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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}
}
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