13 Search Results for "Cicalese, Ferdinando"

Document
DOI: 10.4230/LIPIcs.WABI.2025.17
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT

Authors: Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
String matching problems in bioinformatics are typically for finding exact substring matches between a query and a reference text. Previous formulations often focus on maximum exact matches (MEMs). However, multiple occurrences of substrings of the query in the text that are long enough but not maximal may not be captured by MEMs. Such long matches can be informative, especially when the text is a collection of similar sequences such as genomes. In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount of LEMs, so we only consider those above some length threshold ℒ. These are referred to as long LEMs. The purpose of long LEMs is to capture substring matches between a query and a text that are not necessarily maximal in the pattern but still long enough to be important. Therefore efficient long LEMs finding algorithms are desired for these datasets. However, these datasets are too large to query on traditional string indexes. Fortunately, these datasets are very repetitive. Recently, compressed string indexes that take advantage of the redundancy in the data but retain efficient querying capability have been proposed as a solution. We therefore give an efficient algorithm for computing all the long LEMs of a query and a text in a BWT runs compressed string index. We describe an O(m+occ) expected time algorithm that relies on an O(r) words space string index for outputting all long LEMs of a pattern with respect to a text given the matching statistics of the pattern with respect to the text. Here m is the length of the query, occ is the number of long LEMs outputted, and r is the number of runs in the BWT of the text. The O(r) space string index we describe relies on an adaptation of the move data structure by Nishimoto and Tabei. We are able to support LCP[i] queries in constant time given SA[i]. In other words, we answer PLCP[i] queries in constant time. These PLCP queries enable the efficient long LEM query. Long LEMs may provide useful similarity information between a pattern and a text that MEMs may ignore. This information is particularly useful in pangenome and biobank scale haplotype panel contexts.
Cite as

Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sanaullah_et_al:LIPIcs.WABI.2025.17,
  author =	{Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaojie},
  title =	{{An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{17:1--17:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.17},
  URN =		{urn:nbn:de:0030-drops-239433},
  doi =		{10.4230/LIPIcs.WABI.2025.17},
  annote =	{Keywords: BWT, LEM, Long LEM, MEM, Run Length Compressed BWT, Move Data Structure, Pangenome}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.6
String Problems in the Congested Clique Model

Authors: Shay Golan and Matan Kraus

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, n nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and the communication between the nodes is conducted in rounds. In each round, every node is allowed to send an O(log n)-bit message to every other node in the network. We consider three fundamental string problems in the Congested Clique model. First, we present an O(1) rounds algorithm for string sorting that supports strings of arbitrary length. Second, we present an O(1) rounds combinatorial pattern matching algorithm. Finally, we present an O(log log n) rounds algorithm for the computation of the suffix array and the corresponding Longest Common Prefix array of a given string.
Cite as

Shay Golan and Matan Kraus. String Problems in the Congested Clique Model. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{golan_et_al:LIPIcs.CPM.2025.6,
  author =	{Golan, Shay and Kraus, Matan},
  title =	{{String Problems in the Congested Clique Model}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{6:1--6:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.6},
  URN =		{urn:nbn:de:0030-drops-231003},
  doi =		{10.4230/LIPIcs.CPM.2025.6},
  annote =	{Keywords: String Sorting, Pattern Matching, Suffix Array, Congested Clique, Sorting}
}
Document
DOI: 10.4230/LIPIcs.STACS.2025.38
Two-Dimensional Longest Common Extension Queries in Compact Space

