Shinnosuke SEKI
| Department of Computer and Network Engineering | Associate Professor |
| Cluster I (Informatics and Computer Engineering) | Associate Professor |
Researcher Information
Field Of Study
Career
- Sep. 2018 - Present
Ecole Normale Superieure de Lyon, Invited Professor, France - Sep. 2013 - Mar. 2015
Academy of Finland, Postdoctoral Researcher, Principal Investigator, Finland - Feb. 2012 - Aug. 2013
Aalto University, Department of Information and Computer Science, Postdoctoral Researcher, Finland - 01 May 2011 - 15 Feb. 2012
Kyoto University, 薬学研究科, 博士研究員 - Sep. 2010 - Apr. 2011
University of Western Ontario, Department of Computer Science, Postdoctoral Researcher, Canada
Educational Background
Member History
- Feb. 2024 - Present
Member, Program Committee of the IEEE 3rd Conference on Information Technology and Data Science (CITDS 2024) - Nov. 2023 - Present
Member, Program Committee of the 26th International Conference on Descriptional Complexity of Formal Systems (DCFS 2024), Society - Sep. 2023 - Present
Co-chair, Program Committee of the 30th International Conference on DNA Computing and Molecular Programming (DNA30), Society - Aug. 2023 - Present
Member, Organizing Committee of the 28th International Conference on Implementation and Application of Automata (CIAA 2024), Society - Jul. 2023 - Present
Member, Organizing Committee of the 21st International Conference on Unconventional Computation and Natural Computation (UCNC 2024), Society - Sep. 2022 - Present
Member, Steering Committee of the International Conference on Machines, Computations, and Universality (MCU), Society - Oct. 2021 - Present
Co-chair, Steering Committee of the International Conference on Unconventional Computation and Natural Computation (UCNC), Co-chair - Sep. 2019 - Present
Area Editor, New Generation Computing, Editorial Board, Society - Apr. 2018 - Present
Advisory Board, Springer Natural Computing Book-Series, Society - Aug. 2017 - Present
Member, Steering Committee of International Conference on Developments in Language Theory (DLT), Society - Sep. 2022 - Sep. 2023
Member, Program Committee of the 29th International Conference on DNA Computing and Molecular Programming (DNA29), Society - Sep. 2022 - Sep. 2023
Member, Program Committee of the 27th International Conference on Implementation and Application of Automata (CIAA2023), Society - Jul. 2022 - Jul. 2023
Member, Program Committee of the 25th International Conference on Descriptional Complexity of Formal Systems (DCFS 2023), Society - Apr. 2022 - Jul. 2023
Member, Program Committee of the 19th Conference on Computability in Europe (CiE2023), Society - 01 Apr. 2018
専門委員, 情報処理学会アルゴリズム研究会 - 01 Apr. 2018
関 新之助, 情報処理学会アルゴリズム研究会 - 01 Oct. 2014
関 新之助, 情報処理学会論文誌「数理モデル化と応用」編集委員会, Society
Research Activity Information
Award
Paper
- Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami
Szilárd Zsolt Fazekas; Naoya Iwano; Yu Kihara; Ryuichi Matsuoka; Shinnosuke Seki; Hinano Takeuchi
Corresponding, Theoretical Computer Science, Elsevier BV, 999, 114550-114550, Jun. 2024, Peer-reviwed, Invited
Scientific journal, English - Freezing 1-tag systems with states
Szilard Zsolt Fazekas; Shinnosuke Seki
Corresponding, Electronic Proceedings in Theoretical Computer Science (EPTCS), Proceedings of the 16th International Conference on Automata and Formal Languages (AFL 2023), 386, 82-95, Sep. 2023, Peer-reviwed
International conference proceedings, English - Ok: A kinetic model for locally reconfigurable molecular systems
Pierre Marcus; Nicolas Schabanel; Shinnosuke Seki
Corresponding, Visions of DNA Nanotechnology at 40 for the Next 40, 229-240, May 2023, Peer-reviwed, Invited
Scientific journal, English - Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)
Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Guillaume Theyssier
Proceedings of the 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), LIPIcs 219, 51:1-51:23, 09 Mar. 2022, Peer-reviwed
International conference proceedings, English - Square network on a word
Szilard Zsolt Fazekas; Shinnosuke Seki
Theoretical Computer Science, Elsevier, 894, 26, 121-134, Nov. 2021, Peer-reviwed, Left-aligned last occurrences of squares (double-square) have provided profound insights into the question of how many distinct squares can be packed on a word ω of length n and brought the best known upper bound 11n/6. Other types of alignments such as being center-aligned as well as long distance relations such as being the occurrences of the same square incorporate the squares on ω into a bipartite graph of the squares and positions {1,2,…,n}, which we call the square network. Packing more and more squares in a limited space certainly induces specific kinds of subgraphs once the square density exceeds a threshold, and if one of the subgraphs is known to be forbidden, the threshold provides an upper bound on the number of distinct squares. In this paper, we designate a specific position of double-squares as P1 and obtain certain induced subgraphs as well as forbidden ones guaranteed by the presence of P1-aligned double squares; an induced subgraph of particular interest expresses the global uniqueness of squares involved.
Scientific journal, English - Simple intrinsic simulation of cellular automata in oritatami molecular folding model
Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Yuki Ubukata
Proceedings of the 14th Latin American Theoretical Informatics Symposium (LATIN 2020), Springer, LNCS 12118, 425-436, 05 Jan. 2021, Peer-reviwed
International conference proceedings, English - Linear bounds on the size of the conformations in greedy deterministic oritatami
Szilard Zsolt Fazekas; Hwee Kim; Ryuichi Matsuoka; Reoto Morita; Shinnosuke Seki
International Journal of Foundations of Computer Science, World Scientific Publishing Company, 32, 5, 575-596, 2021, Peer-reviwed
Scientific journal, English - A general architecture of oritatami systems for simulating arbitrary finite automata
Yo-Sub Han; Hwee Kim; Yusei Masuda; Shinnosuke Seki
Theoretical Computer Science, Springer, 870, 16, 29-52, 2021, Peer-reviwed
Scientific journal, English - Counting infinitely by oritatami co-transcriptional folding
Kohei Maruyama; Shinnosuke Seki
Natural Computing, Springer, 20, 2, 329-340, 2021, Peer-reviwed
Scientific journal, English - Transcript design problem of oritatami systems
Yo-Sub Han; Hwee Kim; Shinnosuke Seki
Natural Computing, Springer, 19, 2, 323-335, 2020, Peer-reviwed
Scientific journal, English - Self-attraction removal from oritatami systems
Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
International Journal of Foundations of Computer Science, 30, 6-7, 1047-1067, 2019, Peer-reviwed
Scientific journal, English - On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence.
Szilárd Zsolt Fazekas; Kohei Maruyama; Reoto Morita; Shinnosuke Seki
Proceedings of the 15th International Conference on Theory and Applications of Models of Computation (TAMC 2019), Springer, LNCS 11436, 188-207, 2019, Peer-reviwed
International conference proceedings, English - Oritatami: a computational model for molecular co-transcriptional folding
Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
International Journal of Molecular Sciences, MDPI, 20, 9, 2259, 2019, Peer-reviwed
Scientific journal, English - Single-stranded architectures for computing
Shinnosuke Seki
Proceedings of the 23rd International Conference on Developments in Language Theory (DLT 2019), Springer, LNCS 11647, 41-56, 2019, Peer-reviwed, Invited
International conference proceedings, English - Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki
Natural Computing, Springer, 17, 1, 67-79, 2018, Peer-reviwed
Scientific journal, English - Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
Yusei Masuda; Shinnosuke Seki; Yuki Ubukata
Proceedings of the 23rd International Conference on Implementation and Applications of Automata (CIAA2018), Springer, LNCS, 10977, 261-273, 2018, Peer-reviwed
International conference proceedings, English - Know when to fold 'em: Self-assembly of shapes by folding in oritatami
Erik Demaine; Jacob Hendricks; Meagan Olsen; Matthew J. Patitz; Trent A. Rogers; Nicolas Schabanel; Shinnosuke Seki; Hadley Thoams
Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 19-36, 2018, Peer-reviwed
International conference proceedings, English - Transcript design problem of oritatami systems
Yo-Sub Han; Hwee Kim; Shinnosuke Seki
Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 139-154, 2018, Peer-reviwed
International conference proceedings, English - Proving the Turing universality of oritatami co-transcriptional folding
Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
Proceedings of the 29th International Symposium on Algorithms and Computation (ISAAC2018), Schloss Dagstuhl, LIPIcs 123, 23:1-23:13, 2018, Peer-reviwed
International conference proceedings, English - The Complexity of Fixed-Height Patterned Tile Self-Assembly
Shinnosuke Seki; Andrew Winslow
INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 28, 5, 465-482, Aug. 2017, Peer-reviwed, We characterize the complexity of the PATS problem for patterns of fixed height and color count in variants of the model where seed glues are either chosen or fixed and identical (so-called non-uniform and uniform variants). We prove that both variants are NP-complete for patterns of height 2 or more and admit O(n)-time algorithms for patterns of height 1. We also prove that if the height and number of colors in the pattern is fixed, the non-uniform variant admits a O(n)-time algorithm while the uniform variant remains NP-complete. The NP-completeness results use a new reduction from a constrained version of a problem on finite state transducers.
Scientific journal, English - Self-attraction removal from oritatami systems
Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 10316, 164-176, 2017, Peer-reviwed, RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized (transcribed). Oritatami is a computational model of this phenomenon, which lets its transcript, a sequence of beads (abstract molecules) fold cotranscriptionally via interactions between beads according to its ruleset. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. We provide an algorithm for that with overhead linear in the delay parameter, which should be considerably smaller than the length of its transcript. We also show that this overhead is tight.
