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DOI: 10.4230/LIPIcs.ESA.2021.35
Minimum Common String Partition: Exact Algorithms

Authors: Marek Cygan, Alexander S. Kulikov, Ivan Mihajlin, Maksim Nikolaev, and Grigory Reznikov

Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)

Abstract
In the minimum common string partition problem (MCSP), one gets two strings and is asked to find the minimum number of cuts in the first string such that the second string can be obtained by rearranging the resulting pieces. It is a difficult algorithmic problem having applications in computational biology, text processing, and data compression. MCSP has been studied extensively from various algorithmic angles: there are many papers studying approximation, heuristic, and parameterized algorithms. At the same time, almost nothing is known about its exact complexity. In this paper, we present new results in this direction. We improve the known 2ⁿ upper bound (where n is the length of input strings) to ϕⁿ where ϕ ≈ 1.618... is the golden ratio. The algorithm uses Fibonacci numbers to encode subsets as monomials of a certain implicit polynomial and extracts one of its coefficients using the fast Fourier transform. Then, we show that the case of constant size alphabet can be solved in subexponential time 2^{O(nlog log n/log n)} by a hybrid strategy: enumerate all long pieces and use dynamic programming over histograms of short pieces. Finally, we prove almost matching lower bounds assuming the Exponential Time Hypothesis.
Cite as

Marek Cygan, Alexander S. Kulikov, Ivan Mihajlin, Maksim Nikolaev, and Grigory Reznikov. Minimum Common String Partition: Exact Algorithms. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 35:1-35:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{cygan_et_al:LIPIcs.ESA.2021.35,
  author =	{Cygan, Marek and Kulikov, Alexander S. and Mihajlin, Ivan and Nikolaev, Maksim and Reznikov, Grigory},
  title =	{{Minimum Common String Partition: Exact Algorithms}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{35:1--35:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-204-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{204},
  editor =	{Mutzel, Petra and Pagh, Rasmus and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2021.35},
  URN =		{urn:nbn:de:0030-drops-146167},
  doi =		{10.4230/LIPIcs.ESA.2021.35},
  annote =	{Keywords: similarity measure, string distance, exact algorithms, upper bounds, lower bounds}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX-RANDOM.2019.26
Collapsing Superstring Conjecture

Authors: Alexander Golovnev, Alexander S. Kulikov, Alexander Logunov, Ivan Mihajlin, and Maksim Nikolaev

Published in: LIPIcs, Volume 145, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2019)

Abstract
In the Shortest Common Superstring (SCS) problem, one is given a collection of strings, and needs to find a shortest string containing each of them as a substring. SCS admits 2 11/23-approximation in polynomial time (Mucha, SODA'13). While this algorithm and its analysis are technically involved, the 30 years old Greedy Conjecture claims that the trivial and efficient Greedy Algorithm gives a 2-approximation for SCS. We develop a graph-theoretic framework for studying approximation algorithms for SCS. The framework is reminiscent of the classical 2-approximation for Traveling Salesman: take two copies of an optimal solution, apply a trivial edge-collapsing procedure, and get an approximate solution. In this framework, we observe two surprising properties of SCS solutions, and we conjecture that they hold for all input instances. The first conjecture, that we call Collapsing Superstring conjecture, claims that there is an elementary way to transform any solution repeated twice into the same graph G. This conjecture would give an elementary 2-approximate algorithm for SCS. The second conjecture claims that not only the resulting graph G is the same for all solutions, but that G can be computed by an elementary greedy procedure called Greedy Hierarchical Algorithm. While the second conjecture clearly implies the first one, perhaps surprisingly we prove their equivalence. We support these equivalent conjectures by giving a proof for the special case where all input strings have length at most 3 (which until recently had been the only case where the Greedy Conjecture was proven). We also tested our conjectures on millions of instances of SCS. We prove that the standard Greedy Conjecture implies Greedy Hierarchical Conjecture, while the latter is sufficient for an efficient greedy 2-approximate approximation of SCS. Except for its (conjectured) good approximation ratio, the Greedy Hierarchical Algorithm provably finds a 3.5-approximation, and finds exact solutions for the special cases where we know polynomial time (not greedy) exact algorithms: (1) when the input strings form a spectrum of a string (2) when all input strings have length at most 2.
Cite as

Alexander Golovnev, Alexander S. Kulikov, Alexander Logunov, Ivan Mihajlin, and Maksim Nikolaev. Collapsing Superstring Conjecture. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 145, pp. 26:1-26:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{golovnev_et_al:LIPIcs.APPROX-RANDOM.2019.26,
  author =	{Golovnev, Alexander and Kulikov, Alexander S. and Logunov, Alexander and Mihajlin, Ivan and Nikolaev, Maksim},
  title =	{{Collapsing Superstring Conjecture}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2019)},
  pages =	{26:1--26:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-125-2},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{145},
  editor =	{Achlioptas, Dimitris and V\'{e}gh, L\'{a}szl\'{o} A.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2019.26},
  URN =		{urn:nbn:de:0030-drops-112411},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2019.26},
  annote =	{Keywords: superstring, shortest common superstring, approximation, greedy algorithms, greedy conjecture}
}
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