126 Search Results for "Sanders, Peter"

Volume

LIPIcs, Volume 173

28th Annual European Symposium on Algorithms (ESA 2020)

ESA 2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)

Editors: Fabrizio Grandoni, Grzegorz Herman, and Peter Sanders

Document
DOI: 10.4230/LIPIcs.ESA.2024.69
PHOBIC: Perfect Hashing With Optimized Bucket Sizes and Interleaved Coding

Authors: Stefan Hermann, Hans-Peter Lehmann, Giulio Ermanno Pibiri, Peter Sanders, and Stefan Walzer

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
A minimal perfect hash function (or MPHF) maps a set of n keys to [n] : = {1, …, n} without collisions. Such functions find widespread application e.g. in bioinformatics and databases. In this paper we revisit PTHash - a construction technique particularly designed for fast queries. PTHash distributes the input keys into small buckets and, for each bucket, it searches for a hash function seed that places its keys in the output domain without collisions. The collection of all seeds is then stored in a compressed way. Since the first buckets are easier to place, buckets are considered in non-increasing order of size. Additionally, PTHash heuristically produces an imbalanced distribution of bucket sizes by distributing 60% of the keys into 30% of the buckets. Our main contribution is to characterize, up to lower order terms, an optimal choice for the expected bucket sizes, improving construction throughput for space efficient configurations both in theory and practice. Further contributions include a new encoding scheme for seeds that works across partitions of the data structure and a GPU parallelization. Compared to PTHash, PHOBIC is 0.17 bits/key more space efficient for same query time and construction throughput. For a configuration with fast queries, our GPU implementation can construct an MPHF at 2.17 bits/key in 28 ns/key, which can be queried in 37 ns/query on the CPU.
Cite as

Stefan Hermann, Hans-Peter Lehmann, Giulio Ermanno Pibiri, Peter Sanders, and Stefan Walzer. PHOBIC: Perfect Hashing With Optimized Bucket Sizes and Interleaved Coding. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 69:1-69:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hermann_et_al:LIPIcs.ESA.2024.69,
  author =	{Hermann, Stefan and Lehmann, Hans-Peter and Pibiri, Giulio Ermanno and Sanders, Peter and Walzer, Stefan},
  title =	{{PHOBIC: Perfect Hashing With Optimized Bucket Sizes and Interleaved Coding}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{69:1--69:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.69},
  URN =		{urn:nbn:de:0030-drops-211405},
  doi =		{10.4230/LIPIcs.ESA.2024.69},
  annote =	{Keywords: Compressed Data Structures, Minimal Perfect Hashing, GPU}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.83
Scalable Distributed String Sorting

Authors: Florian Kurpicz, Pascal Mehnert, Peter Sanders, and Matthias Schimek

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
String sorting is an important part of tasks such as building index data structures. Unfortunately, current string sorting algorithms do not scale to massively parallel distributed-memory machines since they either have latency (at least) proportional to the number of processors p or communicate the data a large number of times (at least logarithmic). We present practical and efficient algorithms for distributed-memory string sorting that scale to large p. Similar to state-of-the-art sorters for atomic objects, the algorithms have latency of about p^{1/k} when allowing the data to be communicated k times. Experiments indicate good scaling behavior on a wide range of inputs on up to 49152 cores. Overall, we achieve speedups of up to 4.9 over the current state-of-the-art distributed string sorting algorithms.
Cite as

Florian Kurpicz, Pascal Mehnert, Peter Sanders, and Matthias Schimek. Scalable Distributed String Sorting. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 83:1-83:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kurpicz_et_al:LIPIcs.ESA.2024.83,
  author =	{Kurpicz, Florian and Mehnert, Pascal and Sanders, Peter and Schimek, Matthias},
  title =	{{Scalable Distributed String Sorting}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{83:1--83:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.83},
  URN =		{urn:nbn:de:0030-drops-211541},
  doi =		{10.4230/LIPIcs.ESA.2024.83},
  annote =	{Keywords: sorting, strings, distributed-memory computing, distributed membership filters, scalability}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.97
Engineering Edge Orientation Algorithms