International conference proceedings, English - Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays
Trent A. Rogers; Shinnosuke Seki
FUNDAMENTA INFORMATICAE, IOS PRESS, 154, 1-4, 359-372, 2017, Peer-reviwed, RNA sequences start folding immediately as they are synthesized by RNA polymerase (cotranscriptional folding). The oritatami system (OS) is a novel mathematical model to study computational aspects of cotranscriptional folding. In this paper, we first provide a survey throughout existing research topics and results on oritatami systems and offer research directions of significance. Simulation of an oritatami system in a different ratio (delay) of transcription speed to the speed of folding is one of them. We will introduce a simple notion of simulation, and prove that there is an OS of delay delta that cannot be simulated by any oritatami system at larger delay.
Scientific journal, English - Self-attraction removal from oritatami systems
Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 10316, 164-176, 2017, Peer-reviwed, RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized (transcribed). Oritatami is a computational model of this phenomenon, which lets its transcript, a sequence of beads (abstract molecules) fold cotranscriptionally via interactions between beads according to its ruleset. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. We provide an algorithm for that with overhead linear in the delay parameter, which should be considerably smaller than the length of its transcript. We also show that this overhead is tight.
International conference proceedings, English - The extended equation of Lyndon and Schutzenberger
Florin Manea; Mike Muller; Dirk Nowotka; Shinnosuke Seki
Journal of Computer and System Sciences, Elsevier, 85, 132-167, 26 Nov. 2016, Peer-reviwed
Scientific journal, English - Rule set design problems for oritatami system
Makoto Ota; Shinnosuke Seki
Theoretical Computer Science, Elsevier, 671, 26-35, 22 Sep. 2016, Peer-reviwed
Scientific journal, English - Programming biomolecules that fold greedily during transcription
Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
MFCS 2016: 41st International Symposium on Mathematical Foundations of Computer Science, LIPIcs 58, 43:1-43:14, 22 Aug. 2016, Peer-reviwed
International conference proceedings, English - Binary pattern tile set synthesis is NP-hard
Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki
Algorithmica, Springer, 78, 1, 1-46, 26 Apr. 2016, Peer-reviwed
Scientific journal, English - The Complexity of Fixed-Height Patterned Tile Self-assembly
Shinnosuke Seki; Andrew Winslow
Implementation and Application of Automata, SPRINGER INT PUBLISHING AG, 9705, LNCS 9705, 248-259, 2016, Peer-reviwed, We characterize the complexity of the PATSproblem for patterns of fixed height and color count in variants of the model where seed glues are either chosen or fixed and identical (so-called non-uniform and uniform variants). We prove that both variants are NP-complete for patterns of height 2 or more and admit O(n)-time algorithms for patterns of height 1. We also prove that if the height and number of colors in the pattern is fixed, the non-uniform variant admits a O(n)-time algorithm while the uniform variant remains NP-complete. The NP-completeness results use a new reduction from a constrained version of a problem on finite state transducers.
International conference proceedings, English - Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 9818, 19-34, 2016, Peer-reviwed, The oritatami system (OS) is a model of computation by cotranscriptional folding, being inspired by the recent experimental succeess of RNA origami to self-assemble an RNA tile cotranscriptionally.The OSs implemented so far, including binary counter and Turing machine simulator, are deterministic, that is, uniquely fold into one conformation, while nondeterminism is intrinsic in biomolecular folding.We introduce nondeterminism to OS (NOS) and propose an NOS that chooses an assignment of Boolean values nondeterministically and evaluates a logical formula on the assignment.This NOS is seedless in the sense that it does not require any initial conformation to begin with like the RNA origami.The NOS allows to prove the co-NP hardness of deciding, given two NOSs, if there exists no conformation that one of them folds into but the other does not.
International conference proceedings, English - A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis
Aleck Johnsen; Ming-Yang Kao; Shinnosuke Seki
Journal of Combinatorial Optimization, Springer, 33, 2, 496-529, 24 Nov. 2015, Peer-reviwed
Scientific journal, English - Program Size and Temperature in Self-Assembly
Ho-Lin Chen; David Doty; Shinnosuke Seki
ALGORITHMICA, SPRINGER, 72, 3, 884-899, Jul. 2015, Peer-reviwed, Winfree's abstract Tile Assembly Model is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on their four sides. We show that there is a polynomial-time algorithm that, given an square, finds the minimal tile system (i.e., the system with the smallest number of distinct tile types) that uniquely self-assembles the square, answering an open question of Adleman et al. (Combinatorial optimization problems in self-assembly, STOC 2002). Our investigation leading to this algorithm reveals other positive and negative results about the relationship between the size of a tile system and its "temperature" (the binding strength threshold required for a tile to attach).
Scientific journal, English - Dynamic Simulation of 1D Cellular Automata in the Active aTAM
Natasa Jonoska; Daria Karpenko; Shinnosuke Seki
NEW GENERATION COMPUTING, SPRINGER, 33, 3, 271-295, Jul. 2015, Peer-reviwed, The Active aTAM is a tile based model for self-assembly where tiles are able to transfer signals and change identities according to the signals received. We extend Active aTAM to include deactivation signals and thereby allow detachment of tiles. We show that the model allows a dynamic simulation of cellular automata with assemblies that do not record the entire computational history but only the current updates of the states, and thus provide a way for (a) algorithmic dynamical structural changes in the assembly and (b) reusable space in self-assembly. The simulation is such that at a given location the sequence of tiles that attach and detach corresponds precisely to the sequence of states the synchronous cellular automaton generates at that location.
Scientific journal, English - 3-color bounded patterned self-assembly
Lila Kari; Steffen Kopecki; Shinnosuke Seki
NATURAL COMPUTING, SPRINGER, 14, 2, 279-292, Jun. 2015, Peer-reviwed, The problem of patterned self-assembly tile set synthesis (PATS) is to find a minimal tile set which uniquely self-assembles into a given pattern. Czeizler and Popa proved the NP-completeness of PATS and Seki showed that the PATS problem is already NP-complete for patterns with 60 colors. In search for the minimal number of colors such that PATS remains NP-complete, we introduce multiple bound PATS (MBPATS) where we allow bounds for the numbers of tile types of each color. We show that MBPATS is NP-complete for patterns with just three colors and, as a byproduct of this result, we also obtain a novel proof for the NP-completeness of PATS which is more concise than the previous proofs.
Scientific journal, English - Square-Density Increasing Mappings
Florin Manea; Shinnosuke Seki
COMBINATORICS ON WORDS, WORDS 2015, SPRINGER-VERLAG BERLIN, 9304, 160-169, 2015, Peer-reviwed, The square conjecture claims that the number of distinct squares, factors of the form xx, in a word is at most the length of the word. Being associated with it, it is also conjectured that binary words have the largest square density. That is, it is sufficient to solve the square conjecture for words over binary alphabet. We solve this subsidiary conjecture affirmatively, or more strongly, we prove the irrelevance of the alphabet size in solving the square conjecture, as long as the alphabet is not unary. The tools we employ are homomorphisms with which one can convert an arbitrary word into a word with strictly larger square density over an intended alphabet.
International conference proceedings, English - Semilinear Sets and Counter Machines: a Brief Survey
Oscar H. Ibarra; Shinnosuke Seki
FUNDAMENTA INFORMATICAE, IOS PRESS, 138, 1-2, 61-76, 2015, Peer-reviwed, Semilinear sets are one of the most important concepts in theoretical computer science, as illustrated by the fact that the set of nonnegative integer solutions to any system of Diophantine equations is semilinear. Parikh's theorem enables us to represent any semilinear set as a push-down automaton (PDA). We summarize recent results on the descriptional complexity of conversions among different representations of a semilinear set: as a vector set (conventional), a finite automaton (FA), a PDA, etc.. We also discuss semilinearity-preserving operations like union, intersection, and complement. We use Parikh's theorem to enlarge the class of finite-state machines that can represent semilinear sets. In particular, we give a simpler proof of a known result that characterizes semilinear sets in terms of machines with reversal-bounded counters. We then investigate the power of such a machine with only one counter in the context of a long-standing conjecture about repetition on words.
Scientific journal, English - Binary Pattern Tile Set Synthesis Is NP-hard
Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki
Automata, Languages, and Programming, Pt I, SPRINGER-VERLAG BERLIN, 9134, 1022-1034, 2015, Peer-reviwed, We solve an open problem, stated in 2008, about the feasibility of designing efficient algorithmic self-assembling systems which produce 2-dimensional colored patterns. More precisely, we show that the problem of finding the smallest tile assembly system which will self-assemble an input pattern with 2 colors (i.e., 2-Pats) is NP-hard. One crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof for the four color theorem and the recent important advance on the Erdos discrepancy problem using computer programs. In this paper, these techniques will be brought to a new order of magnitude, computational tasks corresponding to one CPU-year. We massively parallelize our program, and provide a full proof of its correctness. Its source code is freely available online.
International conference proceedings, English - Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise
Remi Lemoy; Alexander Mozeika; Shinnosuke Seki
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, IOP PUBLISHING LTD, 47, 10, 105001-105001, Mar. 2014, Peer-reviwed, Thermal noise in a cellular automaton (CA) refers to a random perturbation in its function which eventually leads the automaton to an equilibrium state controlled by a temperature parameter. We study the one-dimensional majority-3 CA under this model of noise. Without noise, each cell in the automaton decides its next state by majority voting among itself and its left and right neighbour cells. Transfer matrix analysis shows that the automaton always reaches a state in which every cell is in one of its two states with probability 1/2 and thus cannot remember even one bit of information. Numerical experiments, however, support the possibility of reliable computation for a long but finite time.
