42 Search Results for "Raman, Rajeev"

Volume

LIPIcs, Volume 75

16th International Symposium on Experimental Algorithms (SEA 2017)

SEA 2017, June 21-23, 2017, London, UK

Editors: Costas S. Iliopoulos, Solon P. Pissis, Simon J. Puglisi, and Rajeev Raman

Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2021.8
Weighted Ancestors in Suffix Trees Revisited

Authors: Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, and Rajeev Raman

Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)

Abstract
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require Ω(log log n) time for queries provided 𝒪(n polylog n) space is available and weights are from [0..n], where n is the number of tree nodes. However, when applied to suffix trees, the problem, surprisingly, admits an 𝒪(n)-space solution with constant query time, as was shown by Gawrychowski, Lewenstein, and Nicholson (Proc. ESA 2014). This variant of the problem can be reformulated as follows: given the suffix tree of a string s, we need a data structure that can locate in the tree any substring s[p..q] of s in 𝒪(1) time (as if one descended from the root reading s[p..q] along the way). Unfortunately, the data structure of Gawrychowski et al. has no efficient construction algorithm, limiting its wider usage as an algorithmic tool. In this paper we resolve this issue, describing a data structure for weighted ancestors in suffix trees with constant query time and a linear construction algorithm. Our solution is based on a novel approach using so-called irreducible LCP values.
Cite as

Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, and Rajeev Raman. Weighted Ancestors in Suffix Trees Revisited. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 8:1-8:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{belazzougui_et_al:LIPIcs.CPM.2021.8,
  author =	{Belazzougui, Djamal and Kosolobov, Dmitry and Puglisi, Simon J. and Raman, Rajeev},
  title =	{{Weighted Ancestors in Suffix Trees Revisited}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{8:1--8:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-186-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{191},
  editor =	{Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.8},
  URN =		{urn:nbn:de:0030-drops-139594},
  doi =		{10.4230/LIPIcs.CPM.2021.8},
  annote =	{Keywords: suffix tree, weighted ancestors, irreducible LCP, deterministic substring hashing}
}
Document
DOI: 10.4230/LIPIcs.SEA.2020.7
Fast and Simple Compact Hashing via Bucketing

Authors: Dominik Köppl, Simon J. Puglisi, and Rajeev Raman

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

Abstract
Compact hash tables store a set S of n key-value pairs, where the keys are from the universe U = {0,…,u-1}, and the values are v-bit integers, in close to B(u, n) + nv bits of space, where {b(u, n)} = log₂ binom(u,n) is the information-theoretic lower bound for representing the set of keys in S, and support operations insert, delete and lookup on S. Compact hash tables have received significant attention in recent years, and approaches dating back to Cleary [IEEE T. Comput, 1984], as well as more recent ones have been implemented and used in a number of applications. However, the wins on space usage of these approaches are outweighed by their slowness relative to conventional hash tables. In this paper, we demonstrate that compact hash tables based upon a simple idea of bucketing practically outperform existing compact hash table implementations in terms of memory usage and construction time, and existing fast hash table implementations in terms of memory usage (and sometimes also in terms of construction time). A related notion is that of a compact Hash ID map, which stores a set Ŝ of n keys from U, and implicitly associates each key in Ŝ with a unique value (its ID), chosen by the data structure itself, which is an integer of magnitude O(n), and supports inserts and lookups on Ŝ, while using close to B(u,n) bits. One of our approaches is suitable for use as a compact Hash ID map.
Cite as

Dominik Köppl, Simon J. Puglisi, and Rajeev Raman. Fast and Simple Compact Hashing via Bucketing. In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{koppl_et_al:LIPIcs.SEA.2020.7,
  author =	{K\"{o}ppl, Dominik and Puglisi, Simon J. and Raman, Rajeev},
  title =	{{Fast and Simple Compact Hashing via Bucketing}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{7:1--7:14},
  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.2020.7},
  URN =		{urn:nbn:de:0030-drops-120817},
  doi =		{10.4230/LIPIcs.SEA.2020.7},
  annote =	{Keywords: compact hashing, hash table, separate chaining}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.SEA.2017
LIPIcs, Volume 75, SEA'17, Complete Volume

