BDD-Based Analysis of Gapped q-Gram Filters

Recently, there has been a surge of interest in gapped q-gram filters for approximate string matching. Important design parameters for filters are for example the value of q, the filter-threshold and in particular the shape (aka seed) of the filter. A good choice of parameters can improve the performance of a q-gram filter by orders of magnitude and optimising these parameters is a nontrivial combinatorial problem. We describe a new method for analysing gapped q-gram filters. This method is simple and generic. It applies to a variety of filters, overcomes many restrictions that are present in existing algorithms and can easily be extended to new filter variants. To implement our approach, we use an extended version of BDDs (Binary Decision Diagrams), a data structure that efficiently represents sets of bit-strings. In a second step, we define a new class of multi-shape filters and analyse these filters with the BDD-based approach. Experiments show that multi-shape filters can outperfor...

• Type: Conference
• Year: 2004
• Where: STRINGOLOGY
• Authors: Marc Fontaine, Stefan Burkhardt, Juha Kärkkäinen
• Keywords: Approximate String Matching, Gapped Q-gram Filters, Q-gram Filters, STRINGOLOGY 2004, STRINGOLOGY 2008