Java do not permit a functional framework that is completely compatible with object-oriented programming.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"195 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115012984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Verifying design modularity, hierarchy, and interaction locality using data clustering techniques 使用数据聚类技术验证设计模块化、层次结构和交互局部性
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233417
Liguo Yu, S. Ramaswamy
{"title":"Verifying design modularity, hierarchy, and interaction locality using data clustering techniques","authors":"Liguo Yu, S. Ramaswamy","doi":"10.1145/1233341.1233417","DOIUrl":"https://doi.org/10.1145/1233341.1233417","url":null,"abstract":"Modularity, hierarchy, and interaction locality are general approaches to reducing the complexity of any large system. A widely used principle in achieving these goals in designing software systems is striving for high cohesion within a module and low coupling between modules. However, this principle has difficulties in practice. Because a hierarchical system structure often consists of several layers, it is difficult to decide at what layer an interaction should be considered as cohesion, and at what layer an interaction should be considered as coupling. In this paper, we do not differentiate cohesion and coupling, but use a general term interaction to represent the dependencies between software modules. We propose a method to verify the design modularity, hierarchy, and interaction locality of a software system. This approach is based on the component interactions gathered from certain design level artifacts, such as UML diagrams. Data clustering technique is then used to group software components according to the degree of interactions between them. To show how to use this approach, we apply it to Parna's KWIC object-oriented design example, in which sequence diagram is used to derive the degree of component interactions.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123580830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
The Parlor 客厅
ACM-SE 45 Pub Date : 2007-03-23 DOI: 10.1145/1233341.1233462
Shogo Minamikawa
{"title":"The Parlor","authors":"Shogo Minamikawa","doi":"10.1145/1233341.1233462","DOIUrl":"https://doi.org/10.1145/1233341.1233462","url":null,"abstract":"The animation video project \"The Parlor\" was developed in the domains of yakuza (Japanese mafia), animation, and short film because I wanted to explore how one might defeat a yakuza using art, in order to convey the power of art to transform a personal experience of powerlessness into an empowering one. \"The Parlor\" tells the story of an artist and a yakuza who meet in the artist's tattoo parlor, a long time after the yakuza had attacked the artist on the street. The tattoo artist recognizes the yakuza through a series of flashbacks and then the story enters the fantasy world of the tattoo where the artist defeats the yakuza in a comic-surreal fight. Simultaneously, the tattoo is being etched on the yakuza's back and when the animation ends, the tattoo reflects the new power relationship between the yakuza and the artist. In order to move between the different time-zones and different realities, the animation uses a combination of three different visual aesthetics. Thus, this animation explores the idea of power and how art can be the means to empowerment.","PeriodicalId":427658,"journal":{"name":"ACM-SE 45","volume":"443 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123618774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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