Authors: Arnab Ganguly, Daniel Gibney, Rahul Shah, and Sharma V. Thankachan

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
For a length n text over an alphabet of size σ, we can encode the suffix tree data structure in 𝒪(nlog σ) bits of space. It supports suffix array (SA), inverse suffix array (ISA), and longest common extension (LCE) queries in 𝒪(log^ε_σ n) time, which enables efficient pattern matching; here ε > 0 is an arbitrarily small constant. Further improvements are possible for LCE queries, where 𝒪(1) time queries can be achieved using an index of space 𝒪(nlog σ) bits. However, compactly indexing a two-dimensional text (i.e., an n× n matrix) has been a major open problem. We show progress in this direction by first presenting an 𝒪(n²log σ)-bit structure supporting LCE queries in near 𝒪((log_σ n)^{2/3}) time. We then present an 𝒪(n²log σ + n²log log n)-bit structure supporting ISA queries in near 𝒪(log n ⋅ (log_σ n)^{2/3}) time. Within a similar space, achieving SA queries in poly-logarithmic (even strongly sub-linear) time is a significant challenge. However, our 𝒪(n²log σ + n²log log n)-bit structure can support SA queries in 𝒪(n²/(σ log n)^c) time, where c is an arbitrarily large constant, which enables pattern matching in time faster than what is possible without preprocessing. We then design a repetition-aware data structure. The δ_2D compressibility measure for two-dimensional texts was recently introduced by Carfagna and Manzini [SPIRE 2023]. The measure ranges from 1 to n², with smaller δ_2D indicating a highly compressible two-dimensional text. The current data structure utilizing δ_2D allows only element access. We obtain the first structure based on δ_2D for LCE queries. It takes 𝒪^{~}(n^{5/3} + n^{8/5}δ_2D^{1/5}) space and answers queries in 𝒪(log n) time.
Cite as

Arnab Ganguly, Daniel Gibney, Rahul Shah, and Sharma V. Thankachan. Two-Dimensional Longest Common Extension Queries in Compact Space. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 38:1-38:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ganguly_et_al:LIPIcs.STACS.2025.38,
  author =	{Ganguly, Arnab and Gibney, Daniel and Shah, Rahul and Thankachan, Sharma V.},
  title =	{{Two-Dimensional Longest Common Extension Queries in Compact Space}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{38:1--38:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2025.38},
  URN =		{urn:nbn:de:0030-drops-228649},
  doi =		{10.4230/LIPIcs.STACS.2025.38},
  annote =	{Keywords: String matching, text indexing, two-dimensional text}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.60
List Decoding Bounds for Binary Codes with Noiseless Feedback

Authors: Meghal Gupta and Rachel Yun Zhang

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
In an error-correcting code, a sender encodes a message x ∈ {0, 1}^k such that it is still decodable by a receiver on the other end of a noisy channel. In the setting of error-correcting codes with feedback, after sending each bit, the sender learns what was received at the other end and can tailor future messages accordingly. While the unique decoding radius of feedback codes has long been known to be 1/3, the list decoding capabilities of feedback codes is not well understood. In this paper, we provide the first nontrivial bounds on the list decoding radius of feedback codes for lists of size 𝓁. For 𝓁 = 2, we fully determine the 2-list decoding radius to be 3/7. For larger values of 𝓁, we show an upper bound of 1/2 - 1/{2^(𝓁+2) - 2}, and show that the same techniques for the 𝓁 = 2 case cannot match this upper bound in general.
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Meghal Gupta and Rachel Yun Zhang. List Decoding Bounds for Binary Codes with Noiseless Feedback. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 60:1-60:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gupta_et_al:LIPIcs.ITCS.2025.60,
  author =	{Gupta, Meghal and Zhang, Rachel Yun},
  title =	{{List Decoding Bounds for Binary Codes with Noiseless Feedback}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{60:1--60:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.60},
  URN =		{urn:nbn:de:0030-drops-226880},
  doi =		{10.4230/LIPIcs.ITCS.2025.60},
  annote =	{Keywords: error-correcting codes, feedback, list decoding}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2022.38
On Constrained Intersection Representations of Graphs and Digraphs

Authors: Ferdinando Cicalese, Clément Dallard, and Martin Milanič

Published in: LIPIcs, Volume 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022)

Abstract
We study the problem of determining minimal directed intersection representations of DAGs in a model introduced by [Kostochka, Liu, Machado, and Milenkovic, ISIT2019]: vertices are assigned color sets, two vertices are connected by an arc if and only if they share at least one color and the tail vertex has a strictly smaller color set than the head, and the goal is to minimize the total number of colors. We show that the problem is polynomially solvable in the class of triangle-free and Hamiltonian DAGs and also disclose the relationship of this problem with several other models of intersection representations of graphs and digraphs.
Cite as

