7 Search Results for "Hamilton, David"

Document
DOI: 10.4230/LIPIcs.DNA.29.1
Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer

Authors: Ahmed Shalaby, Chris Thachuk, and Damien Woods

Published in: LIPIcs, Volume 276, 29th International Conference on DNA Computing and Molecular Programming (DNA 29) (2023)

Abstract
Polynomial time dynamic programming algorithms play a crucial role in the design, analysis and engineering of nucleic acid systems including DNA computers and DNA/RNA nanostructures. However, in complex multistranded or pseudoknotted systems, computing the minimum free energy (MFE), and partition function of nucleic acid systems is NP-hard. Despite this, multistranded and/or pseudoknotted systems represent some of the most utilised and successful systems in the field. This leaves open the tempting possibility that many of the kinds of multistranded and/or pseudoknotted systems we wish to engineer actually fall into restricted classes, that do in fact have polynomial time algorithms, but we've just not found them yet. Here, we give polynomial time algorithms for MFE and partition function calculation for a restricted kind of multistranded system called the 1D scaffolded DNA computer. This model of computation thermodynamically favours correct outputs over erroneous states, simulates finite state machines in 1D and Boolean circuits in 2D, and is amenable to DNA storage applications. In an effort to begin to ask the question of whether we can naturally compare the expressivity of nucleic acid systems based on the computational complexity of prediction of their preferred energetic states, we show our MFE problem is in logspace (the complexity class L), making it perhaps one of the simplest known, natural, nucleic acid MFE problems. Finally, we provide a stochastic kinetic simulator for the 1D scaffolded DNA computer and evaluate strategies for efficiently speeding up this thermodynamically favourable system in a constant-temperature kinetic regime.
Cite as

Ahmed Shalaby, Chris Thachuk, and Damien Woods. Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 1:1-1:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{shalaby_et_al:LIPIcs.DNA.29.1,
  author =	{Shalaby, Ahmed and Thachuk, Chris and Woods, Damien},
  title =	{{Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded DNA Computer}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{1:1--1:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.29.1},
  URN =		{urn:nbn:de:0030-drops-187840},
  doi =		{10.4230/LIPIcs.DNA.29.1},
  annote =	{Keywords: thermodynamic computation, model of computation, molecular computing, minimum free energy, partition function, DNA computing, DNA self-assembly, DNA strand displacement, kinetics simulation}
}
Document
DOI: 10.4230/LIPIcs.ESA.2023.61
Solving Edge Clique Cover Exactly via Synergistic Data Reduction

Authors: Anthony Hevia, Benjamin Kallus, Summer McClintic, Samantha Reisner, Darren Strash, and Johnathan Wilson

Published in: LIPIcs, Volume 274, 31st Annual European Symposium on Algorithms (ESA 2023)

Abstract
The edge clique cover (ECC) problem - where the goal is to find a minimum cardinality set of cliques that cover all the edges of a graph - is a classic NP-hard problem that has received much attention from both the theoretical and experimental algorithms communities. While small sparse graphs can be solved exactly via the branch-and-reduce algorithm of Gramm et al. [JEA 2009], larger instances can currently only be solved inexactly using heuristics with unknown overall solution quality. We revisit computing minimum ECCs exactly in practice by combining data reduction for both the ECC and vertex clique cover (VCC) problems. We do so by modifying the polynomial-time reduction of Kou et al. [Commun. ACM 1978] to transform a reduced ECC instance to a VCC instance; alternatively, we show it is possible to "lift" some VCC reductions to the ECC problem. Our experiments show that combining data reduction for both problems (which we call synergistic data reduction) enables finding exact minimum ECCs orders of magnitude faster than the technique of Gramm et al., and allows solving large sparse graphs on up to millions of vertices and edges that have never before been solved. With these new exact solutions, we evaluate the quality of recent heuristic algorithms on large instances for the first time. The most recent of these, EO-ECC by Abdullah et al. [ICCS 2022], solves 8 of the 27 instances for which we have exact solutions. It is our hope that our strategy rallies researchers to seek improved algorithms for the ECC problem.
Cite as

Anthony Hevia, Benjamin Kallus, Summer McClintic, Samantha Reisner, Darren Strash, and Johnathan Wilson. Solving Edge Clique Cover Exactly via Synergistic Data Reduction. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 61:1-61:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{hevia_et_al:LIPIcs.ESA.2023.61,
  author =	{Hevia, Anthony and Kallus, Benjamin and McClintic, Summer and Reisner, Samantha and Strash, Darren and Wilson, Johnathan},
  title =	{{Solving Edge Clique Cover Exactly via Synergistic Data Reduction}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{61:1--61:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-295-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{274},
  editor =	{G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2023.61},
  URN =		{urn:nbn:de:0030-drops-187148},
  doi =		{10.4230/LIPIcs.ESA.2023.61},
  annote =	{Keywords: Edge clique cover, Vertex clique cover, Data reduction, Degeneracy}
}
Document
DOI: 10.4230/LIPIcs.FUN.2021.7
1 X 1 Rush Hour with Fixed Blocks Is PSPACE-Complete

