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DOI: 10.4230/LIPIcs.ICALP.2018.34
On Estimating Edit Distance: Alignment, Dimension Reduction, and Embeddings

Authors: Moses Charikar, Ofir Geri, Michael P. Kim, and William Kuszmaul

Published in: LIPIcs, Volume 107, 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018)

Abstract
Edit distance is a fundamental measure of distance between strings and has been widely studied in computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of actually producing an alignment (i.e., the sequence of edits) has received far less attention. Somewhat surprisingly, we show that any algorithm to estimate edit distance can be used in a black-box fashion to produce an approximate alignment of strings, with modest loss in approximation factor and small loss in run time. Plugging in the result of Andoni, Krauthgamer, and Onak, we obtain an alignment that is a (log n)^{O(1/epsilon^2)} approximation in time O~(n^{1 + epsilon}). Closely related to the study of approximation algorithms is the study of metric embeddings for edit distance. We show that min-hash techniques can be useful in designing edit distance embeddings through three results: (1) An embedding from Ulam distance (edit distance over permutations) to Hamming space that matches the best known distortion of O(log n) and also implicitly encodes a sequence of edits between the strings; (2) In the case where the edit distance between the input strings is known to have an upper bound K, we show that embeddings of edit distance into Hamming space with distortion f(n) can be modified in a black-box fashion to give distortion O(f(poly(K))) for a class of periodic-free strings; (3) A randomized dimension-reduction map with contraction c and asymptotically optimal expected distortion O(c), improving on the previous O~(c^{1 + 2 / log log log n}) distortion result of Batu, Ergun, and Sahinalp.
Cite as

Moses Charikar, Ofir Geri, Michael P. Kim, and William Kuszmaul. On Estimating Edit Distance: Alignment, Dimension Reduction, and Embeddings. In 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 107, pp. 34:1-34:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{charikar_et_al:LIPIcs.ICALP.2018.34,
  author =	{Charikar, Moses and Geri, Ofir and Kim, Michael P. and Kuszmaul, William},
  title =	{{On Estimating Edit Distance: Alignment, Dimension Reduction, and Embeddings}},
  booktitle =	{45th International Colloquium on Automata, Languages, and Programming (ICALP 2018)},
  pages =	{34:1--34:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-076-7},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{107},
  editor =	{Chatzigiannakis, Ioannis and Kaklamanis, Christos and Marx, D\'{a}niel and Sannella, Donald},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2018.34},
  URN =		{urn:nbn:de:0030-drops-90383},
  doi =		{10.4230/LIPIcs.ICALP.2018.34},
  annote =	{Keywords: edit distance, alignment, approximation algorithms, embedding, dimension reduction}
}
Document
DOI: 10.4230/LIPIcs.APPROX-RANDOM.2017.1
Min-Cost Bipartite Perfect Matching with Delays

Authors: Itai Ashlagi, Yossi Azar, Moses Charikar, Ashish Chiplunkar, Ofir Geri, Haim Kaplan, Rahul Makhijani, Yuyi Wang, and Roger Wattenhofer

Published in: LIPIcs, Volume 81, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2017)

Abstract
In the min-cost bipartite perfect matching with delays (MBPMD) problem, requests arrive online at points of a finite metric space. Each request is either positive or negative and has to be matched to a request of opposite polarity. As opposed to traditional online matching problems, the algorithm does not have to serve requests as they arrive, and may choose to match them later at a cost. Our objective is to minimize the sum of the distances between matched pairs of requests (the connection cost) and the sum of the waiting times of the requests (the delay cost). This objective exhibits a natural tradeoff between minimizing the distances and the cost of waiting for better matches. This tradeoff appears in many real-life scenarios, notably, ride-sharing platforms. MBPMD is related to its non-bipartite variant, min-cost perfect matching with delays (MPMD), in which each request can be matched to any other request. MPMD was introduced by Emek et al. (STOC'16), who showed an O(log^2(n)+log(Delta))-competitive randomized algorithm on n-point metric spaces with aspect ratio Delta. Our contribution is threefold. First, we present a new lower bound construction for MPMD and MBPMD. We get a lower bound of Omega(sqrt(log(n)/log(log(n)))) on the competitive ratio of any randomized algorithm for MBPMD. For MPMD, we improve the lower bound from Omega(sqrt(log(n))) (shown by Azar et al., SODA'17) to Omega(log(n)/log(log(n))), thus, almost matching their upper bound of O(log(n)). Second, we adapt the algorithm of Emek et al. to the bipartite case, and provide a simplified analysis that improves the competitive ratio to O(log(n)). The key ingredient of the algorithm is an O(h)-competitive randomized algorithm for MBPMD on weighted trees of height h. Third, we provide an O(h)-competitive deterministic algorithm for MBPMD on weighted trees of height h. This algorithm is obtained by adapting the algorithm for MPMD by Azar et al. to the apparently more complicated bipartite setting.
Cite as

Itai Ashlagi, Yossi Azar, Moses Charikar, Ashish Chiplunkar, Ofir Geri, Haim Kaplan, Rahul Makhijani, Yuyi Wang, and Roger Wattenhofer. Min-Cost Bipartite Perfect Matching with Delays. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 81, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{ashlagi_et_al:LIPIcs.APPROX-RANDOM.2017.1,
  author =	{Ashlagi, Itai and Azar, Yossi and Charikar, Moses and Chiplunkar, Ashish and Geri, Ofir and Kaplan, Haim and Makhijani, Rahul and Wang, Yuyi and Wattenhofer, Roger},
  title =	{{Min-Cost Bipartite Perfect Matching with Delays}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2017)},
  pages =	{1:1--1:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-044-6},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{81},
  editor =	{Jansen, Klaus and Rolim, Jos\'{e} D. P. and Williamson, David P. and Vempala, Santosh S.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2017.1},
  URN =		{urn:nbn:de:0030-drops-75509},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2017.1},
  annote =	{Keywords: online algorithms with delayed service, bipartite matching, competitive analysis}
}
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