Authors: Costas S. Iliopoulos, Solon P. Pissis, Simon J. Puglisi, and Rajeev Raman

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
LIPIcs, Volume 75, SEA'17, Complete Volume
Cite as

16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@Proceedings{iliopoulos_et_al:LIPIcs.SEA.2017,
  title =	{{LIPIcs, Volume 75, SEA'17, Complete Volume}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017},
  URN =		{urn:nbn:de:0030-drops-76644},
  doi =		{10.4230/LIPIcs.SEA.2017},
  annote =	{Keywords: Analysis of Algorithms and Problem Complexity, Algorithms}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.SEA.2017.0
Front Matter, Table of Contents, Preface, Conference Organization, External Reviewers

Authors: Costas S. Iliopoulos, Solon P. Pissis, Simon J. Puglisi, and Rajeev Raman

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization, External Reviewers
Cite as

16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{iliopoulos_et_al:LIPIcs.SEA.2017.0,
  author =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization, External Reviewers}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{0:i--0:xiv},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.0},
  URN =		{urn:nbn:de:0030-drops-76006},
  doi =		{10.4230/LIPIcs.SEA.2017.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization, External Reviewers}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.1
Designing Energy-Efficient Heat Recovery Networks using Mixed-Integer Nonlinear Optimisation

Authors: Radu Baltean-Lugojan, Christodoulos A. Floudas, Ruth Misener, and Miten Mistry

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Many industrial processes involve heating and cooling liquids: a quarter of the EU 2012 energy consumption came from industry and industry uses 73% of this energy on heating and cooling. We discuss mixed-integer nonlinear optimisation and its applications to energy efficiency. Our particular emphasis is on algorithms and solution techniques enabling optimisation for large-scale industrial networks. As a first application, optimising heat exchangers networks may increase efficiency in industrial plants. We develop deterministic global optimisation algorithms for a mixed-integer nonlinear optimisation model that simultaneously incorporates utility cost, equipment area, and hot/cold stream matches. We automatically recognise and exploit special mathematical structures common in heat recovery. We also computationally demonstrate the impact on the global optimisation solver ANTIGONE and benchmark large-scale test cases against heuristic approaches. As a second application, we discuss special structure in nonconvex quadratically-constrained optimisation problems, particularly through the lens of stream mixing and intermediate blending on process systems engineering networks. We take a parametric approach to uncovering topological structure and sparsity of the standard pooling problem in its p-formulation. We show that the sparse patterns of active topological structure are associated with a piecewise objective function. Finally, the presentation explains the conditions under which sparsity vanishes and where the combinatorial complexity emerges to cross over the P/NP boundary. We formally present the results obtained and their derivations for various specialised instances.
Cite as

Radu Baltean-Lugojan, Christodoulos A. Floudas, Ruth Misener, and Miten Mistry. Designing Energy-Efficient Heat Recovery Networks using Mixed-Integer Nonlinear Optimisation. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, p. 1:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{balteanlugojan_et_al:LIPIcs.SEA.2017.1,
  author =	{Baltean-Lugojan, Radu and Floudas, Christodoulos A. and Misener, Ruth and Mistry, Miten},
  title =	{{Designing Energy-Efficient Heat Recovery Networks using Mixed-Integer Nonlinear Optimisation}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{1:1--1:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.1},
  URN =		{urn:nbn:de:0030-drops-76288},
  doi =		{10.4230/LIPIcs.SEA.2017.1},
  annote =	{Keywords: Heat exchanger network, Mixed-integer nonlinear optimisation, Log mean temperature difference, Deterministic global optimisation}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.2
Dictionaries Revisited

