Pub Date : 2021-01-01DOI: 10.1137/1.9781611976472.5
C. Boucher, Ondrej Cvacho, T. Gagie, J. Holub, G. Manzini, G. Navarro, Massimiliano Rossi
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.
{"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":"2 1","pages":"60-72"},"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}
Pub Date : 2016-01-01DOI: 10.1007/978-3-319-49487-6_7
M. Fischer, C. Jähn, F. Heide, Ralf Petring
{"title":"Algorithm Engineering Aspects of Real-Time Rendering Algorithms","authors":"M. Fischer, C. Jähn, F. Heide, Ralf Petring","doi":"10.1007/978-3-319-49487-6_7","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_7","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":"28 1","pages":"226-244"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76737851","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}
Pub Date : 2016-01-01DOI: 10.1007/978-3-319-49487-6_5
Benjamin Doerr, Magnus Wahlström
{"title":"How to Generate Randomized Roundings with Dependencies and How to Derandomize Them","authors":"Benjamin Doerr, Magnus Wahlström","doi":"10.1007/978-3-319-49487-6_5","DOIUrl":"https://doi.org/10.1007/978-3-319-49487-6_5","url":null,"abstract":"","PeriodicalId":93608,"journal":{"name":"Proceedings of the ... Workshop on Algorithm Engineering and Experiments : ALENEX","volume":"32 1","pages":"159-184"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77781964","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}
Pub Date : 2016-01-01DOI: 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":"66 1","pages":"330-351"},"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}
Pub Date : 2016-01-01DOI: 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":"64 1","pages":"1-18"},"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}
Pub Date : 2016-01-01DOI: 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":"1 1","pages":"185-225"},"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}
Pub Date : 2016-01-01DOI: 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":"26 1","pages":"352-378"},"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}
Pub Date : 2015-05-19DOI: 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":"8 1","pages":"245-279"},"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}
Pub Date : 2015-04-20DOI: 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":"15 1","pages":"19-80"},"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}
Pub Date : 2014-10-31DOI: 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":"12 1","pages":"379-417"},"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}
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