Authors: Henrik Reinstädtler, Christian Schulz, and Bora Uçar

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
Given an undirected graph G, the edge orientation problem asks for assigning a direction to each edge to convert G into a directed graph. The aim is to minimize the maximum out-degree of a vertex in the resulting directed graph. This problem, which is solvable in polynomial time, arises in many applications. An ongoing challenge in edge orientation algorithms is their scalability, particularly in handling large-scale networks with millions or billions of edges efficiently. We propose a novel algorithmic framework based on finding and manipulating simple paths to face this challenge. Our framework is based on an existing algorithm and allows many algorithmic choices. By carefully exploring these choices and engineering the underlying algorithms, we obtain an implementation which is more efficient and scalable than the current state-of-the-art. Our experiments demonstrate significant performance improvements compared to state-of-the-art solvers. On average our algorithm is 6.59 times faster when compared to the state-of-the-art.
Cite as

Henrik Reinstädtler, Christian Schulz, and Bora Uçar. Engineering Edge Orientation Algorithms. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 97:1-97:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{reinstadtler_et_al:LIPIcs.ESA.2024.97,
  author =	{Reinst\"{a}dtler, Henrik and Schulz, Christian and U\c{c}ar, Bora},
  title =	{{Engineering Edge Orientation Algorithms}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{97:1--97:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.97},
  URN =		{urn:nbn:de:0030-drops-211682},
  doi =		{10.4230/LIPIcs.ESA.2024.97},
  annote =	{Keywords: edge orientation, pseudoarboricity, graph algorithms}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.84
Insights into (k, ρ)-Shortcutting Algorithms

Authors: Alexander Leonhardt, Ulrich Meyer, and Manuel Penschuck

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
A graph is called a (k, ρ)-graph iff every node can reach ρ of its nearest neighbors in at most k hops. This property has proven useful in the analysis and design of parallel shortest-path algorithms [Blelloch et al., 2016; Dong et al., 2021]. Any graph can be transformed into a (k, ρ)-graph by adding shortcuts. Formally, the (k,ρ)-Minimum-Shortcut-Problem (kρ-MSP) asks to find an appropriate shortcut set of minimal cardinality. We show that kρ-MSP is NP-complete in the practical regime of k ≥ 3 and ρ = Θ(n^ε) for ε > 0. With a related construction, we bound the approximation factor of known kρ-MSP heuristics [Blelloch et al., 2016] from below and propose algorithmic countermeasures improving the approximation quality. Further, we describe an integer linear problem (ILP) that optimally solves kρ-MSP. Finally, we compare the practical performance and quality of all algorithms empirically.
Cite as

Alexander Leonhardt, Ulrich Meyer, and Manuel Penschuck. Insights into (k, ρ)-Shortcutting Algorithms. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 84:1-84:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{leonhardt_et_al:LIPIcs.ESA.2024.84,
  author =	{Leonhardt, Alexander and Meyer, Ulrich and Penschuck, Manuel},
  title =	{{Insights into (k, \rho)-Shortcutting Algorithms}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{84:1--84:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.84},
  URN =		{urn:nbn:de:0030-drops-211554},
  doi =		{10.4230/LIPIcs.ESA.2024.84},
  annote =	{Keywords: Complexity, Approximation, Optimal algorithms, Parallel shortest path}
}
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.WABI.2024.13
PLA-index: A k-mer Index Exploiting Rank Curve Linearity

