4 Search Results for "Severson, Eric"

Document
DOI: 10.4230/LIPIcs.DNA.29.9
Optimal Information Encoding in Chemical Reaction Networks

Authors: Austin Luchsinger, David Doty, and David Soloveichik

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

Abstract
Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has been widely studied in the molecular programming and distributed computing communities. While for Turing-universal systems there is a universal measure of optimal information encoding based on Kolmogorov complexity, chemical reaction networks are not Turing universal unless error and unbounded molecular counts are permitted. Nonetheless, here we show that the optimal number of reactions to generate a specific count x ∈ ℕ with probability 1 is asymptotically equal to a "space-aware" version of the Kolmogorov complexity of x, defined as K̃s(x) = min_p {|p|/log|p| + log(space(𝒰(p))) : 𝒰(p) = x}, where p is a program for universal Turing machine 𝒰. This version of Kolmogorov complexity incorporates not just the length of the shortest program for generating x, but also the space usage of that program. Probability 1 computation is captured by the standard notion of stable computation from distributed computing, but we limit our consideration to chemical reaction networks obeying a stronger constraint: they "know when they are done" in the sense that they produce a special species to indicate completion. As part of our results, we develop a module for encoding and unpacking any b bits of information via O(b/log{b}) reactions, which is information-theoretically optimal for incompressible information. Our work provides one answer to the question of how succinctly chemical self-organization can be encoded - in the sense of generating precise molecular counts of species as the desired state.
Cite as

Austin Luchsinger, David Doty, and David Soloveichik. Optimal Information Encoding in Chemical Reaction Networks. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{luchsinger_et_al:LIPIcs.DNA.29.9,
  author =	{Luchsinger, Austin and Doty, David and Soloveichik, David},
  title =	{{Optimal Information Encoding in Chemical Reaction Networks}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{9:1--9:16},
  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.29.9},
  URN =		{urn:nbn:de:0030-drops-187920},
  doi =		{10.4230/LIPIcs.DNA.29.9},
  annote =	{Keywords: chemical reaction networks, Kolmogorov complexity, stable computation}
}
Document
DOI: 10.4230/LIPIcs.DISC.2021.40
Time-Optimal Loosely-Stabilizing Leader Election in Population Protocols

Authors: Yuichi Sudo, Ryota Eguchi, Taisuke Izumi, and Toshimitsu Masuzawa

Published in: LIPIcs, Volume 209, 35th International Symposium on Distributed Computing (DISC 2021)

Abstract
We consider the leader election problem in the population protocol model. In pragmatic settings of population protocols, self-stabilization is a highly desired feature owing to its fault resilience and the benefit of initialization freedom. However, the design of self-stabilizing leader election is possible only under a strong assumption (i.e., the knowledge of the exact size of a network) and rich computational resource (i.e., the number of states). Loose-stabilization is a promising relaxed concept of self-stabilization to address the aforementioned issue. Loose-stabilization guarantees that starting from any configuration, the network will reach a safe configuration where a single leader exists within a short time, and thereafter it will maintain the single leader for a long time, but not necessarily forever. The main contribution of this paper is giving a time-optimal loosely-stabilizing leader election protocol. The proposed protocol with design parameter τ ≥ 1 attains O(τ log n) parallel convergence time and Ω(n^τ) parallel holding time (i.e., the length of the period keeping the unique leader), both in expectation. This protocol is time-optimal in the sense of both the convergence and holding times in expectation because any loosely-stabilizing leader election protocol with the same length of the holding time is known to require Ω(τ log n) parallel time.
Cite as

Yuichi Sudo, Ryota Eguchi, Taisuke Izumi, and Toshimitsu Masuzawa. Time-Optimal Loosely-Stabilizing Leader Election in Population Protocols. In 35th International Symposium on Distributed Computing (DISC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 209, pp. 40:1-40:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

Copy BibTex To Clipboard

@InProceedings{sudo_et_al:LIPIcs.DISC.2021.40,
  author =	{Sudo, Yuichi and Eguchi, Ryota and Izumi, Taisuke and Masuzawa, Toshimitsu},
  title =	{{Time-Optimal Loosely-Stabilizing Leader Election in Population Protocols}},
  booktitle =	{35th International Symposium on Distributed Computing (DISC 2021)},
  pages =	{40:1--40:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-210-5},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{209},
  editor =	{Gilbert, Seth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2021.40},
  URN =		{urn:nbn:de:0030-drops-148427},
  doi =		{10.4230/LIPIcs.DISC.2021.40},
  annote =	{Keywords: population protocols, leader election, loose-stabilization, self-stabilization}
}
Document
DOI: 10.4230/LIPIcs.DISC.2020.6
Message Complexity of Population Protocols

Authors: Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari, and Eric Severson