Scientific journal, English - A Stronger Square Conjecture on Binary Words
Natasa Jonoska; Florin Manea; Shinnosuke Seki
SOFSEM 2014: THEORY AND PRACTICE OF COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, 8327, 339-350, 2014, Peer-reviwed, We propose a stronger conjecture regarding the number of distinct squares in a binary word. Fraenkel and Simpson conjectured in 1998 that the number of distinct squares in a word is upper bounded by the length of the word. Here, we conjecture that in the case of a word of length n over the alphabet {a, b}, the number of distinct squares is upper bounded by 2k-1/2k+2n, where k is the least of the number of a's and the number of b's. We support the conjecture by showing its validity for several classes of binary words. We also prove that the bound is tight.
International conference proceedings, English - Operational State Complexity under Parikh Equivalence
Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
DESCRIPTIONAL COMPLEXITY OF FORMAL SYSTEMS, DCFS 2014, SPRINGER-VERLAG BERLIN, 8614, 294-305, 2014, Peer-reviwed, We investigate, under Parikh equivalence, the state complexity of some language operations which preserve regularity. For union, concatenation, Kleene star, complement, intersection, shuffle, and reversal, we obtain a polynomial state complexity over any fixed alphabet, in contrast to the intrinsic exponential state complexity of some of these operations in the classical version. For projection we prove a superpolynomial state complexity, which is lower than the exponential one of the corresponding classical operation. We also prove that for each two deterministic automata A and B it is possible to obtain a deterministic automaton with a polynomial number of states whose accepted language has as Parikh image the intersection of the Parikh images of the languages accepted by A and B. Finally, we prove that for each finite set there exists a small context-free grammar defining a language with the same Parikh image.
International conference proceedings, English - Generalised Lyndon-Schutzenberger Equations
Florin Manea; Mike Mueller; Dirk Nowotka; Shinnosuke Seki
MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2014, PT I, SPRINGER-VERLAG BERLIN, 8634, 402-+, 2014, Peer-reviwed, We fully characterise the solutions of the generalised Lyndon-Schutzenberger word equations u(1) ... u(l) = v(1) ... v(m)w(1) ... w(n), where u(i) is an element of {u, theta(u)} for all 1 <= i <= l, v(j) is an element of {v, theta(v)} for all 1 < j <= m, w(k) is an element of {w, theta(w)} for all 1 <= k <= n, and theta is an antimorphic involution. More precisely, we show for which f, m, and n such an equation has only theta-periodic solutions, i.e., u, v, w is an element of {t, theta(t)}* for some word t, closing an open problem by Czeizler et al. (2009).
International conference proceedings, English - On computational complexity of graph inference from counting
Szilárd Zsolt Fazekas; Hiro Ito; Yasushi Okuno; Shinnosuke Seki; Kei Taneishi
Natural Computing, Springer, 12, 4, 589-603, Dec. 2013, Peer-reviwed, In de novo drug design, chemical compounds are quantitized as real-valued vectors called chemical descriptors, and an optimization algorithm runs on known drug-like chemical compounds in a database and outputs an optimal chemical descriptor. Since structural information is needed for chemical synthesis, we must infer chemical graphs from the obtained descriptor. This is formalized as a graph inference problem from a real-value vector. By generalizing subword history, which was originally introduced in formal language theory to extract numerical information of words and languages based on counting, we propose a comprehensive framework to investigate the computational complexity of chemical graph inference. We also propose a (pseudo-)polynomial-time algorithm for inferring graphs in a class of practical importance from spectrums. © 2012 Springer Science+Business Media Dordrecht.
Scientific journal, English - On the open problem of Ginsburg concerning semilinear sets and related problems
Oscar H. Ibarra; Shinnosuke Seki
THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 501, 11-19, Aug. 2013, Peer-reviwed, In his 1966 book, "The Mathematical Theory of Context-Free Languages", S. Ginsburg posed the following open problem: Find a decision procedure for determining if an arbitrary semilinear set is a finite union of stratified linear sets. It turns out that this problem (which remains open) is equivalent to the problem of synchronizability of multitape machines. Given an n-tape automaton M of a given type (e.g., nondeterministic pushdown automaton (NPDA), nondeterministic finite automaton (NFA), etc.) with a one-way read-only head per tape and a right end marker on each tape, we say that M is 0-synchronized (or aligned) if for every n-tuple x = (x(1), . . . , x(n)) that is accepted, there is an accepting computation on x such that at any time during the computation, all heads except those that have reached the end marker are on the same position (i.e., aligned). One of our main contributions is to show that Ginsburg's problem is equivalent to deciding for an arbitrary n-tape NFA M accepting L(M) subset of a(1)* x . . . x a(n)* (where n >= 1 and a(1) , . . . , a(n) an are distinct symbols) whether there exists an equivalent 0-synchronized n-tape NPDA M'. Ginsburg's problem is decidable if M' is required to be an NFA, and we will generalize this decidability over bounded inputs. It is known that if the inputs are unrestricted, the problem is undecidable. We also show several other related decidability and undecidability results.
It may appear, as one of the referees suggested in an earlier version of this paper, that our main result can be written in first order logic. We explain why this is not the case in the Introduction. (C) 2013 Elsevier B.V. All rights reserved.
Scientific journal, English - The power of nondeterminism in self-assembly
Nathan Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
Theory of Computing, 9, 1-29, 2013, Peer-reviwed
Scientific journal, English - On the behavior of tile assembly system at high temperatures
Shinnosuke Seki; Yasushi Okuno
Computability, IOS Press, 2, 2, 107-124, 2013, Peer-reviwed, Behavior of Winfree's tile assembly system (TAS) at high temperatures is investigated in combination with integer programming of a specific form called threshold programming. First, we propose a way to build bridges from the Boolean satisfiability problem (SAT) to threshold programming, and further to TAS's behavior, in order to prove the NP-hardness of optimizing temperatures of TASs that behave in a way given as input. These bridges will take us further to two important results on the behavior of TASs at high temperatures. The first says that arbitrarily high temperatures are required to assemble some shape by a TAS of 'reasonable' size. The second is that for any temperature τ ≥ 4 given as a parameter, it is NP-hard to find the minimum size TAS that self-assembles a given shape at a temperature at most τ.
Scientific journal, English - Convering nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata
Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
Information and Computation, Elsevier, 228-229, 1-15, 2013, Peer-reviwed
Scientific journal, English - On the boundedness property of semilinear sets
Oscar H. Ibarra; Shinnosuke Seki
TAMC 2013: Proceedings of the 10th Annual Conference on Theory and Applications of Models of Computation, Springer, LNCS 7876, 156-168, 2013, Peer-reviwed
International conference proceedings, English - Combinatorial optimization in pattern assembly (extended abstract)
Shinnosuke Seki
UCNC 2013: Proceedings of the Unconventional Computation and Natural Computation - 12th International Conference, Springer, LNCS 7956, 220-231, 2013, Peer-reviwed
International conference proceedings, English - 3-Color Bounded Patterned Self-assemblyY
Lila Kari; Steffen Kopecki; Shinnosuke Seki
DNA COMPUTING AND MOLECULAR PROGRAMMING, DNA 2013, SPRINGER-VERLAG BERLIN, 8141, 105-117, 2013, Peer-reviwed, Patterned self-assembly tile set synthesis (Pats) is the problem of finding a minimal tile set which uniquely self-assembles into a given pattern. Czeizler and Popa proved the NP-completeness of Pats and Seki showed that the Pats problem is already NP-complete for patterns with 60 colors. In search for the minimal number of colors such that Pats remains NP-complete, we introduce multiple bound Pats (mbPats) where we allow bounds for the numbers of tile types of each color. We show that mbPats is NP-complete for patterns with just three colors and, as a byproduct of this result, we also obtain a novel proof for the NP-completeness of Pats which is more concise than the previous proofs.
International conference proceedings, English - Computing Minimum Tile Sets to Self-Assemble Color Patterns
Aleck C. Johnsen; Ming-Yang Kao; Shinnosuke Seki
ALGORITHMS AND COMPUTATION, SPRINGER-VERLAG BERLIN, 8283, 699-710, 2013, Peer-reviwed, Patterned self-assembly tile set synthesis (PATS) aims at finding a minimum tile set to uniquely self-assemble a given rectangular pattern. For k >= 1, k-PATS is a variant of PATS that restricts input patterns to those with at most k colors. We prove the NP-hardness of 29-PATS, where the best known is that of 60-PATS.
International conference proceedings, English - One-reversal counter machines and multihead automata: Revisited
Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki
THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 454, 81-87, Oct. 2012, Peer-reviwed, We investigate the power of (1-reversal) counter machines (finite automata with multiple counters, where each counter can "reverse" only once, i.e., once a counter decrements, it can no longer increment) and one-way multihead finite automata (finite automata with multiple one-way input heads) as a language acceptor. They can be non-deterministic as well as augmented with a pushdown stack. First, we prove that adding a pushdown stack properly strengthens the deterministic counter machines. Non-deterministic counter machines with a pushdown stack are then compared with multihead finite automata. The proof of their incomparability involves an interesting technique: an assumption that a language be accepted by a non-deterministic counter machine would bring a contradictory algorithm to decide an undecidable language. Furthermore, we will show that over bounded languages, these two kinds of machines have the same power, and neither non-determinism nor a pushdown stack makes them stronger. (C) 2012 Elsevier B.V. All rights reserved.
Scientific journal, English - CHARACTERIZATIONS OF BOUNDED SEMILINEAR LANGUAGES BY ONE-WAY AND TWO-WAY DETERMINISTIC MACHINES
Oscar H. Ibarra; Shinnosuke Seki
INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 23, 6, 1291-1305, Sep. 2012, Peer-reviwed, A hounded language L subset of x(1)* ... x(k)* (for some k >= 1 and not-necessarily distinct nonempty words x(1), ... , x(k)) is bounded semilinear if the set Q(L) - {(i(1), ..., i(k)) vertical bar x(1)(i1) ... x(k)(ik) is an element of L} is semilinear, We give characterizations of bounded semilinear languages in terms of one-way and two-way deterministic counter machines.