Authors: Md. Hasin Abrar and Paul Medvedev

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

Abstract
Given a sorted list of k-mers S, the rank curve of S is the function mapping a k-mer from the k-mer universe to the location in S where it either first appears or would be inserted. An exciting recent development is the observation that, for certain datasets, the rank curve is predictable and can be exploited to create small search indices. In this paper, we develop a novel search index that first estimates a k-mer’s rank using a piece-wise linear approximation of the rank curve and then does a local search to determine the precise location of the k-mer in the list. We combine ideas from previous approaches and supplement them with an innovative data representation strategy that substantially reduces space usage. Our PLA-index uses an order of magnitude less space than Sapling and uses less than half the space of the PGM-index, for roughly the same query time. For example, using only 9 MiB of memory, it can narrow down the position of k-mer in the suffix array of the human genome to within 255 positions. Furthermore, we demonstrate the potential of our approach to impact a variety of downstream applications. First, the PLA-index halves the time of binary search on the suffix array of the human genome. Second, the PLA-index reduces the space of a direct-access lookup table by 76 percent, without increasing the run time. Third, we plug the PLA-index into a state-of-the-art read aligner Strobealign and replace a 2 GiB component with a PLA-index of size 1.5 MiB, without significantly effecting runtime. The software and reproducibility information is freely available at https://github.com/medvedevgroup/pla-index.
Cite as

Md. Hasin Abrar and Paul Medvedev. PLA-index: A k-mer Index Exploiting Rank Curve Linearity. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{abrar_et_al:LIPIcs.WABI.2024.13,
  author =	{Abrar, Md. Hasin and Medvedev, Paul},
  title =	{{PLA-index: A k-mer Index Exploiting Rank Curve Linearity}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{13:1--13:18},
  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.2024.13},
  URN =		{urn:nbn:de:0030-drops-206578},
  doi =		{10.4230/LIPIcs.WABI.2024.13},
  annote =	{Keywords: K-mer index, Piece-wise linear approximation, Learned index}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.23
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

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

Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.
Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  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.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.17
A*PA2: Up to 19× Faster Exact Global Alignment

Authors: Ragnar Groot Koerkamp

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

Abstract
Motivation. Pairwise alignment is at the core of computational biology. Most commonly used exact methods are either based on O(ns) band doubling or O(n+s²) diagonal transition, where n is the sequence length and s the number of errors. However, as the length of sequences has grown, these exact methods are often replaced by approximate methods based on e.g. seed-and-extend and heuristics to bound the computed region. We would like to develop an exact method that matches the performance of these approximate methods. Recently, Astarix introduced the A* shortest path algorithm with the seed heuristic for exact sequence-to-graph alignment. A*PA adapted and improved this for pairwise sequence alignment and achieves near-linear runtime when divergence (error rate) is low, at the cost of being very slow when divergence is high. Methods. We introduce A*PA2, an exact global pairwise aligner with respect to edit distance. The goal of A*PA2 is to unify the near-linear runtime of A*PA on similar sequences with the efficiency of dynamic programming (DP) based methods. Like Edlib, A*PA2 uses Ukkonen’s band doubling in combination with Myers' bitpacking. A*PA2 1) uses large block sizes inspired by Block Aligner, 2) extends this with SIMD (single instruction, multiple data), 3) introduces a new profile for efficient computations, 4) introduces a new optimistic technique for traceback based on diagonal transition, 5) avoids recomputation of states where possible, and 6) applies the heuristics developed in A*PA and improves them using pre-pruning. Results. With the first 4 engineering optimizations, A*PA2-simple has complexity O(ns) and is 6× to 8× faster than Edlib for sequences ≥ 10 kbp. A*PA2-full also includes the heuristic and is often near-linear in practice for sequences with small divergence. The average runtime of A*PA2 is 19× faster than the exact aligners BiWFA and Edlib on >500 kbp long ONT (Oxford Nanopore Technologies) reads of a human genome having 6% divergence on average. On shorter ONT reads of 11% average divergence the speedup is 5.6× (avg. length 11 kbp) and 0.81× (avg. length 800 bp). On all tested datasets, A*PA2 is competitive with or faster than approximate methods.
Cite as

