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AWLCO: All-Window Length Co-Occurrence

Authors Joshua Sobel, Noah Bertram, Chen Ding, Fatemeh Nargesian, Daniel Gildea

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Author Details

Joshua Sobel
  • Department of Computer Science, University of Rochester, NY, USA
Noah Bertram
  • Department of Mathematics, University of Rochester, NY, USA
Chen Ding
  • Department of Computer Science, University of Rochester, NY, USA
Fatemeh Nargesian
  • Department of Computer Science, University of Rochester, NY, USA
Daniel Gildea
  • Department of Computer Science, University of Rochester, NY, USA

Funding

Partially funded by NSF awards CCF-1717877, IIS-1813823, CCF-1934986 and CNS-1909099.

Acknowledgements

We would like to give special thanks to Lu Zhang and Katherine Seeman for their efforts for the implementation and experimental evaluation of our algorithms. We thank one of our reviewers for suggesting the Aho-Corasick algorithm.

Cite AsGet BibTex

Joshua Sobel, Noah Bertram, Chen Ding, Fatemeh Nargesian, and Daniel Gildea. AWLCO: All-Window Length Co-Occurrence. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 24:1-24:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
https://doi.org/10.4230/LIPIcs.CPM.2021.24

Abstract

Analyzing patterns in a sequence of events has applications in text analysis, computer programming, and genomics research. In this paper, we consider the all-window-length analysis model which analyzes a sequence of events with respect to windows of all lengths. We study the exact co-occurrence counting problem for the all-window-length analysis model. Our first algorithm is an offline algorithm that counts all-window-length co-occurrences by performing multiple passes over a sequence and computing single-window-length co-occurrences. This algorithm has the time complexity O(n) for each window length and thus a total complexity of O(n²) and the space complexity O(|I|) for a sequence of size n and an itemset of size |I|. We propose AWLCO, an online algorithm that computes all-window-length co-occurrences in a single pass with the time complexity of O(n) and space complexity of O(√{n|I|}), assuming perfect hashing. Following this, we generalize our use case to patterns in which we propose an algorithm that computes all-window-length co-occurrence with time complexity O(n|I|), assuming perfect hashing, with an additional pre-processing step and space complexity O(√{n|I|}+|I|), plus the overhead of the Aho-Corasick algorithm [Aho and Corasick, 1975].

Subject Classification

ACM Subject Classification
  • Theory of computation → Streaming, sublinear and near linear time algorithms
Keywords
  • Itemsets
  • Data Sequences
  • Co-occurrence

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