Ferdinando Cicalese, Clément Dallard, and Martin Milanič. On Constrained Intersection Representations of Graphs and Digraphs. In 33rd International Symposium on Algorithms and Computation (ISAAC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 248, pp. 38:1-38:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{cicalese_et_al:LIPIcs.ISAAC.2022.38,
  author =	{Cicalese, Ferdinando and Dallard, Cl\'{e}ment and Milani\v{c}, Martin},
  title =	{{On Constrained Intersection Representations of Graphs and Digraphs}},
  booktitle =	{33rd International Symposium on Algorithms and Computation (ISAAC 2022)},
  pages =	{38:1--38:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-258-7},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{248},
  editor =	{Bae, Sang Won and Park, Heejin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2022.38},
  URN =		{urn:nbn:de:0030-drops-173239},
  doi =		{10.4230/LIPIcs.ISAAC.2022.38},
  annote =	{Keywords: Directed intersection representation, intersection number}
}
Document
DOI: 10.4230/LIPIcs.SEA.2020.12
Pattern Discovery in Colored Strings

Authors: Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
We consider the problem of identifying patterns of interest in colored strings. A colored string is a string in which each position is colored with one of a finite set of colors. Our task is to find substrings that always occur followed by the same color at the same distance. The problem is motivated by applications in embedded systems verification, in particular, assertion mining. The goal there is to automatically infer properties of the embedded system from the analysis of its simulation traces. We show that the number of interesting patterns is upper-bounded by 𝒪(n²) where n is the length of the string. We introduce a baseline algorithm with 𝒪(n²) running time which identifies all interesting patterns for all colors in the string satisfying certain minimality conditions. When one is interested in patterns related to only one color, we provide an algorithm that identifies patterns in 𝒪(n²log n) time, but is faster than the first algorithm in practice, both on simulated and on real-world patterns.
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Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi. Pattern Discovery in Colored Strings. In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 12:1-12:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{liptak_et_al:LIPIcs.SEA.2020.12,
  author =	{Lipt\'{a}k, Zsuzsanna and Puglisi, Simon J. and Rossi, Massimiliano},
  title =	{{Pattern Discovery in Colored Strings}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{12:1--12:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.12},
  URN =		{urn:nbn:de:0030-drops-120862},
  doi =		{10.4230/LIPIcs.SEA.2020.12},
  annote =	{Keywords: property testing, suffix tree, pattern mining}
}
Document
DOI: 10.4230/DagSemProc.09281.1
09281 Abstracts Collection – Search Methodologies

Authors: Rudolf Ahlswede, Ferdinando Cicalese, and Ugo Vaccaro

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
From 05.07.09 to 10.07.09, the Dagstuhl Seminar 09281 on ``Search Methodologies '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. Abstracts of the presentations given during the seminar are put together in this paper. The first section describes the seminar topics and goals in general. We also briefly comment on how the topics were addressed in the talks. Links to extended abstracts or full papers are provided, if available.
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Rudolf Ahlswede, Ferdinando Cicalese, and Ugo Vaccaro. 09281 Abstracts Collection – Search Methodologies. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{ahlswede_et_al:DagSemProc.09281.1,
  author =	{Ahlswede, Rudolf and Cicalese, Ferdinando and Vaccaro, Ugo},
  title =	{{09281 Abstracts Collection – Search Methodologies}},
  booktitle =	{Search Methodologies},
  pages =	{1--15},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.1},
  URN =		{urn:nbn:de:0030-drops-22457},
  doi =		{10.4230/DagSemProc.09281.1},
  annote =	{Keywords: Search algorithms, group testing, fault-tolerance, identification, decision tree, multi-access communication}
}
Document
DOI: 10.4230/DagSemProc.09281.2
Explicit Non-Adaptive Combinatorial Group Testing Schemes

Authors: Ely Porat and Amir Rotschild

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
Group testing is a long studied problem in combinatorics: A small set of r ill people should be identified out of the whole (n people) by using only queries (tests) of the form "Does set X contain an ill human?". In this paper we provide an explicit construction of a testing scheme which is better (smaller) than any known explicit construction. This scheme has \Theta(min[r2 log n, n])tests which is as many as the best non-explicit schemes have. In our construction we use a fact that may have a value by its own right: Linear error-correction codes with parameters [m, k, \delta m]q meeting the Gilbert-Varshamov bound may be constructed quite efficiently, in \Theta[q^{k}m) time.
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Ely Porat and Amir Rotschild. Explicit Non-Adaptive Combinatorial Group Testing Schemes. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{porat_et_al:DagSemProc.09281.2,
  author =	{Porat, Ely and Rotschild, Amir},
  title =	{{Explicit Non-Adaptive Combinatorial Group Testing Schemes}},
  booktitle =	{Search Methodologies},
  pages =	{1--13},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.2},
  URN =		{urn:nbn:de:0030-drops-22414},
  doi =		{10.4230/DagSemProc.09281.2},
  annote =	{Keywords: Prime Numbers, Group Testing, Streaming, Pattern Matching}
}
Document
DOI: 10.4230/DagSemProc.09281.3
Locating and Detecting Arrays for Interaction Faults