Authors: Martin Farach-Colton

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Dictionaries are probably the most well studied class of data structures. A dictionary supports insertions, deletions, membership queries, and usually successor, predecessor, and extract-min. Given their centrality to both the theory and practice of data structures, surprisingly basic questions about them remain unsolved and sometimes even unposed. This talk focuses on questions that arise from the disparity between the way large-scale dictionaries are analyzed and the way they are used in practice.
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Martin Farach-Colton. Dictionaries Revisited. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, p. 2:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{farachcolton:LIPIcs.SEA.2017.2,
  author =	{Farach-Colton, Martin},
  title =	{{Dictionaries Revisited}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{2:1--2:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.2},
  URN =		{urn:nbn:de:0030-drops-76336},
  doi =		{10.4230/LIPIcs.SEA.2017.2},
  annote =	{Keywords: B+-trees, file system, write optimization}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.3
Engineering Streaming Algorithms

Authors: Graham Cormode

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Streaming algorithms must process a large quantity of small updates quickly to allow queries about the input to be answered from a small summary. Initial work on streaming algorithms laid out theoretical results, and subsequent efforts have involved engineering these for practical use. Informed by experiments, streaming algorithms have been widely implemented and used in practice. This talk will survey this line of work, and identify some lessons learned.
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Graham Cormode. Engineering Streaming Algorithms. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, p. 3:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{cormode:LIPIcs.SEA.2017.3,
  author =	{Cormode, Graham},
  title =	{{Engineering Streaming Algorithms}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{3:1--3:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.3},
  URN =		{urn:nbn:de:0030-drops-76270},
  doi =		{10.4230/LIPIcs.SEA.2017.3},
  annote =	{Keywords: Data stream algorithms}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.4
Better Process Mapping and Sparse Quadratic Assignment

Authors: Christian Schulz and Jesper Larsson Träff

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Communication and topology aware process mapping is a powerful approach to reduce communication time in parallel applications with known communication patterns on large, distributed memory systems. We address the problem as a quadratic assignment problem (QAP), and present algorithms to construct initial mappings of processes to processors as well as fast local search algorithms to further improve the mappings. By exploiting assumptions that typically hold for applications and modern supercomputer systems such as sparse communication patterns and hierarchically organized communication systems, we arrive at significantly more powerful algorithms for these special QAPs. Our multilevel construction algorithms employ recently developed, perfectly balanced graph partitioning techniques and excessively exploit the given communication system hierarchy. We present improvements to a local search algorithm of Brandfass et al. (2013), and decrease the running time by reducing the time needed to perform swaps in the assignment as well as by carefully constraining local search neighborhoods. Experiments indicate that our algorithms not only dramatically speed up local search, but due to the multilevel approach also find much better solutions in practice.
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Christian Schulz and Jesper Larsson Träff. Better Process Mapping and Sparse Quadratic Assignment. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 4:1-4:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{schulz_et_al:LIPIcs.SEA.2017.4,
  author =	{Schulz, Christian and Tr\"{a}ff, Jesper Larsson},
  title =	{{Better Process Mapping and Sparse Quadratic Assignment}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{4:1--4:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.4},
  URN =		{urn:nbn:de:0030-drops-76034},
  doi =		{10.4230/LIPIcs.SEA.2017.4},
  annote =	{Keywords: rank reordering, graph algorithms, process mapping, graph partitioning}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.5
The Isomap Algorithm in Distance Geometry

Authors: Leo Liberti and Claudia D'Ambrosio

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
The fundamental problem of distance geometry consists in finding a realization of a given weighted graph in a Euclidean space of given dimension, in such a way that vertices are realized as points and edges as straight segments having the same lengths as their given weights. This problem arises in structural proteomics, wireless sensor networks, and clock synchronization protocols to name a few applications. The well-known Isomap method is a dimensionality reduction heuristic which projects finite but high dimensional metric spaces into the "most significant" lower dimensional ones, where significance is measured by the magnitude of the corresponding eigenvalues. We start from a simple observation, namely that Isomap can also be used to provide approximate realizations of weighted graphs very efficiently, and then derive and benchmark six new heuristics.
Cite as

