EPTCS 252 Proceedings of the 15th International Conference on Automata and Formal Languages Debrecen, Hungary, September 4-6, 2017 Edited by: Erzsebet´ Csuhaj-Varju,´ Pal´ Dom¨ osi¨ and Gyorgy¨ Vaszil Published: 21st August 2017 DOI: 10.4204/EPTCS.252 ISSN: 2075-2180 Open Publishing Association i Table of Contents TableofContents .................................... ...................................... i Preface............................................ ........................................ iii Erzsébet Csuhaj-Varjú, Pál Dömösi and György Vaszil Invited Presentation: Automata and Formal Languages for Next Generation Sequencing Data . 1 Paola Bonizzoni and Gianluca Della Vedova Invited Presentation: Representation of Information in Automata . ................ 3 Henning Bordihn Invited Presentation: On Regular Images of Regular Languages under Extended Word Operations 5 Szilárd Zsolt Fazekas Invited Presentation: Networks of Genetic Processors: From Universality to a Formal Language Characterization ................................... ........................................ 7 José M. Sempere Invited Presentation: Rearrangement Problem of Multidimensional Arrays by Prefix Reversals . 9 Akihiro Yamamura (Tissue) P Systems with Vesicles of Multisets . ..................................... 11 Artiom Alhazov, Rudolf Freund, Sergiu Ivanov and Sergey Verlan Unavoidable Sets of Partial Words of Uniform Length . .................................. 26 Joey Becker, F. Blanchet-Sadri, Laure Flapan and Stephen Watkins On the Descriptional Complexity of Operations on SemilinearSets.............................. 41 Simon Beier, Markus Holzer and Martin Kutrib Dyck Words, Lattice Paths, and Abelian Borders . ................................... 56 F. Blanchet-Sadri, Kun Chen and Kenneth Hawes Constructing Words with High Distinct Square Densities . .................................... 71 F. Blanchet-Sadri and S. Osborne Higher-Order Operator Precedence Languages . .................................... 86 Stefano Crespi Reghizzi and Matteo Pradella The Triple-Pair Construction for Weighted ω-Pushdown Automata..............................101 Manfred Droste, Zoltán Ésik and Werner Kuich ii Reversible Languages Having Finitely Many Reduced Automata................................114 Kitti Gelle and Szabolcs Iván Input-Driven Double-Head Pushdown Automata . ..................................128 Markus Holzer, Martin Kutrib, Andreas Malcher and Matthias Wendlandt Weakly and Strongly Irreversible Regular Languages . ....................................143 Giovanna J. Lavado, Giovanni Pighizzini and Luca Prigioniero Descriptional Complexity of Non-Unary Self-Verifying Symmetric Difference Automata . 157 Laurette Marais and Lynette van Zijl CD Grammar Systems with Two Propagating Scattered Context Components Characterize the Family of Context Sensitive Languages. .....................................170 Alexander Meduna and Jakub Martiško Derivatives of Parsing Expression Grammars. .....................................180 Aaron Moss A New Sensing 5’–>3’ Watson-Crick Automata Concept. ................................195 Benedek Nagy, Shaghayegh Parchami and Hamid Mir-Mohammad-Sadeghi Exact AffineCounter Automata.......................... ....................................205 Masaki Nakanishi, Kamil Khadiev, Krisjanis Prusis, Jevgenijs Vihrovs and Abuzer Yakaryılmaz On h-Lexicalized Restarting Automata . .....................................219 Martin Plátek and Friedrich Otto Generalized Results on Monoids as Memory . ..................................234 Özlem Salehi, Flavio D’Alessandro and A. C. Cem Say Preface The 15th International Conference on Automata and Formal Languages (AFL 2017) was held in Debre- cen, September 4-6, 2017. It was organized by the Faculty of Informatics, University of Debrecen and the Faculty of Informatics, E¨otv¨os Lor´and University, Budapest. The AFL conference series was initiated by Prof. Istv´an Pe´ak (1936-1989). He organized the AFL conferences in 1980, 1982, 1984, 1986 and 1988 and started the organization of AFL’90. These con- ferences were all held in the hills around Salg´otarj´an. In 1986 and 1988, the title of the conference was Automata, Languages and Programming Systems. Since the untimely death of Prof. Istv´an Pe´ak in 1990, the AFL conferences have been organized in every third year. Professors Andr´as Ad´am´ and P´al D¨om¨osi took the lead in the continuation of the series. In 1993 and 1996, two more “Salg´otarj´an conferences” took place, the last three conferences of the series were held in Balatonf¨ured (AFL 2008), Debrecen (AFL’11), and Szeged (AFL 2014). AFL 2017 intended to cover all important areas of automata and formal language theory and their applications such as