Internal Pattern Matching Queries in a Text and Applications

We consider several types of internal queries: questions about subwords of a text. As the main tool we develop an optimal data structure for the problem called here internal pattern matching. This data structure provides constant-time answers to queries about occurrences of one subword $x$ in another subword $y$ of a given text, assuming that $|y|=\mathcal{O}(|x|)$, which allows for a constant-space representation of all occurrences. This problem can be viewed as a natural extension of the well-studied pattern matching problem. The data structure has linear size and admits a linear-time construction algorithm. Using the solution to the internal pattern matching problem, we obtain very efficient data structures answering queries about: primitivity of subwords, periods of subwords, general substring compression, and cyclic equivalence of two subwords. All these results improve upon the best previously known counterparts. The linear construction time of our data structure also allows to improve the algorithm for finding $\delta$-subrepetitions in a text (a more general version of maximal repetitions, also called runs). For any fixed $\delta$ we obtain the first linear-time algorithm, which matches the linear time complexity of the algorithm computing runs. Our data structure has already been used as a part of the efficient solutions for subword suffix rank & selection, as well as substring compression using Burrows-Wheeler transform composed with run-length encoding.Comment: 31 pages, 9 figures; accepted to SODA 201

Pattern avoidance in binary trees

This paper considers the enumeration of trees avoiding a contiguous pattern. We provide an algorithm for computing the generating function that counts n-leaf binary trees avoiding a given binary tree pattern t. Equipped with this counting mechanism, we study the analogue of Wilf equivalence in which two tree patterns are equivalent if the respective n-leaf trees that avoid them are equinumerous. We investigate the equivalence classes combinatorially. Toward establishing bijective proofs of tree pattern equivalence, we develop a general method of restructuring trees that conjecturally succeeds to produce an explicit bijection for each pair of equivalent tree patterns.Comment: 19 pages, many images; published versio