Authors: Josh Brunner, Lily Chung, Erik D. Demaine, Dylan Hendrickson, Adam Hesterberg, Adam Suhl, and Avi Zeff

Published in: LIPIcs, Volume 157, 10th International Conference on Fun with Algorithms (FUN 2021) (2020)

Abstract
Consider n²-1 unit-square blocks in an n × n square board, where each block is labeled as movable horizontally (only), movable vertically (only), or immovable - a variation of Rush Hour with only 1 × 1 cars and fixed blocks. We prove that it is PSPACE-complete to decide whether a given block can reach the left edge of the board, by reduction from Nondeterministic Constraint Logic via 2-color oriented Subway Shuffle. By contrast, polynomial-time algorithms are known for deciding whether a given block can be moved by one space, or when each block either is immovable or can move both horizontally and vertically. Our result answers a 15-year-old open problem by Tromp and Cilibrasi, and strengthens previous PSPACE-completeness results for Rush Hour with vertical 1 × 2 and horizontal 2 × 1 movable blocks and 4-color Subway Shuffle.
Cite as

Josh Brunner, Lily Chung, Erik D. Demaine, Dylan Hendrickson, Adam Hesterberg, Adam Suhl, and Avi Zeff. 1 X 1 Rush Hour with Fixed Blocks Is PSPACE-Complete. In 10th International Conference on Fun with Algorithms (FUN 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 157, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{brunner_et_al:LIPIcs.FUN.2021.7,
  author =	{Brunner, Josh and Chung, Lily and Demaine, Erik D. and Hendrickson, Dylan and Hesterberg, Adam and Suhl, Adam and Zeff, Avi},
  title =	{{1 X 1 Rush Hour with Fixed Blocks Is PSPACE-Complete}},
  booktitle =	{10th International Conference on Fun with Algorithms (FUN 2021)},
  pages =	{7:1--7:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-145-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{157},
  editor =	{Farach-Colton, Martin and Prencipe, Giuseppe and Uehara, Ryuhei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2021.7},
  URN =		{urn:nbn:de:0030-drops-127681},
  doi =		{10.4230/LIPIcs.FUN.2021.7},
  annote =	{Keywords: puzzles, sliding blocks, PSPACE-hardness}
}
Document
DOI: 10.4230/LIPIcs.FUN.2021.9
Magic: The Gathering Is Turing Complete

Authors: Alex Churchill, Stella Biderman, and Austin Herrick

Published in: LIPIcs, Volume 157, 10th International Conference on Fun with Algorithms (FUN 2021) (2020)

Abstract
Magic: The Gathering is a popular and famously complicated trading card game about magical combat. In this paper we show that optimal play in real-world Magic is at least as hard as the Halting Problem. This provides a positive answer to the question "is there a real-world game where perfect play is undecidable under the rules in which it is typically played?", a question that has been open for a decade [David Auger and Oliver Teytaud, 2012; Erik D. Demaine and Robert A. Hearn, 2009]. To do this, we present a methodology for embedding an arbitrary Turing machine into a game of Magic such that the first player is guaranteed to win the game if and only if the Turing machine halts. Our result applies to how real Magic is played, can be achieved using standard-size tournament-legal decks, and does not rely on stochasticity or hidden information. Our result is also highly unusual in that all moves of both players are forced in the construction. This shows that even recognising who will win a game in which neither player has a non-trivial decision to make for the rest of the game is undecidable. We conclude with a discussion of the implications for a unified computational theory of games and remarks about the playability of such a board in a tournament setting.
Cite as

Alex Churchill, Stella Biderman, and Austin Herrick. Magic: The Gathering Is Turing Complete. In 10th International Conference on Fun with Algorithms (FUN 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 157, pp. 9:1-9:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{churchill_et_al:LIPIcs.FUN.2021.9,
  author =	{Churchill, Alex and Biderman, Stella and Herrick, Austin},
  title =	{{Magic: The Gathering Is Turing Complete}},
  booktitle =	{10th International Conference on Fun with Algorithms (FUN 2021)},
  pages =	{9:1--9:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-145-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{157},
  editor =	{Farach-Colton, Martin and Prencipe, Giuseppe and Uehara, Ryuhei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2021.9},
  URN =		{urn:nbn:de:0030-drops-127706},
  doi =		{10.4230/LIPIcs.FUN.2021.9},
  annote =	{Keywords: Turing machines, computability theory, Magic: the Gathering, two-player games}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2019.41
The Paulsen Problem Made Simple

Authors: Linus Hamilton and Ankur Moitra

Published in: LIPIcs, Volume 124, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019)

Abstract
The Paulsen problem is a basic problem in operator theory that was resolved in a recent tour-de-force work of Kwok, Lau, Lee and Ramachandran. In particular, they showed that every epsilon-nearly equal norm Parseval frame in d dimensions is within squared distance O(epsilon d^{13/2}) of an equal norm Parseval frame. We give a dramatically simpler proof based on the notion of radial isotropic position, and along the way show an improved bound of O(epsilon d^2).
Cite as