Authors: Charles J. Colbourn and Daniel W. McClary

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
The identification of interaction faults in component-based systems has focused on indicating the presence of faults, rather than their location and magnitude. While this is a valuable step in screening a system for interaction faults prior to its release, it provides little information to assist in the correction of such faults. Consequently tests to reveal the location of interaction faults are of interest. The problem of nonadaptive location of interaction faults is formalized under the hypothesis that the system contains (at most) some number d of faults, each involving (at most) some number t of interacting factors. Restrictions on the number and size of the putative faults lead to numerous variants of the basic problem. The relationships between this class of problems and interaction testing using covering arrays to indicate the presence of faults, designed experiments to measure and model faults, and combinatorial group testing to locate faults in a more general testing scenario, are all examined. While each has some definite similarities with the fault location problems for component-based systems, each has some striking differences as well. In this paper, we formulate the combinatorial problems for locating and detecting arrays to undertake interaction fault location. Necessary conditions for existence are established, and using a close connection to covering arrays, asymptotic bounds on the size of minimal locating and detecting arrays are established. A final version of this paper appears in J Comb Optim (2008) 15: 17-48.
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Charles J. Colbourn and Daniel W. McClary. Locating and Detecting Arrays for Interaction Faults. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{colbourn_et_al:DagSemProc.09281.3,
  author =	{Colbourn, Charles J. and McClary, Daniel W.},
  title =	{{Locating and Detecting Arrays for Interaction Faults}},
  booktitle =	{Search Methodologies},
  pages =	{1--34},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.3},
  URN =		{urn:nbn:de:0030-drops-22405},
  doi =		{10.4230/DagSemProc.09281.3},
  annote =	{Keywords: Covering array, Orthogonal array, Factorial design, Cover-free family, Disjunct matrix, Locating array, Detecting array}
}
Document
DOI: 10.4230/DagSemProc.09281.4
Minimax Trees in Linear Time with Applications

Authors: Pawel Gawrychowski and Travis Gagie

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
A minimax tree is similar to a Huffman tree except that, instead of minimizing the weighted average of the leaves' depths, it minimizes the maximum of any leaf's weight plus its depth. Golumbic (1976) introduced minimax trees and gave a Huffman-like, $O (n log n)$-time algorithm for building them. Drmota and Szpankowski (2002) gave another $O (n log n)$-time algorithm, which takes linear time when the weights are already sorted by their fractional parts. In this paper we give the first linear-time algorithm for building minimax trees for unsorted real weights.
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Pawel Gawrychowski and Travis Gagie. Minimax Trees in Linear Time with Applications. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{gawrychowski_et_al:DagSemProc.09281.4,
  author =	{Gawrychowski, Pawel and Gagie, Travis},
  title =	{{Minimax Trees in Linear Time with Applications}},
  booktitle =	{Search Methodologies},
  pages =	{1--11},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.4},
  URN =		{urn:nbn:de:0030-drops-22421},
  doi =		{10.4230/DagSemProc.09281.4},
  annote =	{Keywords: Data structures, data compression, prefix-free coding}
}
Document
DOI: 10.4230/DagSemProc.09281.5
Pattern matching with don't cares and few errors

Authors: Raphael Clifford, Klim Efremo, Ely Porat, and Amir Rotschild

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
We present solutions for the k-mismatch pattern matching problem with don't cares. Given a text t of length n and a pattern p of length m with don't care symbols and a bound k, our algorithms find all the places that the pattern matches the text with at most k mismatches. We first give an \Theta(n(k + logmlog k) log n) time randomised algorithm which finds the correct answer with high probability. We then present a new deter- ministic \Theta(nk^2 log^m)time solution that uses tools originally developed for group testing. Taking our derandomisation approach further we de- velop an approach based on k-selectors that runs in \Theta(nk polylogm) time. Further, in each case the location of the mismatches at each alignment is also given at no extra cost.
Cite as

