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Documents authored by Theofilatos, Michail

Document
DOI: 10.4230/LIPIcs.SEA.2020.21
Crystal Structure Prediction via Oblivious Local Search

Authors: Dmytro Antypov, Argyrios Deligkas, Vladimir Gusev, Matthew J. Rosseinsky, Paul G. Spirakis, and Michail Theofilatos

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

Abstract
We study Crystal Structure Prediction, one of the major problems in computational chemistry. This is essentially a continuous optimization problem, where many different, simple and sophisticated, methods have been proposed and applied. The simple searching techniques are easy to understand, usually easy to implement, but they can be slow in practice. On the other hand, the more sophisticated approaches perform well in general, however almost all of them have a large number of parameters that require fine tuning and, in the majority of the cases, chemical expertise is needed in order to properly set them up. In addition, due to the chemical expertise involved in the parameter-tuning, these approaches can be biased towards previously-known crystal structures. Our contribution is twofold. Firstly, we formalize the Crystal Structure Prediction problem, alongside several other intermediate problems, from a theoretical computer science perspective. Secondly, we propose an oblivious algorithm for Crystal Structure Prediction that is based on local search. Oblivious means that our algorithm requires minimal knowledge about the composition we are trying to compute a crystal structure for. In addition, our algorithm can be used as an intermediate step by any method. Our experiments show that our algorithms outperform the standard basin hopping, a well studied algorithm for the problem.
Cite as

Dmytro Antypov, Argyrios Deligkas, Vladimir Gusev, Matthew J. Rosseinsky, Paul G. Spirakis, and Michail Theofilatos. Crystal Structure Prediction via Oblivious Local Search. In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 21:1-21:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{antypov_et_al:LIPIcs.SEA.2020.21,
  author =	{Antypov, Dmytro and Deligkas, Argyrios and Gusev, Vladimir and Rosseinsky, Matthew J. and Spirakis, Paul G. and Theofilatos, Michail},
  title =	{{Crystal Structure Prediction via Oblivious Local Search}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{21:1--21:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.21},
  URN =		{urn:nbn:de:0030-drops-120950},
  doi =		{10.4230/LIPIcs.SEA.2020.21},
  annote =	{Keywords: crystal structure prediction, local search, combinatorial neighborhood}
}
Document
Brief Announcement
DOI: 10.4230/LIPIcs.DISC.2018.46
Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time

Authors: David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, and Michail Theofilatos

Published in: LIPIcs, Volume 121, 32nd International Symposium on Distributed Computing (DISC 2018)

Abstract
We study population protocols: networks of anonymous agents whose pairwise interactions are chosen uniformly at random. The size counting problem is that of calculating the exact number n of agents in the population, assuming no leader (each agent starts in the same state). We give the first protocol that solves this problem in sublinear time. The protocol converges in O(log n log log n) time and uses O(n^60) states (O(1) + 60 log n bits of memory per agent) with probability 1-O((log log n)/n). The time to converge is also O(log n log log n) in expectation. Crucially, unlike most published protocols with omega(1) states, our protocol is uniform: it uses the same transition algorithm for any population size, so does not need an estimate of the population size to be embedded into the algorithm.
Cite as

David Doty, Mahsa Eftekhari, Othon Michail, Paul G. Spirakis, and Michail Theofilatos. Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time. In 32nd International Symposium on Distributed Computing (DISC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 121, pp. 46:1-46:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{doty_et_al:LIPIcs.DISC.2018.46,
  author =	{Doty, David and Eftekhari, Mahsa and Michail, Othon and Spirakis, Paul G. and Theofilatos, Michail},
  title =	{{Brief Announcement: Exact Size Counting in Uniform Population Protocols in Nearly Logarithmic Time}},
  booktitle =	{32nd International Symposium on Distributed Computing (DISC 2018)},
  pages =	{46:1--46:3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-092-7},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{121},
  editor =	{Schmid, Ulrich and Widder, Josef},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2018.46},
  URN =		{urn:nbn:de:0030-drops-98359},
  doi =		{10.4230/LIPIcs.DISC.2018.46},
  annote =	{Keywords: population protocol, counting, leader election, polylogarithmic time}
}
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