Leo Liberti and Claudia D'Ambrosio. The Isomap Algorithm in Distance Geometry. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{liberti_et_al:LIPIcs.SEA.2017.5,
  author =	{Liberti, Leo and D'Ambrosio, Claudia},
  title =	{{The Isomap Algorithm in Distance Geometry}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{5:1--5:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.5},
  URN =		{urn:nbn:de:0030-drops-76079},
  doi =		{10.4230/LIPIcs.SEA.2017.5},
  annote =	{Keywords: distance geometry problem, protein conformation, heuristics}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.6
Distributed Domain Propagation

Authors: Robert Lion Gottwald, Stephen J. Maher, and Yuji Shinano

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Portfolio parallelization is an approach that runs several solver instances in parallel and terminates when one of them succeeds in solving the problem. Despite its simplicity, portfolio parallelization has been shown to perform well for modern mixed-integer programming (MIP) and boolean satisfiability problem (SAT) solvers. Domain propagation has also been shown to be a simple technique in modern MIP and SAT solvers that effectively finds additional domain reductions after the domain of a variable has been reduced. In this paper we introduce distributed domain propagation, a technique that shares bound tightenings across solvers to trigger further domain propagations. We investigate its impact in modern MIP solvers that employ portfolio parallelization. Computational experiments were conducted for two implementations of this parallelization approach. While both share global variable bounds and solutions, they communicate differently. In one implementation the communication is performed only at designated points in the solving process and in the other it is performed completely asynchronously. Computational experiments show a positive performance impact of communicating global variable bounds and provide valuable insights in communication strategies for parallel solvers.
Cite as

Robert Lion Gottwald, Stephen J. Maher, and Yuji Shinano. Distributed Domain Propagation. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 6:1-6:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{gottwald_et_al:LIPIcs.SEA.2017.6,
  author =	{Gottwald, Robert Lion and Maher, Stephen J. and Shinano, Yuji},
  title =	{{Distributed Domain Propagation}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{6:1--6:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.6},
  URN =		{urn:nbn:de:0030-drops-76236},
  doi =		{10.4230/LIPIcs.SEA.2017.6},
  annote =	{Keywords: mixed integer programming, parallelization, domain propagation, portfolio solvers}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.7
Efficient Algorithms for k-Regret Minimizing Sets

Authors: Pankaj K. Agarwal, Nirman Kumar, Stavros Sintos, and Subhash Suri

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
A regret minimizing set Q is a small size representation of a much larger database P so that user queries executed on Q return answers whose scores are not much worse than those on the full dataset. In particular, a k-regret minimizing set has the property that the regret ratio between the score of the top-1 item in Q and the score of the top-k item in P is minimized, where the score of an item is the inner product of the item's attributes with a user's weight (preference) vector. The problem is challenging because we want to find a single representative set Q whose regret ratio is small with respect to all possible user weight vectors. We show that k-regret minimization is NP-Complete for all dimensions d>=3, settling an open problem from Chester et al. [VLDB 2014]. Our main algorithmic contributions are two approximation algorithms, both with provable guarantees, one based on coresets and another based on hitting sets. We perform extensive experimental evaluation of our algorithms, using both real-world and synthetic data, and compare their performance against the solution proposed in [VLDB 14]. The results show that our algorithms are significantly faster and scalable to much larger sets than the greedy algorithm of Chester et al. for comparable quality answers.
Cite as

Pankaj K. Agarwal, Nirman Kumar, Stavros Sintos, and Subhash Suri. Efficient Algorithms for k-Regret Minimizing Sets. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{agarwal_et_al:LIPIcs.SEA.2017.7,
  author =	{Agarwal, Pankaj K. and Kumar, Nirman and Sintos, Stavros and Suri, Subhash},
  title =	{{Efficient Algorithms for k-Regret Minimizing Sets}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.7},
  URN =		{urn:nbn:de:0030-drops-76321},
  doi =		{10.4230/LIPIcs.SEA.2017.7},
  annote =	{Keywords: regret minimizing sets, skyline, top-k query, coreset, hitting set}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.8
Engineering an Approximation Scheme for Traveling Salesman in Planar Graphs

