3 Search Results for "Kolmogorov, Mikhail"


Document
Information Distance Revisited

Authors: Bruno Bauwens

Published in: LIPIcs, Volume 154, 37th International Symposium on Theoretical Aspects of Computer Science (STACS 2020)


Abstract
We consider the notion of information distance between two objects x and y introduced by Bennett, Gács, Li, Vitanyi, and Zurek [C. H. Bennett et al., 1998] as the minimal length of a program that computes x from y as well as computing y from x, and study different versions of this notion. In the above paper, it was shown that the prefix version of information distance equals max (K(x|y),K(y|x)) up to additive logarithmic terms. It was claimed by Mahmud [Mahmud, 2009] that this equality holds up to additive O(1)-precision. We show that this claim is false, but does hold if the distance is at least logarithmic. This implies that the original definition provides a metric on strings that are at superlogarithmically separated.

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Bruno Bauwens. Information Distance Revisited. In 37th International Symposium on Theoretical Aspects of Computer Science (STACS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 154, pp. 46:1-46:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@InProceedings{bauwens:LIPIcs.STACS.2020.46,
  author =	{Bauwens, Bruno},
  title =	{{Information Distance Revisited}},
  booktitle =	{37th International Symposium on Theoretical Aspects of Computer Science (STACS 2020)},
  pages =	{46:1--46:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-140-5},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{154},
  editor =	{Paul, Christophe and Bl\"{a}ser, Markus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2020.46},
  URN =		{urn:nbn:de:0030-drops-119071},
  doi =		{10.4230/LIPIcs.STACS.2020.46},
  annote =	{Keywords: Kolmogorov complexity, algorithmic information distance}
}
Document
Synteny Paths for Assembly Graphs Comparison

Authors: Evgeny Polevikov and Mikhail Kolmogorov

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Despite the recent developments of long-read sequencing technologies, it is still difficult to produce complete assemblies of eukaryotic genomes in an automated fashion. Genome assembly software typically output assembled fragments (contigs) along with assembly graphs, that encode all possible layouts of these contigs. Graph representation of the assembled genome can be useful for gene discovery, haplotyping, structural variations analysis and other applications. To facilitate the development of new graph-based approaches, it is important to develop algorithms for comparison and evaluation of assembly graphs produced by different software. In this work, we introduce synteny paths: maximal paths of homologous sequence between the compared assembly graphs. We describe Asgan - an algorithm for efficient synteny paths decomposition, and use it to evaluate assembly graphs of various bacterial assemblies produced by different approaches. We then apply Asgan to discover structural variations between the assemblies of 15 Drosophila genomes, and show that synteny paths are robust to contig fragmentation. The Asgan tool is freely available at: https://github.com/epolevikov/Asgan.

Cite as

Evgeny Polevikov and Mikhail Kolmogorov. Synteny Paths for Assembly Graphs Comparison. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{polevikov_et_al:LIPIcs.WABI.2019.24,
  author =	{Polevikov, Evgeny and Kolmogorov, Mikhail},
  title =	{{Synteny Paths for Assembly Graphs Comparison}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{24:1--24:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.24},
  URN =		{urn:nbn:de:0030-drops-110545},
  doi =		{10.4230/LIPIcs.WABI.2019.24},
  annote =	{Keywords: Assembly graphs, Genome assembly, Synteny blocks, Comparative Genomics}
}
Document
Plain Stopping Time and Conditional Complexities Revisited

Authors: Mikhail Andreev, Gleb Posobin, and Alexander Shen

Published in: LIPIcs, Volume 117, 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)


Abstract
In this paper we analyze the notion of "stopping time complexity", the amount of information needed to specify when to stop while reading an infinite sequence. This notion was introduced by Vovk and Pavlovic [Vovk and Pavlovic, 2016]. It turns out that plain stopping time complexity of a binary string x could be equivalently defined as (a) the minimal plain complexity of a Turing machine that stops after reading x on a one-directional input tape; (b) the minimal plain complexity of an algorithm that enumerates a prefix-free set containing x; (c) the conditional complexity C(x|x*) where x in the condition is understood as a prefix of an infinite binary sequence while the first x is understood as a terminated binary string; (d) as a minimal upper semicomputable function K such that each binary sequence has at most 2^n prefixes z such that K(z)<n; (e) as maxC^X(x) where C^X(z) is plain Kolmogorov complexity of z relative to oracle X and the maximum is taken over all extensions X of x. We also show that some of these equivalent definitions become non-equivalent in the more general setting where the condition y and the object x may differ, and answer an open question from Chernov, Hutter and Schmidhuber [Alexey V. Chernov et al., 2007].

Cite as

Mikhail Andreev, Gleb Posobin, and Alexander Shen. Plain Stopping Time and Conditional Complexities Revisited. In 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 117, pp. 2:1-2:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@InProceedings{andreev_et_al:LIPIcs.MFCS.2018.2,
  author =	{Andreev, Mikhail and Posobin, Gleb and Shen, Alexander},
  title =	{{Plain Stopping Time and Conditional Complexities Revisited}},
  booktitle =	{43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)},
  pages =	{2:1--2:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-086-6},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{117},
  editor =	{Potapov, Igor and Spirakis, Paul and Worrell, James},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2018.2},
  URN =		{urn:nbn:de:0030-drops-95842},
  doi =		{10.4230/LIPIcs.MFCS.2018.2},
  annote =	{Keywords: Kolmogorov complexity, stopping time complexity, structured conditional complexity, algorithmic information theory}
}
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