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There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
Consider any locally checkable labeling problem $\Pi$ in rooted regular trees: there is a finite set of labels $\Sigma$, and for each label $x \in \Sigma$ we specify what are permitted label combinations of the children for an internal node…
Consider the following generalization of the classic binary search problem: a searcher is required to find a hidden vertex $x$ in a tree $T$. To do so, they iteratively perform queries to an oracle, each about a chosen vertex $v$. After…
Arising from structural graph theory, treewidth has become a focus of study in fixed-parameter tractable algorithms in various communities including combinatorics, integer-linear programming, and numerical analysis. Many NP-hard problems…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Unbounded SubsetSum is a classical textbook problem: given integers $w_1,w_2,\cdots,w_n\in [1,u],~c,u$, we need to find if there exists $m_1,m_2,\cdots,m_n\in \mathbb{N}$ satisfying $c=\sum_{i=1}^n w_im_i$. In its all-target version, $t\in…
Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…
A tree $t$-spanner $T$ of a graph $G$ is a spanning tree of $G$ such that the distance in $T$ between every pair of verices is at most $t$ times the distance in $G$ between them. There are efficient algorithms that find a tree $t\cdot…
We present a novel self-stabilizing algorithm for minimum spanning tree (MST) construction. The space complexity of our solution is $O(\log^2n)$ bits and it converges in $O(n^2)$ rounds. Thus, this algorithm improves the convergence time of…
We study two models of growing recursive trees. For both models, initially the tree only contains one vertex $u_1$ and at each time $n\geq 2$ a new vertex $u_n$ is added to the tree and its parent is chosen randomly according to some rule.…
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…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
The Weighted Tree Augmentation Problem (WTAP) is a fundamental well-studied problem in the field of network design. Given an undirected tree $G=(V,E)$, an additional set of edges $L \subseteq V\times V$ disjoint from $E$ called…
The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their…
Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…
Given an undirected graph $G = (V, E)$ and a weight function $w:E \to \mathbb{R}$, the \textsc{Minimum Dominating Tree} problem asks to find a minimum weight sub-tree of $G$, $T = (U, F)$, such that every $v \in V \setminus U$ is adjacent…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
There are various approaches to exploiting "hidden structure" in instances of hard combinatorial problems to allow faster algorithms than for general unstructured or random instances. For SAT and its counting version #SAT, hidden structure…