Scientific journal, English - Absoluteness of subword inequality is undecidable
Shinnosuke Seki
THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 418, 116-120, Feb. 2012, Peer-reviwed, In a given word, one can count the number of occurrences of other words as a scattered subword. These counts can be "added" and/or "multiplied." A subword history gives an instruction of what words to be counted and how these counts to be added and multiplied with other counts or integer constants, and hence, determines its unique value in a given word. Mateescu, Salomaa, and Yu asked: "is it decidable whether the value of a given subword history is non-negative in all words over a given alphabet?" (absoluteness problem). Another important problem is of whether there exists a word in which the value of a given subword history becomes 0 (equality problem). In this paper, we prove the undecidability of the equality problem and show that the equality problem is polynomial-time Karp reducible to the absoluteness problem: thus, the absoluteness problem is also undecidable. This approach solves the open problem actually under stronger conditions than supposed originally. (C) 2011 Elsevier B.V. All rights reserved.
Scientific journal, English - Iterated Hairpin Completions of Non-crossing Words
Lila Kari; Steffen Kopecki; Shinnosuke Seki
SOFSEM 2012: THEORY AND PRACTICE OF COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, 7147, 337-+, 2012, Peer-reviwed, Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive language and for some words it is known to be non-context-free. However, it is unknown whether regularity of iterated hairpin completion of a given word is decidable. Also the question whether iterated hairpin completion of a word can be context-free but not regular was asked in literature. In this paper we investigate iterated hairpin completions of non-crossing words and, within this setting, we are able to answer both questions. For non-crossing words we prove that the regularity of iterated hairpin completions is decidable and that if iterated hairpin completion of a non-crossing word is not regular, then it is not context-free either.
International conference proceedings, English - Triangular and hexagonal tile self-assembly systems
Lila Kari; Shinnosuke Seki; Zhi Xu
WTCS 2012: Proceedings of the International Workshop on Theoretical Computer Science, Springer, LNCS 7160, 357-375, 2012, Peer-reviwed
International conference proceedings, English - Converting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
DLT 2012: Proceedings of the 16th International Conference on Developments in Language Theory, Springer, LNCS 7410, 284-295, 2012, Peer-reviwed
International conference proceedings, English - SCHEMA FOR PARALLEL INSERTION AND DELETION: REVISITED
Lila Kari; Shinnosuke Seki
INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 22, 7, 1655-1668, Nov. 2011, Peer-reviwed, A general framework of parallel insertion and deletion based on p-schemata is proposed. A p-schema is a set of tuples of words. When being used for parallel insertion of a language into a word, an element of p-schema specifies how to split the word into factors between which the language to be inserted. As its inverse operation, parallel deletion based on the p-schema is defined. Several algebraic properties of these operations such as closure properties of language classes under them are proved. The main contribution of this paper is to propose algorithms to solve language equations involving p-schema-based insertions or deletions based on syntactic congruence. These algorithms not only decide whether a given equation has a solution but construct the set of all of its maximal or minimal solutions. The algorithms are extensible so as to solve some multiple-variables equations and inequalities. Related undecidability results are also presented.
Scientific journal, English - An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki
INFORMATION AND COMPUTATION, ACADEMIC PRESS INC ELSEVIER SCIENCE, 209, 4, 717-730, Apr. 2011, Peer-reviwed, One of the particularities of information encoded as DNA strands is that a string u contains basically the same information as its Watson Crick complement, denoted here as theta(u). Thus, any expression consisting of repetitions of u and theta(u) can be considered in some sense periodic. In this paper, we give a generalization of Lyndon and Schutzenberger's classical result about equations of the form u(l) = V(n)W(m) to cases where both sides involve repetitions of words as well as their complements. Our main results show that, for such extended equations, if l >= 5, n, m >= 3, then all three words involved can be expressed in terms of a common word t and its complement theta(t). Moreover, if l >= 5, then n = m = 3 is an optimal bound. These results are established based on a complete characterization of all possible overlaps between two expressions that involve only some word u and its complement theta(u), which is also obtained in this paper. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.
Scientific journal, English - Block insertion and deletion on trajectories
Bo Cui; Lila Kari; Shinnosuke Seki
THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 412, 8-10, 714-728, Mar. 2011, Peer-reviwed, In this paper, we introduce block insertion and deletion on trajectories, which provide us with a new framework to study properties of language operations. With the parallel syntactical constraint provided by trajectories, these operations properly generalize several sequential as well as parallel binary language operations such as catenation, sequential insertion, k-insertion, parallel insertion, quotient, sequential deletion, k-deletion, etc.
We establish some relationships between the new operations and shuffle and deletion on trajectories, and obtain several closure properties of the families of regular and context-free languages under the new operations. Moreover, we obtain several decidability results of three types of language equation problems which involve the new operations. The first one is to answer, given languages L-1, L-2, L-3 and a trajectory set T. whether the result of an operation between L-1 and L-2 on the trajectory set T is equal to L-3. The second one is to answer, for three given languages L-1, L-2, L-3, whether there exists a set of trajectories such that the block insertion or deletion between L-1 and L-2 on this trajectory set is equal to L-3. The third problem is similar to the second one, but the language L-1 is unknown while languages L-2, L-3 as well as a trajectory set T are given. Crown Copyright (C) 2010 Published by Elsevier B.V. All rights reserved.
Scientific journal, English - PROPERTIES OF PSEUDO-PRIMITIVE WORDS AND THEIR APPLICATIONS
Lila Kari; Benoit Masson; Shinnosuke Seki
INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 22, 2, 447-471, Feb. 2011, Peer-reviwed, A pseudo-primitive word with respect to an antimorphic involution theta is a word which cannot be written as a catenation of occurrences of a strictly shorter word t and theta(t). Properties of pseudo-primitive words are investigated in this paper. These properties link pseudo-primitive words with essential notions in combinatorics on words such as primitive words, (pseudo)-palindromes, and (pseudo)-commutativity. Their applications include an improved solution to the extended Lyndon-Schutzenberger equation u(1) u(2) ... u(l) = v(1) ... v(n) w(1) ... w(m), where u(1),..., u(l) is an element of {u, theta(u)}, v(1),..., v(n) is an element of (v, theta(v)}, and w(1),..., w(m) is an element of {w, theta(w)} for some words u, v, w, integers l,n,m >= 2, and an antimorphic involution theta. We prove that for l >= 4, n, m >= 3, this equation implies that u, v, w can be expressed in terms of a common word t and its image theta(t). Moreover, several cases of this equation where l = 3 are examined.
Scientific journal, English - Triangular Tile Self-assembly Systems
Lila Kari; Shinnosuke Seki; Zhi Xu
DNA COMPUTING AND MOLECULAR PROGRAMMING, SPRINGER-VERLAG BERLIN, 6518, 89-99, 2011, Peer-reviwed, We discuss theoretical aspects of the self-assembly of triangular tiles; in particular, right triangular tiles and equilateral triangular tiles. Contrary to intuition, we show that triangular tile assembly systems and square tile assembly systems are not comparable in general. More precisely, there exists a square tile assembly system S such that no triangular tile assembly system that is a division of S produces the same final supertile. There also exists a deterministic triangular tile assembly system T such that no square tile assembly system produces the same final supertiles while preserving border glues. We discuss the assembly of triangles by triangular tiles and show triangular systems with Theta(log N/log log N) tiles that can self-assemble into a triangular supertile of size Theta(N(2)). Lastly, we show that triangular tile assembly systems, either right-triangular or equilateral, are Turing universal.
International conference proceedings, English - Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement
Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
DNA COMPUTING AND MOLECULAR PROGRAMMING, SPRINGER-VERLAG BERLIN, 6518, 25-36, 2011, Peer-reviwed, We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. The design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. The design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. This means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes.
International conference proceedings, English - ORTHOGONAL SHUFFLE ON TRAJECTORIES
Mark Daley; Lila Kari; Shinnosuke Seki; Petr Sosik
INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, WORLD SCIENTIFIC PUBL CO PTE LTD, 22, 1, 213-222, Jan. 2011, Peer-reviwed, A language L is called the orthogonal shuffle of the language L(1) with the language L(2), along the trajectory set T if every word in L is uniquely obtained as the shuffle between a word in L(1), a word in L(2) along a trajectory word in T. In this paper we investigate properties of the orthogonal shuffle on trajectories, as well as several types of language equations using this language operation. As a corollary, we obtain several properties of orthogonal catenation, orthogonal literal shuffle and orthogonal insertion.
Scientific journal, English - K-Comma Codes and Their Generalizations
Bo Cui; Lila Kari; Shinnosuke Seki
FUNDAMENTA INFORMATICAE, IOS PRESS, 107, 1, 1-18, 2011, Peer-reviwed, In this paper, we introduce the notion of k-comma codes-a proper generalization of the notion of comma-free codes. For a given positive integer k, a k-comma code is a set L over an alphabet Sigma with the property that L Sigma(k) L boolean AND Sigma(+) L Sigma(+) = empty set. Informally, in a k-comma code, no codeword can be a subword of the catenation of two other codewords separated by a "comma" of length k. A k-comma code is indeed a code, that is, any sequence of codewords is uniquely decipherable. We extend this notion to that of k-spacer codes, with commas of length less than or equal to a given k. We obtain several basic properties of k-comma codes and their generalizations, k-comma intercodes, and some relationships between the families of k-comma intercodes and other classical families of codes, such as infix codes and bifix codes. Moreover, we introduce the notion of n-k-comma intercodes, and obtain, for each k >= 0, several hierarchical relationships among the families of n-k-comma intercodes, as well as a characterization of the family of 1-k-comma intercodes.
