Related papers: Internal Dictionary Matching
Words are fundamental linguistic units that connect thoughts and things through meaning. However, words do not appear independently in a text sequence. The existence of syntactic rules induces correlations among neighboring words. Using an…
Reading comprehension models are based on recurrent neural networks that sequentially process the document tokens. As interest turns to answering more complex questions over longer documents, sequential reading of large portions of text…
We propose a general framework for end-to-end learning of data structures. Our framework adapts to the underlying data distribution and provides fine-grained control over query and space complexity. Crucially, the data structure is learned…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a…
We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…
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…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
Geometric data structures have been extensively studied in the regime where the dimension is much smaller than the number of input points. But in many scenarios in Machine Learning, the dimension can be much higher than the number of points…
We describe a data structure that supports access, rank and select queries, as well as symbol insertions and deletions, on a string $S[1,n]$ over alphabet $[1..\sigma]$ in time $O(\lg n/\lg\lg n)$, which is optimal even on binary sequences…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
A lattice is a partially-ordered set in which every pair of elements has a unique meet (greatest lower bound) and join (least upper bound). We present new data structures for lattices that are simple, efficient, and nearly optimal in terms…
We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…
Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter,…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
Consider observation data, comprised of n observation vectors with values on a set of attributes. This gives us n points in attribute space. Having data structured as a tree, implied by having our observations embedded in an ultrametric…
A choice dictionary is a data structure that can be initialized with a parameter $n\in\{1,2,\ldots\}$ and subsequently maintains an initially empty subset $S$ of $\{1,\ldots,n\}$ under insertion, deletion, membership queries and an…