Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX最新文献

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PFP Compressed Suffix Trees 压缩后缀树
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2021-01-01 DOI: 10.1137/1.9781611976472.5
C. Boucher, Ondrej Cvacho, T. Gagie, J. Holub, G. Manzini, G. Navarro, Massimiliano Rossi
{"title":"PFP Compressed Suffix Trees","authors":"C. Boucher, Ondrej Cvacho, T. Gagie, J. Holub, G. Manzini, G. Navarro, Massimiliano Rossi","doi":"10.1137/1.9781611976472.5","DOIUrl":"https://doi.org/10.1137/1.9781611976472.5","url":null,"abstract":"Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string S, it produces a dictionary D and a parse P of overlapping phrases such that BWT(S) can be computed from D and P in time and workspace bounded in terms of their combined size |PFP(S)|. In practice D and P are significantly smaller than S and computing BWT(S) from them is more efficient than computing it from S directly, at least when S is the concatenation of many genomes. In this paper, we consider PFP(S) as a data structure and show how it can be augmented to support full suffix tree functionality, still built and fitting within O(|PFP(S)|) space. This entails the efficient computation of various primitives to simulate the suffix tree: computing a longest common extension (LCE) of two positions in S; reading any cell of its suffix array (SA), of its inverse (ISA), of its BWT, and of its longest common prefix array (LCP); and computing minima over ranges and next/previous smaller value queries over the LCP. Our experimental results show that the PFP suffix tree can be efficiently constructed for very large repetitive datasets and that its operations perform competitively with other compressed suffix trees that can only handle much smaller datasets.","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72974611","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: 14
Algorithm Engineering Aspects of Real-Time Rendering Algorithms 实时渲染算法的算法工程方面
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2016-01-01 DOI: 10.1007/978-3-319-49487-6_7
M. Fischer, C. Jähn, F. Heide, Ralf Petring
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引用次数: 0
How to Generate Randomized Roundings with Dependencies and How to Derandomize Them 如何生成具有依赖关系的随机轮询以及如何去随机化它们
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2016-01-01 DOI: 10.1007/978-3-319-49487-6_5
Benjamin Doerr, Magnus Wahlström
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引用次数: 1
Integrating Sequencing and Scheduling: A Generic Approach with Two Exemplary Industrial Applications 整合排序和调度:一个通用的方法与两个示范工业应用
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2016-01-01 DOI: 10.1007/978-3-319-49487-6_10
Wiebke Höhn, R. Möhring
{"title":"Integrating Sequencing and Scheduling: A Generic Approach with Two Exemplary Industrial Applications","authors":"Wiebke Höhn, R. Möhring","doi":"10.1007/978-3-319-49487-6_10","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_10","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83935256","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
Engineering a Lightweight and Efficient Local Search SAT Solver 设计一个轻量级和高效的局部搜索SAT求解器
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2016-01-01 DOI: 10.1007/978-3-319-49487-6_1
A. Balint, U. Schöning
{"title":"Engineering a Lightweight and Efficient Local Search SAT Solver","authors":"A. Balint, U. Schöning","doi":"10.1007/978-3-319-49487-6_1","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_1","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85596357","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
External-Memory State Space Search 外部内存状态空间搜索
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2016-01-01 DOI: 10.1007/978-3-319-49487-6_6
S. Edelkamp
{"title":"External-Memory State Space Search","authors":"S. Edelkamp","doi":"10.1007/978-3-319-49487-6_6","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_6","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90656965","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: 3
Engineering a Bipartite Matching Algorithm in the Semi-Streaming Model 设计半流模型的二部匹配算法
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2016-01-01 DOI: 10.1007/978-3-319-49487-6_11
Lasse Kliemann
{"title":"Engineering a Bipartite Matching Algorithm in the Semi-Streaming Model","authors":"Lasse Kliemann","doi":"10.1007/978-3-319-49487-6_11","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_11","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81850456","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: 3
Algorithm Engineering in Robust Optimization 鲁棒优化中的算法工程
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2015-05-19 DOI: 10.1007/978-3-319-49487-6_8
M. Goerigk, A. Schöbel
{"title":"Algorithm Engineering in Robust Optimization","authors":"M. Goerigk, A. Schöbel","doi":"10.1007/978-3-319-49487-6_8","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_8","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73630180","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: 130
Route Planning in Transportation Networks 交通网络中的路线规划
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2015-04-20 DOI: 10.1007/978-3-319-49487-6_2
H. Bast, D. Delling, A. Goldberg, M. Müller-Hannemann, Thomas Pajor, P. Sanders, D. Wagner, Renato F. Werneck
{"title":"Route Planning in Transportation Networks","authors":"H. Bast, D. Delling, A. Goldberg, M. Müller-Hannemann, Thomas Pajor, P. Sanders, D. Wagner, Renato F. Werneck","doi":"10.1007/978-3-319-49487-6_2","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_2","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82406624","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: 651
Engineering Art Galleries 工程艺术馆
Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX Pub Date : 2014-10-31 DOI: 10.1007/978-3-319-49487-6_12
P. J. Rezende, C. C. Souza, Stephan Friedrichs, M. Hemmer, A. Kröller, Davi C. Tozoni
{"title":"Engineering Art Galleries","authors":"P. J. Rezende, C. C. Souza, Stephan Friedrichs, M. Hemmer, A. Kröller, Davi C. Tozoni","doi":"10.1007/978-3-319-49487-6_12","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_12","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78605052","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: 23
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