Ragnar Groot Koerkamp. A*PA2: Up to 19× Faster Exact Global Alignment. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{grootkoerkamp:LIPIcs.WABI.2024.17,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{A*PA2: Up to 19× Faster Exact Global Alignment}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{17:1--17:25},
  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.2024.17},
  URN =		{urn:nbn:de:0030-drops-206610},
  doi =		{10.4230/LIPIcs.WABI.2024.17},
  annote =	{Keywords: Edit distance, Pairwise alignment, A*, Shortest path, Dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.SAT.2024.25
Trusted Scalable SAT Solving with On-The-Fly LRAT Checking

Authors: Dominik Schreiber

Published in: LIPIcs, Volume 305, 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)

Abstract
Recent advances have enabled powerful distributed SAT solvers to emit proofs of unsatisfiability, which renders them as trustworthy as sequential solvers. However, this mode of operation is still lacking behind conventional distributed solving in terms of scalability. We argue that the core limiting factor of such approaches is the requirement of a single, persistent artifact at the end of solving that is then checked independently (and sequentially). As an alternative, we propose a bottleneck-free setup that exploits recent advancements in producing and processing LRAT information to immediately check all solvers' reasoning on-the-fly during solving. In terms of clause sharing, our approach transfers the guarantee of a derived clause’s soundness from the sending to the receiving side via cryptographic signatures. Experiments with up to 2432 cores (32 nodes) indicate that our approach reduces the running time overhead incurred by proof checking by an order of magnitude, down to a median overhead of ≤ 42% over non trusted solving.
Cite as

Dominik Schreiber. Trusted Scalable SAT Solving with On-The-Fly LRAT Checking. In 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 305, pp. 25:1-25:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{schreiber:LIPIcs.SAT.2024.25,
  author =	{Schreiber, Dominik},
  title =	{{Trusted Scalable SAT Solving with On-The-Fly LRAT Checking}},
  booktitle =	{27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)},
  pages =	{25:1--25:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-334-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{305},
  editor =	{Chakraborty, Supratik and Jiang, Jie-Hong Roland},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2024.25},
  URN =		{urn:nbn:de:0030-drops-205477},
  doi =		{10.4230/LIPIcs.SAT.2024.25},
  annote =	{Keywords: SAT solving, distributed algorithms, proofs}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.20
Targeted Branching for the Maximum Independent Set Problem Using Graph Neural Networks

Authors: Kenneth Langedal, Demian Hespe, and Peter Sanders

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
Identifying a maximum independent set is a fundamental NP-hard problem. This problem has several real-world applications and requires finding the largest possible set of vertices not adjacent to each other in an undirected graph. Over the past few years, branch-and-bound and branch-and-reduce algorithms have emerged as some of the most effective methods for solving the problem exactly. Specifically, the branch-and-reduce approach, which combines branch-and-bound principles with reduction rules, has proven particularly successful in tackling previously unmanageable real-world instances. This progress was largely made possible by the development of more effective reduction rules. Nevertheless, other key components that can impact the efficiency of these algorithms have not received the same level of interest. Among these is the branching strategy, which determines which vertex to branch on next. Until recently, the most widely used strategy was to choose the vertex of the highest degree. In this work, we present a graph neural network approach for selecting the next branching vertex. The intricate nature of current branch-and-bound solvers makes supervised and reinforcement learning difficult. Therefore, we use a population-based genetic algorithm to evolve the model’s parameters instead. Our proposed approach results in a speedup on 73% of the benchmark instances with a median speedup of 24%.
Cite as

Kenneth Langedal, Demian Hespe, and Peter Sanders. Targeted Branching for the Maximum Independent Set Problem Using Graph Neural Networks. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{langedal_et_al:LIPIcs.SEA.2024.20,
  author =	{Langedal, Kenneth and Hespe, Demian and Sanders, Peter},
  title =	{{Targeted Branching for the Maximum Independent Set Problem Using Graph Neural Networks}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{20:1--20:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.20},
  URN =		{urn:nbn:de:0030-drops-203853},
  doi =		{10.4230/LIPIcs.SEA.2024.20},
  annote =	{Keywords: Graphs, Independent Set, Vertex Cover, Graph Neural Networks, Branch-and-Reduce}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2024.5
The Flower Calculus

