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The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses…
The problem of {\em efficiently} finding the best match for a query in a given set with respect to the Euclidean distance or the cosine similarity has been extensively studied in literature. However, a closely related problem of efficiently…
Thin spanning trees lie at the intersection of graph theory, approximation algorithms, and combinatorial optimization. They are central to the long-standing \emph{thin tree conjecture}, which asks whether every $k$-edge-connected graph…
An active research line within the broader field of network science is the one concerning link prediction. Close in scope to network reconstruction, link prediction targets specific connections with the aim of uncovering the missing ones,…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time…
Branching bisimilarity is a behavioural equivalence relation on labelled transition systems that takes internal actions into account. It has the traditional advantage that algorithms for branching bisimilarity are more efficient than all…
We show fast deterministic algorithms for fundamental problems on forests in the challenging low-space regime of the well-known Massive Parallel Computation (MPC) model. A recent breakthrough result by Coy and Czumaj [STOC'22] shows that,…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Broadcasting and convergecasting are pivotal services in distributed systems, in particular, in wireless ad-hoc and sensor networks, which are characterized by time- varying communication graphs. We study the question of whether it is…
We present a new algorithm for iterating over all permutations of a sequence. The algorithm leverages elementary~$O(1)$ operations on recursive lists. As a result, no new nodes are allocated during the computation. Instead, all elements are…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications-from biological networks to social…
Plenty of algorithms for link prediction have been proposed and were applied to various real networks. Among these works, the weights of links are rarely taken into account. In this paper, we use local similarity indices to estimate the…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
The Tree Augmentation Problem (TAP) is a fundamental network design problem in which we are given a tree and a set of additional edges, also called \emph{links}. The task is to find a set of links, of minimum size, whose addition to the…
Given a directed graph $G$ on $n$ vertices with a special vertex $s$, the directed minimum degree spanning tree problem requires computing a incoming spanning tree rooted at $s$ whose maximum tree in-degree is the smallest among all such…
In this paper we describe an algorithm that embeds a graph metric $(V,d_G)$ on an undirected weighted graph $G=(V,E)$ into a distribution of tree metrics $(T,D_T)$ such that for every pair $u,v\in V$, $d_G(u,v)\leq d_T(u,v)$ and…
We study the widely used hierarchical agglomerative clustering (HAC) algorithm on edge-weighted graphs. We define an algorithmic framework for hierarchical agglomerative graph clustering that provides the first efficient $\tilde{O}(m)$ time…