Scientific journal, English - On the Regularity of Iterated Hairpin Completion of a Single Word
Lila Kari; Shinnosuke Seki; Steffen Kopecki
FUNDAMENTA INFORMATICAE, IOS PRESS, 110, 1-4, 201-215, 2011, Peer-reviwed, Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand w = x alpha y (alpha) over bar, and outputs w ' = x alpha y (alpha) over bar(x) over bar, where (x) over bar denotes the Watson-Crick complement of x. In this paper, we focus on the problem of finding conditions under which the iterated hairpin completion of a given word is regular. According to the numbers of words alpha and (alpha) over bar that initiate hairpin completion and how they are scattered, we classify the set of all words w. For some basic classes of words w containing small numbers of occurrences of alpha and (alpha) over bar, we prove that the iterated hairpin completion of w is regular. For other classes with higher numbers of occurrences of alpha and (alpha) over bar, we prove a necessary and sufficient condition for the iterated hairpin completion of a word in these classes to be regular.
Scientific journal, English - The Power of Nondeterminism in Self-Assembly
Nathaniel Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
PROCEEDINGS OF THE TWENTY-SECOND ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, SIAM, 590-602, 2011, Peer-reviwed, We investigate the role of nondeterminism in Winfree's abstract tile assembly model, which was conceived to model artificial molecular self-assembling systems constructed from DNA. By nondeterminism we do not mean a magical ability such as that possessed by a nondeterministic algorithm to search an exponential-size space in polynomial time. Rather, we study realistically implementable systems that retain a different sense of determinism in that they are guaranteed to produce a unique shape but are nondeterministic in that they do not guarantee which tile types will be placed where within the shape.
We show a "molecular computability" result: there is an infinite shape S that is uniquely assembled by a tile system but not by any deterministic tile system. We show a "molecular complexity" result: there is a finite shape S that is uniquely assembled by a tile system with c tile types, but every deterministic tile system that uniquely assembles S has more than c tile types. In fact we extend the technique to derive a stronger (classical complexity theoretic) result, showing that the problem of finding the minimum number of tile types that uniquely assemble a given finite shape is Sigma(P)(2)- complete. In contrast, the problem of finding the minimum number of deterministic tile types that uniquely assemble a shape is NP-complete [5].
International conference proceedings, English - One-Reversal Counter Machines and Multihead Automata: Revisited
Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki
SOFSEM 2011: THEORY AND PRACTICE OF COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, 6543, 166-177, 2011, Peer-reviwed, Among the many models of language acceptors that have been studied in the literature are multihead finite automata (finite automata with multiple one-way input heads) and 1-reversal counter machines (finite automata with multiple counters, where each counter can only "reverse" once, i.e., once a counter decrements, it can no longer increment). The devices can be deterministic or nondeterministic and can be augmented with a pushdown stack. We investigate the relative computational power of these machines. Our results (where C-1 and C-2 are classes of machines) are of the following types:
1. Machines in C-1 and C-2 are incomparable.
2. Machines in C-1 are strictly weaker than machines in C-2.
In obtaining results of these types, we use counting and "cut-and-paste" arguments as well as an interesting technique that shows that if a language were accepted by a device in a given class, then all recursively enumerable languages would be decidable.
International conference proceedings, English - Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
Oscar H. Ibarra; Shinnosuke Seki
AFL 2011: Proceedings of the 13th International Conference on Automata and Formal Languages, 211-224, 2011, Peer-reviwed
International conference proceedings, English - Program Size and Temperature in Self-assembly
Ho-Lin Chen; David Doty; Shinnosuke Seki
ALGORITHMS AND COMPUTATION, SPRINGER-VERLAG BERLIN, 7074, 445-+, 2011, Peer-reviwed, Winfree's abstract Tile Assembly Model (aTAM) is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on their four sides. We show that there is a polynomial-time algorithm that, given an n x n square, finds the minimal tile system (i.e., the system with the smallest number of distinct tile types) that uniquely self-assembles the square, answering an open question of Adleman, Cheng, God, Huang, Kempe, Moisset de Espanes, and Rothemund (Combinatorial Optimization Problems in Self-Assembly, STOC 2002). Our investigation leading to this algorithm reveals other positive and negative results about the relationship between the size of a tile system and its "temperature" (the binding strength threshold required for a tile to attach).
International conference proceedings, English - On a special class of primitive words
Elena Czeizler; Lila Kari; Shinnosuke Seki
THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 411, 3, 617-630, Jan. 2010, Peer-reviwed, When representing DNA molecules as words, it is necessary to take into account the fact that a word u encodes basically the same information as its Watson-Crick complement theta(u), where theta denotes the Watson-Crick complementarity function. Thus, an expression which involves only a word u and its complement can be still considered as a repeating sequence. In this context, we define and investigate the properties of a special class of primitive words, called pseudo-primitive words relative to theta or simply theta-primitive words, which cannot be expressed as such repeating sequences. For instance, we prove the existence of a unique theta-primitive root of a given word, and we give some constraints forcing two distinct words to share their theta-primitive root. Also, we present an extension of the well-known Fine and Wilf theorem, for which we give an optimal bound. (C) 2009 Elsevier B.V. All rights reserved.
Scientific journal, English - An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality
Lila Kari; Shinnosuke Seki
FUNDAMENTA INFORMATICAE, IOS PRESS, 101, 3, 215-236, 2010, Peer-reviwed, Considering two DNA molecules which are Watson-Crick (WK) complementary to each other "equivalent" with respect to the information they encode enables us to extend the classical notions of repetition, period, and power. WK-complementarity has been modelled mathematically by an antimorphic involution theta, i.e., a function theta such that theta( xy) = theta(y)theta(x) for any x, y is an element of Sigma*, and theta(2) is the identity. The WK-complementarity being thus modelled, any word which is a repetition of u and theta(u) such as u u, u theta(u)u, and u theta(u)theta(u)theta(u) can be regarded repetitive in this sense, and hence, called a theta-power of u. Taking the notion of theta-power into account, the Fine and Wilf's theorem was extended as "given an antimorphic involution theta and words u, v, if a theta-power of u and a theta-power of v have a common prefix of length at least b (vertical bar u vertical bar, vertical bar v vertical bar) = 2 vertical bar u vertical bar + vertical bar v vertical bar - gcd (vertical bar u vertical bar, vertical bar v vertical bar), then u and v are theta-powers of a same word." In this paper, we obtain an improved bound b' (vertical bar u vertical bar, vertical bar v vertical bar) = b (vertical bar u vertical bar, vertical bar v vertical bar) -[gcd (vertical bar u vertical bar, vertical bar v vertical bar)/2.. Then we show all the cases when this bound is optimal by providing all the pairs of words (u,v) such that they are not theta-powers of a same word, but one can construct a theta-power of u and a theta-power of v whose maximal common prefix is of length equal to b'(vertical bar u vertical bar, vertical bar v vertical bar) - 1. Furthermore, we characterize such words in terms of Sturmian words.
Scientific journal, English - Schema for Parallel Insertion and Deletion
Lila Kari; Shinnosuke Seki
DEVELOPMENTS IN LANGUAGE THEORY, SPRINGER-VERLAG BERLIN, 6224, 267-278, 2010, Peer-reviwed, We propose a general framework for parallel insertion/deletion operations based on p-schemata. A p-schema is a set of tuples of words. When being used for parallel insertion of a language into a word, an element of a p-schema specifies how to split the given word into factors between which the insertion of the language will take place. Parallel deletion based on a p-schema is defined as an "inverse" operation of parallel insertion based on the p-schema. Several well-known language operations are particular cases of p-schema-based insertions or deletions: catenation, Kleene star, reverse catenation, sequential insertion, parallel insertion, insertion next to a given letter, contextual insertion, right and left quotient, sequential deletion, parallel deletion. Additional operations that can be defined using p-schemata include contextual parallel insertion, as well as parallel insertion (deletion) of exactly n words, at most n words, an arbitrary number of words. We also consider the decidability and undecidability of existence of solutions of language equations involving p-schema-based parallel insertion/deletion.
International conference proceedings, English - Twin-roots of words and their properties
Lila Kari; Kalpana Mahalingam; Shinnosuke Seki
THEORETICAL COMPUTER SCIENCE, ELSEVIER SCIENCE BV, 410, 24-25, 2393-2400, May 2009, Peer-reviwed, In this paper we generalize the notion of an iota-symmetric word, from an antimorphic involution, to an arbitrary involution iota as follows: a nonempty word w is said to be iota-symmetric if w = alpha beta = iota(beta alpha) for some words alpha, beta. We propose the notion of iota-twin-roots (x, y) of an iota-symmetric word w. We prove the existence and uniqueness of the iota-twin-roots of ail iota-symmetric word, and show that the left factor alpha and right factor beta of any factorization of w as w = alpha beta = iota(beta alpha), can be expressed in terms of the iota-twin-roots of w. In addition, we show that for any involution iota, the catenation of the iota-twin-roots of w equals the primitive root of w. We also provide several characterizations of the iota-twin-rots of a word, for iota being a morphic or antimorphic involution. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.
Scientific journal, English - On pseudoknot-bordered words and their properties
Lila Kari; Shinnosuke Seki
JOURNAL OF COMPUTER AND SYSTEM SCIENCES, ACADEMIC PRESS INC ELSEVIER SCIENCE, 75, 2, 113-121, Feb. 2009, Peer-reviwed, We Study a generalization of the classical notions of [)ordered and unbordered words, motivated by biomolecular Computing. DNA strands can be viewed as finite strings over the alphabet [A, G, C, T), and are used in biomolecular computing to encode information. Due to the fact that A is Witson-Crick complementary to T and G to C, DNA single strands that are Watson-Crick complementary can bind to each other or to themselves forming so-called secondary structures, Most of these secondary structures are undesirable for biomolecular computational purposes since the strands they involve cannot further interact with other strands. This paper studies pseudoknot-bordered words, a mathematical formalization of pseudoknot-like inter- and intra-molecular structures. In this context, pseudoknot-unbordered words model DNA or RNA strands that will be free of such secondary structures. We obtain several properties of pseudoknot-bordered and -unbordered words. We also address Following problem: Given a pseudoknot-unbordered word u, does {u}(+) consist of pseudoknot-unbordered words only? We show that this is not generally true. We find that a sufficient condition for {u}(+) to consist of pseudoknot-unbordered words only is that it be not primitive. All of our results hold for arbitrary antimorphic involutions, of which the DNA Watson-Crick complementarity function is a particular case. Crown Copyright (c) 2008 Published by Elsevier Inc. All rights reserved.