Linus Hamilton and Ankur Moitra. The Paulsen Problem Made Simple. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 124, pp. 41:1-41:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{hamilton_et_al:LIPIcs.ITCS.2019.41,
  author =	{Hamilton, Linus and Moitra, Ankur},
  title =	{{The Paulsen Problem Made Simple}},
  booktitle =	{10th Innovations in Theoretical Computer Science Conference (ITCS 2019)},
  pages =	{41:1--41:6},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-095-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{124},
  editor =	{Blum, Avrim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2019.41},
  URN =		{urn:nbn:de:0030-drops-101347},
  doi =		{10.4230/LIPIcs.ITCS.2019.41},
  annote =	{Keywords: radial isotropic position, operator scaling, Paulsen problem}
}
Document
DOI: 10.4230/LIPIcs.SWAT.2018.6
On Romeo and Juliet Problems: Minimizing Distance-to-Sight

Authors: Hee-Kap Ahn, Eunjin Oh, Lena Schlipf, Fabian Stehn, and Darren Strash

Published in: LIPIcs, Volume 101, 16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018)

Abstract
We introduce a variant of the watchman route problem, which we call the quickest pair-visibility problem. Given two persons standing at points s and t in a simple polygon P with no holes, we want to minimize the distance these persons travel in order to see each other in P. We solve two variants of this problem, one minimizing the longer distance the two persons travel (min-max) and one minimizing the total travel distance (min-sum), optimally in linear time. We also consider a query version of this problem for the min-max variant. We can preprocess a simple n-gon in linear time so that the minimum of the longer distance the two persons travel can be computed in O(log^2 n) time for any two query positions where the two persons lie.
Cite as

Hee-Kap Ahn, Eunjin Oh, Lena Schlipf, Fabian Stehn, and Darren Strash. On Romeo and Juliet Problems: Minimizing Distance-to-Sight. In 16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 101, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{ahn_et_al:LIPIcs.SWAT.2018.6,
  author =	{Ahn, Hee-Kap and Oh, Eunjin and Schlipf, Lena and Stehn, Fabian and Strash, Darren},
  title =	{{On Romeo and Juliet Problems: Minimizing Distance-to-Sight}},
  booktitle =	{16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018)},
  pages =	{6:1--6:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-068-2},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{101},
  editor =	{Eppstein, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2018.6},
  URN =		{urn:nbn:de:0030-drops-88322},
  doi =		{10.4230/LIPIcs.SWAT.2018.6},
  annote =	{Keywords: Visibility polygon, shortest-path, watchman problems}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2016.14
Deterministic Population Protocols for Exact Majority and Plurality

Authors: Leszek Gasieniec, David Hamilton, Russell Martin, Paul G. Spirakis, and Grzegorz Stachowiak

Published in: LIPIcs, Volume 70, 20th International Conference on Principles of Distributed Systems (OPODIS 2016)

Abstract
In this paper we study space-efficient deterministic population protocols for several variants of the majority problem including plurality consensus. We focus on space efficient majority protocols in populations with an arbitrary number of colours C represented by k-bit labels, where k = ceiling (log C). In particular, we present asymptotically space-optimal (with respect to the adopted k-bit representation of colours) protocols for (1) the absolute majority problem, i.e., a protocol which decides whether a single colour dominates all other colours considered together, and (2) the relative majority problem, also known in the literature as plurality consensus, in which colours declare their volume superiority versus other individual colours. The new population protocols proposed in this paper rely on a dynamic formulation of the majority problem in which the colours originally present in the population can be changed by an external force during the communication process. The considered dynamic formulation is based on the concepts studied by D. Angluin et al. and O. Michail et al. about stabilizing inputs and composition of population protocols. Also, the protocols presented in this paper use a composition of some known protocols for static and dynamic majority.
Cite as

Leszek Gasieniec, David Hamilton, Russell Martin, Paul G. Spirakis, and Grzegorz Stachowiak. Deterministic Population Protocols for Exact Majority and Plurality. In 20th International Conference on Principles of Distributed Systems (OPODIS 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 70, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{gasieniec_et_al:LIPIcs.OPODIS.2016.14,
  author =	{Gasieniec, Leszek and Hamilton, David and Martin, Russell and Spirakis, Paul G. and Stachowiak, Grzegorz},
  title =	{{Deterministic Population Protocols for Exact Majority and Plurality}},
  booktitle =	{20th International Conference on Principles of Distributed Systems (OPODIS 2016)},
  pages =	{14:1--14:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-031-6},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{70},
  editor =	{Fatourou, Panagiota and Jim\'{e}nez, Ernesto and Pedone, Fernando},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2016.14},
  URN =		{urn:nbn:de:0030-drops-70837},
  doi =		{10.4230/LIPIcs.OPODIS.2016.14},
  annote =	{Keywords: Deterministic population protocols, majority, plurality consenus}
}
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