Authors: Amariah Becker, Eli Fox-Epstein, Philip N. Klein, and David Meierfrankenfeld

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
We present an implementation of a linear-time approximation scheme for the traveling salesman problem on planar graphs with edge weights. We observe that the theoretical algorithm involves constants that are too large for practical use. Our implementation, which is not subject to the theoretical algorithm's guarantee, can quickly find good tours in very large planar graphs.
Cite as

Amariah Becker, Eli Fox-Epstein, Philip N. Klein, and David Meierfrankenfeld. Engineering an Approximation Scheme for Traveling Salesman in Planar Graphs. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 8:1-8:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{becker_et_al:LIPIcs.SEA.2017.8,
  author =	{Becker, Amariah and Fox-Epstein, Eli and Klein, Philip N. and Meierfrankenfeld, David},
  title =	{{Engineering an Approximation Scheme for Traveling Salesman in Planar Graphs}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{8:1--8:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.8},
  URN =		{urn:nbn:de:0030-drops-76305},
  doi =		{10.4230/LIPIcs.SEA.2017.8},
  annote =	{Keywords: Traveling Salesman, Approximation Schemes, Planar Graph Algorithms, Algorithm Engineering}
}
Document
DOI: 10.4230/LIPIcs.SEA.2017.9
Approximating the Smallest 2-Vertex-Connected Spanning Subgraph via Low-High Orders

Authors: Loukas Georgiadis, Giuseppe F. Italiano, and Aikaterini Karanasiou

Published in: LIPIcs, Volume 75, 16th International Symposium on Experimental Algorithms (SEA 2017)

Abstract
Let G = (V, E) be a 2-vertex-connected directed graph with m edges and n vertices. We consider the problem of approximating the smallest 2-vertex connected spanning subgraph (2VCSS) of G, and provide new efficient algorithms for this problem based on a clever use of low-high orders. The best previously known algorithms were able to compute a 3/2-approximation in O(m n+n 2) time, or a 3-approximation faster in linear time. In this paper, we present a linear-time algorithm that achieves a better approximation ratio of 2, and another algorithm that matches the previous 3/2-approximation in O(m n + n 2 ) time. We conducted a thorough experimental evaluation of all the above algorithms on a variety of input graphs. The experimental results show that both our two new algorithms perform well in practice. In particular, in our experiments the new 3/2-approximation algorithm was always faster than the previous 3/2-approximation algorithm, while their two approximation ratios were close. On the other side, our new linear-time algorithm yielded consistently better approximation ratios than the previously known linear-time algorithm, at the price of a small overhead in the running time.
Cite as

Loukas Georgiadis, Giuseppe F. Italiano, and Aikaterini Karanasiou. Approximating the Smallest 2-Vertex-Connected Spanning Subgraph via Low-High Orders. In 16th International Symposium on Experimental Algorithms (SEA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 75, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

Copy BibTex To Clipboard

@InProceedings{georgiadis_et_al:LIPIcs.SEA.2017.9,
  author =	{Georgiadis, Loukas and Italiano, Giuseppe F. and Karanasiou, Aikaterini},
  title =	{{Approximating the Smallest 2-Vertex-Connected Spanning Subgraph via Low-High Orders}},
  booktitle =	{16th International Symposium on Experimental Algorithms (SEA 2017)},
  pages =	{9:1--9:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-036-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{75},
  editor =	{Iliopoulos, Costas S. and Pissis, Solon P. and Puglisi, Simon J. and Raman, Rajeev},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2017.9},
  URN =		{urn:nbn:de:0030-drops-76299},
  doi =		{10.4230/LIPIcs.SEA.2017.9},
  annote =	{Keywords: 2-vertex connectivity, approximation algorithms, directed graphs}
}
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