Scientific journal, English - An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots
Shinnosuke Seki; Satoshi Kobayashi
NATURAL COMPUTING, PROCEEDINGS, SPRINGER, 1, 179-+, 2009, Peer-reviwed, Pseudoknots, one of the key components of RNA secondary structures, have been almost systematically intractable because of the difficulty in modeling them. Tree adjoining grammars have proved to be promising for this problem but the question of how to make TAG-based applications practical enough to analyze RNAs of thousands nucleotides remains open. This paper addresses this problem. It makes use of biological properties of pseudoknots, the scarcity and short-bp property. Experiments showed that our algorithm can align RNAs of the length tip to about 2400 nucleotides with biologically meaningful outputs extremely fast on the standard workstation environment. An executable version of our implementation is available at http://www.csd.uwo.ca/(similar to)sseki/
International conference proceedings, English - Towards the Sequence Design Preventing Pseudoknot Formation
Lila Kari; Shinnosuke Seki
NATURAL COMPUTING, PROCEEDINGS, SPRINGER, 1, 101-110, 2009, Peer-reviwed, This paper addresses a pseudoknot-freeness problem of DNA and RNA sequences, motivated by biomolecular computing. Watson-Crick (WK) complementarity forces DNA strands to fold into themselves and form so-called secondary structures, which are usually undesirable for biomolecular computational purposes. This paper studies pseudoknot-bordered words, a mathematical formalization of a common secondary structure, the pseudoknot. We obtain several properties of WK-pseudoknot-bordered and -unbordered words. One of the main results of the paper is that a sufficient condition for a WK-pseudoknot-unbordered word u to result in all words in u(+) being WK-pseudoknot-unbordered is for u not to be a primitive word.
International conference proceedings, English - Duplication in DNA Sequences
Masami Ito; Lila Kari; Zachary Kincaid; Shinnosuke Seki
ALGORITHMIC BIOPROCESSES, SPRINGER-VERLAG BERLIN, LNCS 5257, 43-+, 2009, Peer-reviwed, The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.
International conference proceedings, English - On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes
Bo Cui; Lila Kari; Shinnosuke Seki
ALGEBRAIC INFORMATICS, SPRINGER-VERLAG BERLIN, 5725, 204-219, 2009, Peer-reviwed, This paper studies Conditions under which the operation of parallel insertion can be reversed by parallel deletion. i.e.. when does the equality (L(1) double left arrow L(2)) double right arrow L(2) = L(1) hold for languages L(1) and L(2). We obtain a complete characterization of the solutions in the special M. se when both languages involved are singleton words. We also define comma codes, a family of codes with the property that, if L(2) is a comma code, then the above equation holds for any language L(1) subset of Sigma*. Lastly, we generalize the notion of comma codes to that of comma intercodes of index m. Besides several properties, we prove that the families of comma intercedes of index m form an infinite proper inclusion hierarchy, the first element which is a subset of the family of infix codes, and the last element of which is a subset of the family of bifix codes.
International conference proceedings, English - An Extension of the Lyndon Schutzenberger Result to Pseudoperiodic Words
Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki
DEVELOPMENTS IN LANGUAGE THEORY, PROCEEDINGS, SPRINGER-VERLAG BERLIN, 5583, 183-+, 2009, Peer-reviwed, One of the particularities of information encoded as DNA strands is that a string u contains basically the same information as its Watson-Crick complement, denoted here as theta(u). Thus, any expression consisting of repetitions of u and theta(u) can be considered in some sense periodic. In this paper we give a generalization of Lyndon and Schutzenberger's classical result about equations of the form u(l) = upsilon(n)omega(m), to cases where both sides involve repetitions of words as well as their complements. Our main results show that, for such extended equations, if l >= 5, n, m >= 3, then all three words involved can be expressed in terms of a common word t and its complement theta(t). Moreover. if l >= 5, then n = m = 3 is an optimal bound. We also obtain a complete characterization of all possible overlaps between two expressions that involve only some word u and its complement theta(u).
International conference proceedings, English - On a special class of primitive words
Elena Czeizler; Lila Kari; Shinnosuke Seki
MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2008, PROCEEDINGS, SPRINGER-VERLAG BERLIN, 5162, 265-277, 2008, Peer-reviwed, When representing DNA molecules as words, it is necessary to take into account the fact that a word u encodes basically the same information as its Watson-Crick complement theta(u), where theta denotes the Watson-Crick complementarity function. Thus, an expression which involves only a word u and its complement can be still considered as a, repeating sequence. In this context, we define and investigate the properties of a special class of primitive words, called theta-primitive, which cannot be expressed as such repeating sequences. For instance, we prove the existence of a unique theta-primitive root of a given word, and we give some constraints forcing two distinct words to share their theta-primitive root. Also, we present an extension of the well-known Fine and Wilf Theorem, for which we give an optimal bound.
International conference proceedings, English - A grammatical approach to the alignment of structure-annotated strings
S Seki; S Kobayashi
IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, IEICE-INST ELECTRONICS INFORMATION COMMUNICATIONS ENG, E88D, 12, 2727-2737, Dec. 2005, Peer-reviwed, In this paper, we are concerned with a structural ambiguity problem of tree adjoining grammars (TAGS), which is an essential problem when we try to model consensus structures of given set of ribonucleic acid (RNA) secondary structures by TAGS. RNA secondary structures can be represented as strings with structural information, and TAGS have a descriptive capability of this kind of strings, what we call structure-annotated strings. Thus, we can model RNA secondary structures by TAGs. It is sufficient to use existing alignment methods for just computing the optimal alignment between RNA secondary structures. However, when we also want to model the resulting alignment by grammars, if we adopt these existing methods, then we may fail in modeling the alignment result by grammars. Therefore, it is important to introduce a new alignment method whose alignment results can be appropriately modeled by grammars. In this paper, we will propose an alignment method based on TAG'S derivations each corresponding to a given RNA secondary structure. For an RNA secondary structure, there exist a number of derivations of TAGS which correspond to the structure. From the grammatical point of view, the property of TAGS drives us to the question how we should choose a derivation from these candidates in order to obtain an optimal alignment. This is the structural ambiguity problem of TAGS, which will be mainly discussed in this paper. For dealing with this problem appropriately, we will propose an edit distance between two structure-annotated strings, and then present an algorithm which computes an optimal alignment based on the edit distance.
Scientific journal, English - Efficient learning of k-reversible context-free grammars from positive structural examples
S Seki; S Kobayashi
GRAMMATICAL INFERENCE: ALGORITHMS AND APPLICATIONS, PROCEEDINGS, SPRINGER-VERLAG BERLIN, 3264, 285-287, 2004, Peer-reviwed, This paper discusses on the learnability of context free grammars(CFGs) within the framework of identification in the limit from positive structural examples. We will introduce a new subclass of CFGs, called a class of k-reversible context-free grammars and propose an O(kdn(3)) algorithm for learning this new subclass of CFGs, where d is the maximum of the ranks of given skeletal trees, and n is the total size of the given examples.
Scientific journal, English - Hierarchical Alignment of RNA secondary structures including pseudoknots
Shinnosuke Seki; Atsushi Kijima; Satoshi Kobayashi; Genichi Sanpei
GIW 2004: Proceedings of the 15th International Conference on Genome Informatics, 117-1-117-2, 2004, Peer-reviwed
International conference proceedings, English
MISC
- RNA折り紙
関 新之助
Lead, 2019, 電子情報通信学会誌, 102, 4, 330-334, Japanese, Peer-reviwed, Invited - Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists
Shinnosuke Seki
SIAM (Society for Industrial and Applied Mathematics), 01 May 2017, SIAM News, Not assigned yet, English, Peer-reviwed, Introduction scientific journal
Books and other publications
- Special issue of New Generation Computing devoted to Hagiya-sensei's 64th birthday.
English, Joint editor, Springer, Aug. 2022 - Special issue of Natural Computing devoted to the International Conference on Unconventional Computation and Natural Computation (UCNC 2019)
Ian McQuillan; Shinnosuke Seki
English, Joint editor, Springer, 2021 - Special issue of International Journal of Foundations of Computer Science (IJFCS) devoted to Developments in Language Theory 2018
Shinnosuke Seki
English, Editor, World Scientific, Sep. 2020 - Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation (UCNC2019, Tokyo, Japan, June 3-7, 2019)
English, Joint editor, Springer, 2019 - Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation
English, Joint editor, Springer, 2019 - Proceedings of the 22nd International Conference on Developments in Language Theory (DLT2018, Tokyo, Japan, September 10-14, 2018)
Scholarly book, English, Joint editor, Springer, 06 Aug. 2018 - Encyclopedia of Algorithms
Shinnosuke Seki
Dictionary or encycropedia, English, Single work, Patterned Self-Assembly Tile Set Synthesis, Springer, 2016 - Handbook of Natural Computing
Lila Kari; Shinnosuke Seki; Petr Sosik
Scholarly book, English, Contributor, Springer, 2012 - Proc. 14th International Conference on Developments in Language Theory
Yuan Gao; Hanlin Lu; Shinnosuke Seki; Sheng Yu
Scholarly book, English, Editor, Springer, 2010
Lectures, oral presentations, etc.
- How complex shapes can RNA fold into?
