Related papers: Binary Jumbled Pattern Matching via All-Pairs Shor…
The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…
We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
We present an approach to implement binary search trees in the rule-based graph programming language GP 2. Our implementation uses GP 2's rooted graph transformation rules to be fast and supports insertion, deletion and query operations. We…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
Let $A$ be a static array storing $n$ elements from a totally ordered set. We present a data structure of optimal size at most $n\log_2(3+2\sqrt{2})+o(n)$ bits that allows us to answer the following queries on $A$ in constant time, without…
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…
We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…
For every fixed $d \in \mathbb{N}$, we design a data structure that represents a binary $n \times n$ matrix that is $d$-twin-ordered. The data structure occupies $O_d(n)$ bits, which is the least one could hope for, and can be queried for…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
Abelian string matching problems are becoming an object of considerable interest in last years. Very recently, Alatabbi et al. \cite{AILR2015} presented the first solution for the longest common Abelian factor problem for a pair of strings,…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…
We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…
Embedding image features into a binary Hamming space can improve both the speed and accuracy of large-scale query-by-example image retrieval systems. Supervised hashing aims to map the original features to compact binary codes in a manner…
We present a complete classification of the deterministic distributed time complexity for a family of graph problems: binary labeling problems in trees. These are locally checkable problems that can be encoded with an alphabet of size two…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…