Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction

Ramtin Afshar; Amihood Amir; Michael T. Goodrich; Pedro Matias

doi:10.1007/978-3-030-59212-7_12

Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction

Ramtin Afshar, Amihood Amir, Michael T. Goodrich, Pedro Matias

Department of Computer Science

University of California at Irvine

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new and improved bounds for exact string reconstruction for settings where either the string or the queries are “mixed-up”.

Original language	English
Title of host publication	String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Proceedings
Editors	Christina Boucher, Sharma V. Thankachan
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	155-174
Number of pages	20
ISBN (Print)	9783030592110
DOIs	https://doi.org/10.1007/978-3-030-59212-7_12
State	Published - 2020
Event	27th International Symposium on String Processing and Information Retrieval, SPIRE 2020 - Orlando, United States Duration: 13 Oct 2020 → 15 Oct 2020

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	12303 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	27th International Symposium on String Processing and Information Retrieval, SPIRE 2020
Country/Territory	United States
City	Orlando
Period	13/10/20 → 15/10/20

Bibliographical note

Publisher Copyright:
© 2020, Springer Nature Switzerland AG.

Funding

Acknowledgments. This research was funded in part by the U.S. National Science Foundation under grant 1815073. Amihood Amir was partly supported by BSF grant 2018141 and ISF grant 1475-18.

Funders	Funder number
National Science Foundation
Directorate for Computer and Information Science and Engineering	1815073
Bonfils-Stanton Foundation	2018141
Israel Science Foundation	1475-18

Keywords

DNA sequencing
Exact learning
Hybridization
Information security
Jumbled-index queries
Periodicity
String reconstruction
Stringology
Substrings

Access to Document

10.1007/978-3-030-59212-7_12

Cite this

Afshar, R., Amir, A., Goodrich, M. T., & Matias, P. (2020). Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction. In C. Boucher, & S. V. Thankachan (Eds.), String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Proceedings (pp. 155-174). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12303 LNCS). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-030-59212-7_12

Afshar, Ramtin ; Amir, Amihood ; Goodrich, Michael T. et al. / Adaptive Exact Learning in a Mixed-Up World : Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction. String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Proceedings. editor / Christina Boucher ; Sharma V. Thankachan. Springer Science and Business Media Deutschland GmbH, 2020. pp. 155-174 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Afshar, R, Amir, A, Goodrich, MT & Matias, P 2020, Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction. in C Boucher & SV Thankachan (eds), String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12303 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 155-174, 27th International Symposium on String Processing and Information Retrieval, SPIRE 2020, Orlando, United States, 13/10/20. https://doi.org/10.1007/978-3-030-59212-7_12

Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction. / Afshar, Ramtin; Amir, Amihood; Goodrich, Michael T. et al.
String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Proceedings. ed. / Christina Boucher; Sharma V. Thankachan. Springer Science and Business Media Deutschland GmbH, 2020. p. 155-174 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12303 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Afshar R, Amir A, Goodrich MT, Matias P. Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction. In Boucher C, Thankachan SV, editors, String Processing and Information Retrieval - 27th International Symposium, SPIRE 2020, Proceedings. Springer Science and Business Media Deutschland GmbH. 2020. p. 155-174. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-59212-7_12

Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction

Abstract

Publication series

Conference

Bibliographical note

Funding

Keywords

Access to Document

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Cite this