Published in: LIPIcs, Volume 179, 34th International Symposium on Distributed Computing (DISC 2020)

Abstract
The standard population protocol model assumes that when two agents interact, each observes the entire state of the other. We initiate the study of message complexity for population protocols, where an agent’s state is divided into an externally-visible message and externally-hidden local state. We consider the case of O(1) message complexity. When time is unrestricted, we obtain an exact characterization of the stably computable predicates based on the number of internal states s(n): If s(n) = o(n) then the protocol computes semilinear predicates (unlike the original model, which can compute non-semilinear predicates with s(n) = O(log n)), and otherwise it computes a predicate decidable by a nondeterministic O(n log s(n))-space-bounded Turing machine. We then introduce novel O(polylog(n)) expected time protocols for junta/leader election and general purpose broadcast correct with high probability, and approximate and exact population size counting correct with probability 1. Finally, we show that the main constraint on the power of bounded-message-size protocols is the size of the internal states: with unbounded internal states, any computable function can be computed with probability 1 in the limit by a protocol that uses only 1-bit messages.
Cite as

Talley Amir, James Aspnes, David Doty, Mahsa Eftekhari, and Eric Severson. Message Complexity of Population Protocols. In 34th International Symposium on Distributed Computing (DISC 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 179, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

Copy BibTex To Clipboard

@InProceedings{amir_et_al:LIPIcs.DISC.2020.6,
  author =	{Amir, Talley and Aspnes, James and Doty, David and Eftekhari, Mahsa and Severson, Eric},
  title =	{{Message Complexity of Population Protocols}},
  booktitle =	{34th International Symposium on Distributed Computing (DISC 2020)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-168-9},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{179},
  editor =	{Attiya, Hagit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2020.6},
  URN =		{urn:nbn:de:0030-drops-130848},
  doi =		{10.4230/LIPIcs.DISC.2020.6},
  annote =	{Keywords: population protocol, message complexity, space-optimal}
}
Document
DOI: 10.4230/LIPIcs.DNA.2020.3
Composable Computation in Leaderless, Discrete Chemical Reaction Networks

Authors: Hooman Hashemi, Ben Chugg, and Anne Condon

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)

Abstract
We classify the functions f:ℕ^d → ℕ that are stably computable by leaderless, output-oblivious discrete (stochastic) Chemical Reaction Networks (CRNs). CRNs that compute such functions are systems of reactions over species that include d designated input species, whose initial counts represent an input x ∈ ℕ^d, and one output species whose eventual count represents f(x). Chen et al. showed that the class of functions computable by CRNs is precisely the semilinear functions. In output-oblivious CRNs, the output species is never a reactant. Output-oblivious CRNs are easily composable since a downstream CRN can consume the output of an upstream CRN without affecting its correctness. Severson et al. showed that output-oblivious CRNs compute exactly the subclass of semilinear functions that are eventually the minimum of quilt-affine functions, i.e., affine functions with different intercepts in each of finitely many congruence classes. They call such functions the output-oblivious functions. A leaderless CRN can compute only superadditive functions, and so a leaderless output-oblivious CRN can compute only superadditive, output-oblivious functions. In this work we show that a function f:ℕ^d → ℕ is stably computable by a leaderless, output-oblivious CRN if and only if it is superadditive and output-oblivious.
Cite as

Hooman Hashemi, Ben Chugg, and Anne Condon. Composable Computation in Leaderless, Discrete Chemical Reaction Networks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

Copy BibTex To Clipboard

@InProceedings{hashemi_et_al:LIPIcs.DNA.2020.3,
  author =	{Hashemi, Hooman and Chugg, Ben and Condon, Anne},
  title =	{{Composable Computation in Leaderless, Discrete Chemical Reaction Networks}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{3:1--3:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.3},
  URN =		{urn:nbn:de:0030-drops-129560},
  doi =		{10.4230/LIPIcs.DNA.2020.3},
  annote =	{Keywords: Chemical Reaction Networks, Stable Function Computation, Output-Oblivious, Output-Monotonic}
}
  • Refine by Author
  • 2 Doty, David
  • 1 Amir, Talley
  • 1 Aspnes, James
  • 1 Chugg, Ben
  • 1 Condon, Anne
  • Show More...

  • Refine by Classification
  • 2 Theory of computation → Distributed algorithms
  • 2 Theory of computation → Models of computation
  • 1 Theory of computation → Formal languages and automata theory

  • Refine by Keyword
  • 1 Chemical Reaction Networks
  • 1 Kolmogorov complexity
  • 1 Output-Monotonic
  • 1 Output-Oblivious
  • 1 Stable Function Computation
  • Show More...

  • Refine by Type
  • 4 document

  • Refine by Publication Year
  • 2 2020
  • 1 2021
  • 1 2023

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH Imprint Privacy Contact