Authors: Pablo Donato

Published in: LIPIcs, Volume 299, 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)

Abstract
We introduce the flower calculus, a deep inference proof system for intuitionistic first-order logic inspired by Peirce’s existential graphs. It works as a rewriting system over inductive objects called "flowers", that enjoy both a graphical interpretation as topological diagrams, and a textual presentation as nested sequents akin to coherent formulas. Importantly, the calculus dispenses completely with the traditional notion of symbolic connective, operating solely on nested flowers containing atomic predicates. We prove both the soundness of the full calculus and the completeness of an analytic fragment with respect to Kripke semantics. This provides to our knowledge the first analyticity result for a proof system based on existential graphs, adapting semantic cut-elimination techniques to a deep inference setting. Furthermore, the kernel of rules targetted by completeness is fully invertible, a desirable property for both automated and interactive proof search.
Cite as

Pablo Donato. The Flower Calculus. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 5:1-5:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{donato:LIPIcs.FSCD.2024.5,
  author =	{Donato, Pablo},
  title =	{{The Flower Calculus}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{5:1--5:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-323-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{299},
  editor =	{Rehof, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2024.5},
  URN =		{urn:nbn:de:0030-drops-203343},
  doi =		{10.4230/LIPIcs.FSCD.2024.5},
  annote =	{Keywords: deep inference, graphical calculi, existential graphs, intuitionistic logic, Kripke semantics, cut-elimination}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2024.135
A Finite Presentation of Graphs of Treewidth at Most Three

Authors: Amina Doumane, Samuel Humeau, and Damien Pous

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
We provide a finite equational presentation of graphs of treewidth at most three, solving an instance of an open problem by Courcelle and Engelfriet. We use a syntax generalising series-parallel expressions, denoting graphs with a small interface. We introduce appropriate notions of connectivity for such graphs (components, cutvertices, separation pairs). We use those concepts to analyse the structure of graphs of treewidth at most three, showing how they can be decomposed recursively, first canonically into connected parallel components, and then non-deterministically. The main difficulty consists in showing that all non-deterministic choices can be related using only finitely many equational axioms.
Cite as

Amina Doumane, Samuel Humeau, and Damien Pous. A Finite Presentation of Graphs of Treewidth at Most Three. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 135:1-135:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{doumane_et_al:LIPIcs.ICALP.2024.135,
  author =	{Doumane, Amina and Humeau, Samuel and Pous, Damien},
  title =	{{A Finite Presentation of Graphs of Treewidth at Most Three}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{135:1--135:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.135},
  URN =		{urn:nbn:de:0030-drops-202787},
  doi =		{10.4230/LIPIcs.ICALP.2024.135},
  annote =	{Keywords: Graphs, treewidth, connectedness, axiomatisation, series-parallel expressions}
}
Document
DOI: 10.4230/LIPIcs.ESA.2023.19
High Performance Construction of RecSplit Based Minimal Perfect Hash Functions

Authors: Dominik Bez, Florian Kurpicz, Hans-Peter Lehmann, and Peter Sanders

Published in: LIPIcs, Volume 274, 31st Annual European Symposium on Algorithms (ESA 2023)

