Related papers: Counting on General Run-Length Grammars
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
Compression of integer sets and sequences has been extensively studied for settings where elements follow a uniform probability distribution. In addition, methods exist that exploit clustering of elements in order to achieve higher…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
In his Ph.D. thesis, Ira Gessel proved a reciprocity formula for noncommutative symmetric functions which enables one to count words and permutations with restrictions on the lengths of their increasing runs. We generalize Gessel's theorem…
In past work (Onokpasa, Wild, Wong, DCC 2023), we showed that (a) for joint compression of RNA sequence and structure, stochastic context-free grammars are the best known compressors and (b) that grammars which have better compression…
Re-Pair is an effective grammar-based compression scheme achieving strong compression rates in practice. Let $n$, $\sigma$, and $d$ be the text length, alphabet size, and dictionary size of the final grammar, respectively. In their original…
We present a new similarity measure based on information theoretic measures which is superior than Normalized Compression Distance for clustering problems and inherits the useful properties of conditional Kolmogorov complexity. We show that…
Given a pattern $p = s_1x_1s_2x_2\cdots s_{r-1}x_{r-1}s_r$ such that $x_1,x_2,\ldots,x_{r-1}\in\{x,\overset{{}_{\leftarrow}}{x}\}$, where $x$ is a variable and $\overset{{}_{\leftarrow}}{x}$ its reversal, and $s_1,s_2,\ldots,s_r$ are…
We introduce annotated grammars, an extension of context-free grammars which allows annotations on terminals. Our model extends the standard notion of regular spanners, and is more expressive than the extraction grammars recently introduced…
We show that, given a string $s$ of length $n$, with constant memory and logarithmic passes over a constant number of streams we can build a context-free grammar that generates $s$ and only $s$ and whose size is within an $\Oh{\min (g \log…
Permutation $\sigma$ appears in permutation $\pi$ if there exists a subsequence of $\pi$ that is order-isomorphic to $\sigma$. The natural question is to check if $\sigma$ appears in $\pi$, and if so count the number of occurrences. We know…
We consider several types of internal queries, that is, questions about fragments of a given text $T$ specified in constant space by their locations in $T$. Our main result is an optimal data structure for Internal Pattern Matching (IPM)…
Context-free grammars are not able to model cross-serial dependencies in natural languages. To overcome this issue, Seki et al. introduced a generalization called $m$-multiple context-free grammars ($m$-MCFGs), which deal with $m$-tuples of…
We propose a new grammar-based language for defining information-extractors from documents (text) that is built upon the well-studied framework of document spanners for extracting structured data from text. While previously studied…
We study a generalization of the recently introduced order-preserving pattern matching, where instead of looking for an exact copy of the pattern, we only require that the relative order between the elements is the same. In our variant, we…
In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…
Since its introduction prediction by partial matching (PPM) has always been a de facto gold standard in lossless text compression, where many variants improving the compression ratio and speed have been proposed. However, reducing the high…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…