Shinnosuke Seki
Invited oral presentation, English, 17th International Conference on Reachability Problems (RP 2023), Invited, Peer-reviewed
13 Oct. 2023
11 Oct. 2023- 13 Oct. 2023 - Freezing 1-Tag systems with states
Szilard Zsolf Fazekas
Oral presentation, English, 16th International Conference on Automata and Formal Languages (AFL 2023), Peer-reviewed
06 Sep. 2023
05 Sep. 2023- 07 Sep. 2023 - On algorithmic self-assembly of squares by co-transcriptional folding
Ryuichi Matsuoka
Oral presentation, English, The 33rd International Symposium on Algorithms and Computation (ISAAC 2022), Hanyang University, Seoul, Republic of Korea, Peer-reviewed
20 Dec. 2022
19 Dec. 2022- 21 Dec. 2022 - Single-stranded architectures for computing by RNA co-transcriptional folding
Shinnosuke Seki
Public discourse, English, Invited, Ajou University, Suwon, Republic of Korea
15 Dec. 2022 - Single-stranded architectures for RNA co-transcriptional folding
Shinnosuke Seki
Invited oral presentation, English, Moving and Computing 2022 (MaC2022), Invited, University of Pisa, Pisa, Italy, International conference
19 Sep. 2022 - Single-stranded architectures for RNA co-transcriptional folding
Shinnosuke Seki
Invited oral presentation, English, Dagstuhl seminar 22381: Rational Design of Ribonucleic Acids, Invited, Schloss Dagstuhl, Dagstuhl, Germany, International conference
19 Sep. 2022 - Turedo a new computational model for molecular nanobots?
Nicolas Schabanel
Invited oral presentation, English, Computability in Europe (CiE 2022), Invited, Swansea University, International conference
14 Jul. 2022 - Oritatami systems assemble shapes no less complex than tile assembly model
Nicolas Schabanel
Oral presentation, English, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), International conference
15 Mar. 2022 - Algorithmic self-assembly of squares in oritatami
松岡 龍一
Oral presentation, English, 2021年度 冬のLAシンポジウム, 京都大学数理解析研究所, Domestic conference
01 Feb. 2021 - Simple intrinsic simulation of cellular automata in oritatami molecular folding model
Daria Pchelina
Oral presentation, English, 14th Latin American Symposium on Theoretical Informatics (LATIN 2020), Invited, International conference
05 Jan. 2021 - Les oritatamis tracent des dessins indécidables
Nicolas Schabanel
Oral presentation, French, Journées SDA2 2020: Systèmes Dynamiques, Automates et Algorithmes, Caen, France, International conference
04 Dec. 2020 - Single-stranded architectures for computing
Shinnosuke Seki
Oral presentation, English, 1st International Conference on Information Technology and Data Science, Invited, University of Debrecen, Debrecen, Hungary, International conference
06 Nov. 2020 - A single-stranded architecture for infinite counting
Shinnosuke Seki
Public discourse, English, Invited, Politecnico di Torino (Torino, Italy)
27 Jan. 2020 - Counting infinitely by oritatami co-transcriptional folding
Kohei Maruyama
Oral presentation, English, SOFSEM2020: 46th International Conference on Current Trends in Theory and Practice of Informatics, Limassol, Cyprus, International conference
20 Jan. 2020 - Single-stranded architectures for computing
Shinnosuke Seki
Invited oral presentation, English, 23rd International Conference on Developments in Language Theory (DLT 2019), Invited, University of Warsaw, Warsaw, Poland, International conference
05 Aug. 2019 - A general architecture of oritatami systems for simulating arbitrary finite automata
Shinnosuke Seki
Oral presentation, English, CIAA2019: 24th International Conference on Implementation and Application of Automata, Slovak Academy of Science, Kosice, Slovakia, International conference
22 Jul. 2019 - On the power of oritatami cotranscriptional folding with unary bead sequence
Kohei Maruyama; Reoto Morita
Oral presentation, English, TAMC2019: 15th Annual Conference on Theory and Applications of Models of Computation, International conference
13 Apr. 2019 - Proving the Turing universality of oritatami cotranscriptional folding
Nicolas Schabanel
Oral presentation, English, 29th International Symposium on Algorithms and Computation (ISAAC2018), International conference
16 Dec. 2018 - Know when to fold 'em: Self-assembly of shapes by folding in oritatami
Nicolas Schabanel
Oral presentation, English, DNA24: 24th International Conference on DNA Computing and Molecular Programming, International conference
08 Oct. 2018 - Transcript desing problem of oritatami systems
Hwee Kim
Oral presentation, English, DNA24: 24th International Conference on DNA Computing and Molecular Programming, International conference
08 Oct. 2018 - Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
Yusei Masuda; Yuki Ubukata
Oral presentation, English, 23rd International Conference on Implementation and Application of Automata (CIAA 2018), International conference
30 Jul. 2018 - Proving Turing universality of cotranscriptional folding
Shinnosuke Seki
Oral presentation, English, 2018 Zassenhaus Groups and Friends Conference, Invited, University of South Florida, Tampa, FL, USA, International conference
06 Apr. 2018 - Self-Assembly of shapes by cotranscriptional folding
Shinnosuke Seki
Oral presentation, English, Invited, Department of Mathematics and Statistics, University of South Florida
02 Apr. 2018 - Cotranscriptional Folding: A Frontier in Molecular Engineering
Shinnosuke Seki
Oral presentation, English, 京都大学数理解析研究所RIMS共同研究（公開型）「代数系、論理、言語とその周辺領域」, Domestic conference
20 Feb. 2018 - Proving Turing universality of cotranscriptional folding
Shinnosuke Seki
Oral presentation, Japanese, 京都大学数理解析研究所RIMS共同研究（公開型）「アルゴリズムと計算理論の基礎と応用」, Domestic conference
05 Feb. 2018 - Turing completeness of RNA cotarnsccriptional folding
Shinnosuke Seki
Invited oral presentation, English, SICE Molecular Robotics Seminar, 4th JST Seminar on Ethical Issues for Molecular Robots, Invited, Hakata, Japan, Domestic conference
19 Jan. 2018 - Self-attraction removal from oritatami systems
Hwee Kim
Oral presentation, English, 19th International Conference on Descriptional Complexity of Formal Systems, Milan, Italy, International conference
03 Jul. 2017 - Bit string bifurcation by cotranscriptional folding
Yusei Masuda; Yuki Ubukata
Oral presentation, English, 1st International Workshop on Oritatami, Shinnosuke Seki, University of Arkansas, International conference
06 Jun. 2017 - Bit string bifurcation by cotranscriptional folding
Yusei Masuda; Yuki Ubukata
Oral presentation, English, 11th International Workshop on Natural Computing, Akita International University, International conference
13 May 2017 - Self-assembly at nano scale by molecular Xerox
Shinnosuke Seki
Invited oral presentation, English, 11th International Workshop on Natural Computing, Invited, Akita International University, Akita, Japan, International conference
13 May 2017 - Nano-scale self-assembly using molecular Xerox
Shinnosuke Seki
Oral presentation, Japanese, 第2回 若手研究者のための熱利用・環境技術ワークショップ, Invited, 化学工学会エネルギー部会熱利用分科会, 東京都八王子市, Domestic conference
02 Dec. 2016 - Oritatami, a novel frontier in molecular self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Yonsei University
21 Nov. 2016 - Oritatami, a novel mathematical model of RNA cotranscriptional folding
Shinnosuke Seki
Public discourse, English, Invited, Akita University, Akita, Japan
20 Oct. 2016 - Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Hwee Kim
Oral presentation, English, The 22nd International Conference on DNA Computing and Molecular Programming (DNA 22), Munich, Germany, International conference
04 Sep. 2016 - Programming biomolecules that fold greedily during transcription
Pierre-Etienne Meunier
Oral presentation, English, 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016), International conference
22 Aug. 2016 - The complexity of fixed-height patterned tile self-assembly
Shinnosuke Seki
Oral presentation, English, 21st International Conference on Implementation and Application of Automata (CIAA 2016), Seoul, Republic of Korea, International conference
19 Jul. 2016 - Folding Turing is hard but feasible
Nicolas Schabanel
Oral presentation, English, Highlights of Algorithms (HALG 2016), Paris, France, International conference
06 Jun. 2016 - Molecular cotranscriptional folding: A novel challenge in theory and applications of self-assembly
Shinnosuke Seki
Public discourse, English, Invited, University of South Florida, Tampa, Florida, USA
25 Jan. 2016 - Molecular cotranscriptional folding: A novel topic in theory and applications of self-assembly
Shinnosuke Seki
Invited oral presentation, English, 5th Interdisciplinary Research and Global Outlook (IRAGO2015)
22 Oct. 2015 - Square-density increasing mappings
Shinnosuke Seki
Oral presentation, English, 10th International Conference on Combinatorics on Words (WORDS2015), International conference
14 Sep. 2015 - Computational complexity of inverse word search problem
Hiro Ito
Oral presentation, English, 12th International Symposium on Operations Research and Its Applications (ISORA2015), International conference
21 Aug. 2015 - Efficient universal computation by molecular cotranscriptional folding
Shinnosuke Seki
Oral presentation, English, 21st International Conference on DNA Computing and Molecular Programming (DNA21), Wyss Institute for Biologically inspired Engineering at Harvard University, International conference
17 Aug. 2015 - Binary pattern tile set synthesis is NP-hard
Shinnosuke Seki
Oral presentation, English, 42nd International Colloquium on Automata, Languages, and Programming (ICALP2015), International conference
04 Jul. 2015 - Oritatami, a model of cotranscriptional folding
Shinnosuke Seki
Public discourse, English, Invited, Turku, Finland, International conference
04 Mar. 2015 - Generalized Lyndon-Schutzenberger equations
Florin Manea
Oral presentation, English, MFCS2014: 39th International Symposium on Mathematical Foundations of Computer Science, Budapest, Hungary, International conference
25 Aug. 2014 - Operational state complexity under Parikh equivalence
Shinnosuke Seki
Public symposium, English, DCFS2014: 16th International Workshop on Descriptional Complexity of Formal Systems, Turku, Finland, International conference
05 Aug. 2014 - DNA pattern self-assembly: Introduction and recent breakthroughs
Nicolas Schabanel
Invited oral presentation, English, Complexite et Algorithmes: Algorithmes naturels, Invited, Universite Paris Diderot, LIAFA, Paris, France, International conference
09 Jun. 2014 - Stronger square conjecture on binary words
Shinnosuke Seki
Oral presentation, English, SOFSEM2014: 40th International Conference on Current Trends in Theory and Practice of Computer Science, International conference
25 Jan. 2014 - A stronger square conjecture on binary words
Shinnosuke Seki
Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia
24 Jan. 2014 - Computing minimum tile sets to self-assembly color patterns
Aleck Johnson
Oral presentation, English, ISAAC2013: 24th International Symposium on Algorithms and Computation, Hong Kong, International conference