Abstract
A minimal perfect hash function (MPHF) bijectively maps a set S of objects to the first |S| integers. It can be used as a building block in databases and data compression. RecSplit [Esposito et al., ALENEX'20] is currently the most space efficient practical minimal perfect hash function. It heavily relies on trying out hash functions in a brute force way. We introduce rotation fitting, a new technique that makes the search more efficient by drastically reducing the number of tried hash functions. Additionally, we greatly improve the construction time of RecSplit by harnessing parallelism on the level of bits, vectors, cores, and GPUs. In combination, the resulting improvements yield speedups up to 239 on an 8-core CPU and up to 5438 using a GPU. The original single-threaded RecSplit implementation needs 1.5 hours to construct an MPHF for 5 Million objects with 1.56 bits per object. On the GPU, we achieve the same space usage in just 5 seconds. Given that the speedups are larger than the increase in energy consumption, our implementation is more energy efficient than the original implementation.
Cite as

Dominik Bez, Florian Kurpicz, Hans-Peter Lehmann, and Peter Sanders. High Performance Construction of RecSplit Based Minimal Perfect Hash Functions. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 19:1-19:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bez_et_al:LIPIcs.ESA.2023.19,
  author =	{Bez, Dominik and Kurpicz, Florian and Lehmann, Hans-Peter and Sanders, Peter},
  title =	{{High Performance Construction of RecSplit Based Minimal Perfect Hash Functions}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{19:1--19:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-295-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{274},
  editor =	{G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. 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.2023.19},
  URN =		{urn:nbn:de:0030-drops-186728},
  doi =		{10.4230/LIPIcs.ESA.2023.19},
  annote =	{Keywords: compressed data structure, parallel perfect hashing, bit parallelism, GPU, SIMD, parallel computing, vector instructions}
}
Document
DOI: 10.4230/LIPIcs.ESA.2023.46
Learned Monotone Minimal Perfect Hashing

Authors: Paolo Ferragina, Hans-Peter Lehmann, Peter Sanders, and Giorgio Vinciguerra

Published in: LIPIcs, Volume 274, 31st Annual European Symposium on Algorithms (ESA 2023)

Abstract
A Monotone Minimal Perfect Hash Function (MMPHF) constructed on a set S of keys is a function that maps each key in S to its rank. On keys not in S, the function returns an arbitrary value. Applications range from databases, search engines, data encryption, to pattern-matching algorithms. In this paper, we describe LeMonHash, a new technique for constructing MMPHFs for integers. The core idea of LeMonHash is surprisingly simple and effective: we learn a monotone mapping from keys to their rank via an error-bounded piecewise linear model (the PGM-index), and then we solve the collisions that might arise among keys mapping to the same rank estimate by associating small integers with them in a retrieval data structure (BuRR). On synthetic random datasets, LeMonHash needs 34% less space than the next larger competitor, while achieving about 16 times faster queries. On real-world datasets, the space usage is very close to or much better than the best competitors, while achieving up to 19 times faster queries than the next larger competitor. As far as the construction of LeMonHash is concerned, we get an improvement by a factor of up to 2, compared to the competitor with the next best space usage. We also investigate the case of keys being variable-length strings, introducing the so-called LeMonHash-VL: it needs space within 13% of the best competitors while achieving up to 3 times faster queries than the next larger competitor.
Cite as

Paolo Ferragina, Hans-Peter Lehmann, Peter Sanders, and Giorgio Vinciguerra. Learned Monotone Minimal Perfect Hashing. In 31st Annual European Symposium on Algorithms (ESA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 274, pp. 46:1-46:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{ferragina_et_al:LIPIcs.ESA.2023.46,
  author =	{Ferragina, Paolo and Lehmann, Hans-Peter and Sanders, Peter and Vinciguerra, Giorgio},
  title =	{{Learned Monotone Minimal Perfect Hashing}},
  booktitle =	{31st Annual European Symposium on Algorithms (ESA 2023)},
  pages =	{46:1--46:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-295-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{274},
  editor =	{G{\o}rtz, Inge Li and Farach-Colton, Martin and Puglisi, Simon J. 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.2023.46},
  URN =		{urn:nbn:de:0030-drops-186990},
  doi =		{10.4230/LIPIcs.ESA.2023.46},
  annote =	{Keywords: compressed data structure, monotone minimal perfect hashing, retrieval}
}
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