grammars, acceptors and transducers for strings, trees, graphs, arrays, algebraic theories for automata and languages, combinatorial properties of words and languages, formal power series, decision problems, efficient algorithms for automata and languages, relations to complexity theory and logic, picture description and analysis, quantum computing, cryptography, concurrency, applications of automata and language theory in biology, natural language processing, and other fields. The Programme Committee invited lectures from Paola Bonizzoni (University of Milan-Bicocca, Italy), Henning Bordihn (University of Potsdam, Germany), Szil´ard Zsolt Fazekas (Akita University, Japan), Jos´eM. Sempere (Technical University of Valencia, Spain), Akihiro Yamamura (Akita University, Japan). A special memorial session in honor of late Zolt´an Esik,´ steering committee member and organizer of AFL conferences, consisted of talks presented by Szabolcs Iv´an (University of Szeged, Hungary) and Werner Kuich (Technical University of Vienna, Austria). This volume contains the abstracts of invited lectures and the texts of the 17 papers accepted from the 23 submissions to AFL 2017. The members of the International Program Committee were Francine Blanchet-Sadri (Greensboro), Gy¨orgy Mar´oti (Veszpr´em), Victor Bovdi (Al Ain), Alexander Meduna (Brno), Erzs´ebet Csuhaj-Varj´u(Budapest, co-chair), Victor Mitrana (Bucharest, Madrid), J¨urgen Dassow (Magdeburg), Andreas Maletti (Stuttgart), P´al D¨om¨osi (Debrecen, co-chair), Benedek Nagy (Famagusta), Henning Fernau (Trier), Chrystopher Nehaniv (Hertfordshire), Zolt´an F¨ul¨op (Szeged), Friedrich Otto (Kassel), Viliam Geffert (Koˇsice), Gheorghe P˘aun (Bucharest), E. Csuhaj-Varj´u, P. D¨om¨osi, Gy. Vaszil (Eds.): 15th International Conference on Automata and Formal Languages (AFL 2017) EPTCS 252, 2017, pp. iii–v, doi:10.4204/EPTCS.252.0 iv Preface Marian Gheorghe (Bradford), Giovanni Pighizzini (Milano), Oscar H. Ibarra (Santa Barbara, CA), Agust´ın Riscos-N´u˜nez (Sevilla), Szabolcs Iv´an (Szeged), Jeffrey Shallit (Waterloo, Canada), Galina Jir´askov´a(Koˇsice), Petr Sos´ık (Opava), Juhani Karhum¨aki (Turku), Bianca Truthe (Giessen), Alica Kelemenov´a(Opava), Gy¨orgy Vaszil (Debrecen, co-chair), Mikl´os Kr´esz (Szeged), Laurent Vuillon (Chamb´ery), Martin Kutrib (Giessen), Claudio Zandron (Milano). We thank the members of the Programme Committee for the evaluation of the submissions and their subreferees for their excellent cooperation in this work. We are grateful to the contributors of the conference AFL 2017, in particular to the invited speakers for presenting interesting new developments. We are grateful to the Department of Computer Science and the Faculty of Informatics of the University of Debrecen for the local organization and for the financial support of AFL 2017. September 2017 Erzs´ebet Csuhaj-Varj´u, Budapest P´al D¨om¨osi, Gy¨orgy Vaszil, Debrecen E. Csuhaj-Varj´u, P. D¨om¨osi, Gy. Vaszil v AFL 2017 Organizing Committee G´eza Horv´ath (Debrecen, co-chair) Ern˝on´eK´asa (Debrecen) Gy¨orgy Vaszil (Debrecen, co-chair) Ildik´oCserh´atin´eVecsei (Debrecen) AFL Steering Committee Andr´as Ad´am´ (Budapest, honorary chair) Istv´an Babcs´anyi (Budapest) Erzs´ebet Csuhaj-Varj´u(Budapest) P´al D¨om¨osi (Debrecen, chair) Zolt´an F¨ul¨op (Szeged) L´aszl´oHunyadv´ari (Budapest) L´aszl´oK´aszonyi (Szombathely) Attila Nagy (Budapest) Gy¨orgy Vaszil (Debrecen) List of subreviewers Zuzana Bedn´arov´a Robert Mercas¸ Emilie Charlier Mark-Jan Nederhof Lucie Ciencialov´a Pascal Ochem James Currie Erik Paul Stefan D¨uck Luca Prigioniero Zsolt Gazdag Michael Rao Kitti Gelle Juraj Sebejˇ Markus Holzer Shinnosuke Seki G´eza Horv´ath S´andor V´agv¨olgyi Sylvain Lombardy Matthias Wendlandt Ian McQuillan Automata and Formal Languages for Next Generation Sequencing Data Paola Bonizzoni Gianluca Della Vedova Department of Informatics, Systems and Communications Department of Informatics, Systems and Communications University of Milan-Bicocca, Milan, Italy University of Milan-Bicocca, Milan, Italy [email protected] [email protected] The advent of Next Generation Sequencing (NGS) technologies is characterized by the production of massive data consisting of short sequences (reads) and it has enabled the completion of several sequencing projects on entire populations. This talk focuses on the application of concepts from automata theory and formal languages to Bioinformatics, motivated by the repetitive nature that is intrinsic to the sequences that are produced with NGS technologies. The analysis of such data raises the need of formal tools that are able to take advantage of the similarities among sequences to index and compare NGS data in a memory (and hence time) efficient manner. We will explore some