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We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any $n$-node static tree can be represented in $2n + o(n)$ bits and a number of operations on the tree can be supported in…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
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…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results.…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
We present a randomized algorithm that computes a constant approximation of a graph's arboricity, using $\tilde{O}(n/\lambda)$ queries to adjacency lists and in the same time bound. Here, $n$ and $\lambda$ denote the number of nodes and the…
A key principle in string processing is local consistency: using short contexts to handle matching fragments of a string consistently. String synchronizing sets [Kempa, Kociumaka; STOC 2019] are an influential instantiation of this…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
Given a set $S$ of $n$ points in the plane, we consider the problem of answering range selection queries on $S$: that is, given an arbitrary $x$-range $Q$ and an integer $k > 0$, return the $k$-th smallest $y$-coordinate from the set of…
We consider the problem of finding a minimum cut of a weighted graph presented as a single-pass stream. While graph sparsification in streams has been intensively studied, the specific application of finding minimum cuts in streams is less…
Given a string $T$ of length $n$ over an alphabet $\Sigma\subset \{1,2,\ldots,n^{O(1)}\}$ of size $\sigma$, we are to preprocess $T$ so that given a range $[i,j]$, we can return a representation of a shortest string over $\Sigma$ that is…
Given a string $S$ of length $N$ on a fixed alphabet of $\sigma$ symbols, a grammar compressor produces a context-free grammar $G$ of size $n$ that generates $S$ and only $S$. In this paper we describe data structures to support the…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Explorable heap selection is the problem of selecting the $n$th smallest value in a binary heap. The key values can only be accessed by traversing through the underlying infinite binary tree, and the complexity of the algorithm is measured…
Approximate nearest-neighbor search is a fundamental algorithmic problem that continues to inspire study due its essential role in numerous contexts. In contrast to most prior work, which has focused on point sets, we consider…
We consider the problem of encoding a string of length $n$ from an integer alphabet of size $\sigma$ so that access and substring equality queries (that is, determining the equality of any two substrings) can be answered efficiently. Any…