16 Dec. 2013 - How many repetitions can you put on a sequence?
Shinnosuke Seki
Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA
07 Nov. 2013 - Combinatorial optimization in pattern-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA
06 Nov. 2013 - Combinatorial optimization in pattern-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Northwestern University, Evanston, IL, USA
13 Oct. 2013 - 3-color bounded patterned self-assembly
Steffen Kopecki
Oral presentation, English, DNA 19: 19th International Conference on DNA Computing and Molecular Programming, Tempe, Arizona, USA, International conference
22 Sep. 2013 - Combinatorial optimization in pattern assembly (extended abstract)
Shinnosuke Seki
Oral presentation, English, UCNC2013: 12th International Conference on Unconventional Computation and Natural Computation, Milan, Italy, International conference
01 Jul. 2013 - On the boundedness property of semilinear sets
Shinnosuke Seki
Oral presentation, English, TAMC2013: 10th Annual Conference on Theory and Applications of Models of Computation, Hong Kong, International conference
20 May 2013 - DNA pattern self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Yonsei University, Seoul, Republic of Korea
15 May 2013 - DNA pattern self-assembly
Shinnosuke Seki
Invited oral presentation, English, Helsinki Institute for Information Technology (HIIT), Helsinki, Finland
24 Apr. 2013 - Roles that temperature plays in self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, University of South Florida, Tampa, FL, USA
30 Nov. 2012 - Combinatorial optimization in pattern assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, California Institute of Technology, Pasadena, California, USA
02 Nov. 2012 - Descriptional complexity in Parikh equivalence
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada
18 Oct. 2012 - Conveting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
Giovanni Pighizzini
Oral presentation, English, DLT2012: 16th International Conference on Developments in Language Theory, Taipei, Taiwan, International conference
14 Aug. 2012 - On the behavior of tile assembly system at high temperatures
Shinnosuke Seki
Oral presentation, English, CiE2012: Turing Centenary Conference - How the World Computes, Cambridge, UK, International conference
18 Jun. 2012 - Triangular and hexagonal tile self-assembly systems
Zhi Xu
Oral presentation, English, WTCS2012: International Workshop on Theoretical Computer Science, Auckland, New Zealand, International conference
21 Feb. 2012 - On the behavior of tile assembly system at high temperatures
Shinnosuke Seki
Invited oral presentation, English, Slovak Academy of Science, Kosice, Slovakia
30 Jan. 2012 - Iterated hairpin completions of non-crossing words
Shinnosuke Seki
Oral presentation, English, SOFSEM2012: 38th International Conference on Current Trends in Theory and Practice of Computer Science, Spindleruv Mlyn, Czech Republic, International conference
21 Jan. 2012 - In the century of communication
Shinnosuke Seki
Invited oral presentation, English, Invited, 島根大学, 松江、日本
13 Dec. 2011 - Program size and temperature in self-assembly
David Doty
Oral presentation, English, ISAAC2011: 22nd International Symposium on Algorithms and Computation, Yokohama, Japan, International conference
05 Dec. 2011 - Roles that temperature play in self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada
10 Nov. 2011 - Number theory and computational efficiency in chemoinformatics
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada
03 Nov. 2011 - Number theory and computational efficiency in chemoinformatics
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Pavol Jozef Safarik, Kosice, Slovakia
25 Aug. 2011 - An introduction to the world of self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia
24 Aug. 2011 - Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
Shinnosuke Seki
Oral presentation, English, AFL2011: 13th International Conference on Automata and Formal Languages, Debrecen, Hungary, International conference
20 Aug. 2011 - Scalable, time-responsive, digital, energy-efficient, moleculer circuits using DNA strand displacement
David Doty
Poster presentation, English, DNA16: 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, International conference
14 Jun. 2011 - One-reversal counter machines and multihead automata: revisited
Shinnosuke Seki
Oral presentation, English, SOFSEM2011: 37th International Conference on Current Trends in Theory and Practice of Computer Science, High Tatras, Slovakia, International conference
22 Jan. 2011 - Power of nondeterminism in self-assembly
David Doty
Oral presentation, English, SODA2011: ACM-SIAM Symposium on Discrete Algorithms, San Fransisco, California, USA, International conference
22 Jan. 2011 - Schema for parallel insertion and deletion
Shinnosuke Seki
Oral presentation, English, DLT2010: 14th International Conference on Developments in Language Theory, London, ON, Canada, International conference
17 Aug. 2010 - Triangular tile self-assembly systems
Shinnosuke Seki
Poster presentation, English, DNA16: 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, International conference
14 Jun. 2010 - Schema for parallel insertion and deletion
Shinnosuke Seki
Invited oral presentation, English, Workshop on Formal Languages and Automata III, Invited, Kyoto Sangyo University, Kyoto, Japan, International conference
12 Dec. 2009 - An extension of fundamental notions in combinatorics on words inspired by DNA information encoding
Shinnosuke Seki
Invited oral presentation, English, Invited, Universitate Potsdam, Potsdam, Germany
06 Jul. 2009 - An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
Shinnosuke Seki
Oral presentation, English, DLT2009: 13th International Conference on Developments in Language Theory, Stuttgard, Germany, International conference
30 Jun. 2009 - On the reversibility of parallel insertion, and its relation to comma codes
Bo Cui
Oral presentation, English, CAI2009: 3rd International Conference on Algebraic Informatics, Thessaloniki, Greece, International conference
19 May 2009 - Duplication in DNA sequences
Zachary Kincaid
Oral presentation, English, DLT2008: 12th International Conference on Developments in Language Theory, Kyoto, Japan, International conference
16 Sep. 2008 - On a special class of primitive words
Elena Czeizler
Oral presentation, English, MFCS2008: 33rd International Symposium on Mathematical Foundations of Computer Science, Torun, Poland, International conference
27 Aug. 2008 - Towards the sequence design preventing pseudoknot formation
Shinnosuke Seki
Oral presentation, English, IWNC2007: 2nd International Workshop on Natural Computing, Nagoya, Japan, International conference
10 Dec. 2007 - An efficient multiple alignment method for DNA secondary structures including pseudoknots
Shinnosuke Seki
Oral presentation, English, IWNC2007: 2nd International Workshop on Natural Computing, Nagoya, Japan, International conference
10 Dec. 2007 - Hierarchical alignment of RNA secondary structures including pseudoknots
Shinnosuke Seki
Poster presentation, English, GIW2004: 15th International Workshop on Genome Informatics, Yokohama, Japan, International conference
13 Dec. 2004 - Efficient learning of k-reversible context-free grammars from positive structural examples
Shinnosuke Seki
Poster presentation, English, ICGI: 7th International Colloquium on Grammatical Inferences, Athens, Greece, International conference
11 Oct. 2004
Courses
- Formal Language Theory
Oct. 2021 - Present
The University of Electro-Communications - MICS実験第2
Oct. 2020 - Present
The University of Electro-Communications - 情報領域演習第2
Apr. 2020 - Present
The University of Electro-Communications - 大学院技術英語
Apr. 2020 - Present
The University of Electro-Communications - Exercise in Informatics 1
Oct. 2017 - Mar. 2023
The University of Electro-Communications - MICS実験第一
The University of Electro-Communications - K過程輪講
The University of Electro-Communications - 総合コミュニケーション科学
The University of Electro-Communications - Combinatorics
Aalto University
Research Themes
- 文字列の辞書式順序の組合せ論とその応用
坂内 英夫
01 Apr. 2020 - 31 Mar. 2024 - 共転写性フォールディングの本質的計算完全性
01 Apr. 2020 - 31 Mar. 2023 - 万能折り畳みシステムの小型化とその限界
29 Jun. 2018 - 31 Mar. 2020 - 国際会議UCNC2019への助成
Shinnosuke Seki
Tateishi Science and Technology Foundation
25 Sep. 2018 - 07 Jun. 2019 - 国際会議DLT2018への助成
Shinnosuke Seki
National Institute of Information and Communications Technology (NICT), Support for the 22nd International Conference on Developments in Language Theory (DLT 2018), Principal investigator
01 Apr. 2018 - 共転写性フォールディングによる自己組織化システムの実際的設計と最適化
01 Apr. 2016 - 31 Mar. 2018 - 国際会議DLT2018への助成
Shinnosuke Seki
The Telecommunications Advancement Foundation, シンポジウム・セミナー 振興普及援助
01 Sep. 2017 - 機関選抜のため、研究テーマはなし
Shinnosuke Seki
Japan Science and Technology Agency, Principal investigator
06 Aug. 2015 - 31 Mar. 2017 - 国際会議DLT2018への助成
（株）久保田情報技研, 国際会議DLT2018開催支援寄付金
2017 - 共転写性フォールディングの数理モデル化とチューリング完全性
Shinnosuke Seki
Principal investigator
01 Apr. 2015 - 31 Mar. 2016 - Practical designs of molecular self-assembly systems and their optimization
Shinnosuke Seki
Academy of Finland, Principal investigator
01 Sep. 2013 - 31 Mar. 2015