Raphael Clifford, Klim Efremo, Ely Porat, and Amir Rotschild. Pattern matching with don't cares and few errors. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{clifford_et_al:DagSemProc.09281.5,
  author =	{Clifford, Raphael and Efremo, Klim and Porat, Ely and Rotschild, Amir},
  title =	{{Pattern matching with don't cares and few errors}},
  booktitle =	{Search Methodologies},
  pages =	{1--19},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.5},
  URN =		{urn:nbn:de:0030-drops-22442},
  doi =		{10.4230/DagSemProc.09281.5},
  annote =	{Keywords: Prime Numbers, Group Testing, Streaming, Pattern Matching}
}
Document
DOI: 10.4230/DagSemProc.09281.6
Rounds in Combinatorial Search

Authors: Gábor Wiener

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
The search complexity of a separating system ${cal H} subseteq 2^{[m]}$ is the minimum number of questions of type ``$xin H$? hinspace '' (where $H in {cal H}$) needed in the worst case to determine a hidden element $xin [m]$. If we are allowed to ask the questions in at most $k$ batches then we speak of the emph{$k$-round} (or emph{$k$-stage}) complexity of ${cal H}$, denoted by $hbox{c}_k ({cal H})$. While $1$-round and $m$-round complexities (called non-adaptive and adaptive complexities, respectively) are widely studied (see for example Aigner cite{A}), much less is known about other possible values of $k$, though the cases with small values of $k$ (tipically $k=2$) attracted significant attention recently, due to their applications in DNA library screening. It is clear that $ |{cal H}| geq hbox{c}_{1} ({cal H}) geq hbox{c}_{2} ({cal H}) geq ldots geq hbox{c}_{m} ({cal H})$. A group of problems raised by {G. O. H. Katona} cite{Ka} is to characterize those separating systems for which some of these inequalities are tight. In this paper we are discussing set systems ${cal H}$ with the property $|{cal H}| = hbox{c}_{k} ({cal H}) $ for any $kgeq 3$. We give a necessary condition for this property by proving a theorem about traces of hypergraphs which also has its own interest.
Cite as

Gábor Wiener. Rounds in Combinatorial Search. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{wiener:DagSemProc.09281.6,
  author =	{Wiener, G\'{a}bor},
  title =	{{Rounds in Combinatorial Search}},
  booktitle =	{Search Methodologies},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.6},
  URN =		{urn:nbn:de:0030-drops-22399},
  doi =		{10.4230/DagSemProc.09281.6},
  annote =	{Keywords: Search, group testing, adaptiveness, hypergraph, trace}
}
Document
DOI: 10.4230/DagSemProc.09281.7
Some Aspects of Finite State Channel related to Hidden Markov Process

Authors: Kingo Kobayashi

Published in: Dagstuhl Seminar Proceedings, Volume 9281, Search Methodologies (2009)

Abstract
We have no satisfactory capacity formula for most channels with finite states. Here, we consider some interesting examples of finite state channels, such as Gilbert-Elliot channel, trapdoor channel, etc., to reveal special characters of problems and difficulties to determine the capacities. Meanwhile, we give a simple expression of the capacity formula for Gilbert-Elliot channel by using a hidden Markov source for the optimal input process. This idea should be extended to other finite state channels.
Cite as

Kingo Kobayashi. Some Aspects of Finite State Channel related to Hidden Markov Process. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{kobayashi:DagSemProc.09281.7,
  author =	{Kobayashi, Kingo},
  title =	{{Some Aspects of Finite State Channel related to Hidden Markov Process}},
  booktitle =	{Search Methodologies},
  pages =	{1--16},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9281},
  editor =	{Rudolf Ahlswede and Ferdinando Cicalese and Ugo Vaccaro},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09281.7},
  URN =		{urn:nbn:de:0030-drops-22434},
  doi =		{10.4230/DagSemProc.09281.7},
  annote =	{Keywords: Finite state channel, Hidden Markov source, Gilbert-Elliot channel, Trapdoor Channel}
}
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