Formally Verified Suffix Array Construction Formally Verified Suffix Array Construction

Suffix arrays are a data structure with numerous real-world applications. They are extensively used in text retrieval and data compression applications, including query suggestion mechanisms in web search, and in bioinformatics tools for DNA sequencing and matching. This wide applicability means tha...

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Published inJournal of automated reasoning Vol. 69; no. 3; p. 21
Main Authors Cheung, Louis, Moffat, Alistair, Rizkallah, Christine
Format Journal Article
LanguageEnglish
Published Dordrecht Springer Netherlands 01.09.2025
Springer Nature B.V
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ISSN0168-7433
1573-0670
1573-0670
DOI10.1007/s10817-025-09735-8

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Abstract Suffix arrays are a data structure with numerous real-world applications. They are extensively used in text retrieval and data compression applications, including query suggestion mechanisms in web search, and in bioinformatics tools for DNA sequencing and matching. This wide applicability means that algorithms for constructing suffix arrays are of great practical importance. The SA-IS algorithm is an efficient but conceptually complex suffix array construction technique, and implementing it requires a deep understanding of its underlying theory. As a critical step towards developing a provably correct and efficient implementation, we have developed the SA-IS algorithm in Isabelle/HOL and formally verified that it is equivalent to a mathematical functional specification of suffix arrays, a task that required verifying a wide range of underlying properties of strings and suffixes. We also used Isabelle’s code extraction facilities to extract an executable Haskell implementation of SA-IS, which albeit is inefficient due to using lists and natural numbers rather than arrays and machine words, demonstrates that our verified HOL implementation of SA-IS can be refined to an executable implementation in its current form.
AbstractList Suffix arrays are a data structure with numerous real-world applications. They are extensively used in text retrieval and data compression applications, including query suggestion mechanisms in web search, and in bioinformatics tools for DNA sequencing and matching. This wide applicability means that algorithms for constructing suffix arrays are of great practical importance. The SA-IS algorithm is an efficient but conceptually complex suffix array construction technique, and implementing it requires a deep understanding of its underlying theory. As a critical step towards developing a provably correct and efficient implementation, we have developed the SA-IS algorithm in Isabelle/HOL and formally verified that it is equivalent to a mathematical functional specification of suffix arrays, a task that required verifying a wide range of underlying properties of strings and suffixes. We also used Isabelle’s code extraction facilities to extract an executable Haskell implementation of SA-IS, which albeit is inefficient due to using lists and natural numbers rather than arrays and machine words, demonstrates that our verified HOL implementation of SA-IS can be refined to an executable implementation in its current form.
ArticleNumber 21
Author Cheung, Louis
Moffat, Alistair
Rizkallah, Christine
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Issue 3
Keywords Suffix Array Construction
Formal Verification
SA-IS Algorithm
Isabelle/HOL
Data Structures
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  doi: 10.1145/3549992
– ident: 9735_CR41
  doi: 10.1109/SFCS.1997.646102
– volume: 31
  start-page: 15
  issue: 3
  year: 2013
  ident: 9735_CR32
  publication-title: ACM Transactions on Information Systems
  doi: 10.1145/2493175.2493180
– ident: 9735_CR60
  doi: 10.3233/978-1-58603-976-9-267
– ident: 9735_CR64
  doi: 10.1145/2951913.2951940
– ident: 9735_CR22
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Snippet Suffix arrays are a data structure with numerous real-world applications. They are extensively used in text retrieval and data compression applications,...
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SubjectTerms Algorithms
Arrays
Artificial Intelligence
Bioinformatics
Computer Science
Construction
Data compression
Data structures
Gene sequencing
Mathematical Logic and Formal Languages
Mathematical Logic and Foundations
Number theory
Symbolic and Algebraic Manipulation
Subtitle Formally Verified Suffix Array Construction
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Title Formally Verified Suffix Array Construction
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