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We study dynamic $(1+\epsilon)$-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected $n$-node $m$-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with…
Determinantal point processes (DPPs) have attracted significant attention as an elegant model that is able to capture the balance between quality and diversity within sets. DPPs are parameterized by a positive semi-definite kernel matrix.…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
The Directed Rural Postman Problem (DRPP) can be formulated as follows: given a strongly connected directed multigraph $D=(V,A)$ with nonnegative integral weights on the arcs, a subset $R$ of $A$ and a nonnegative integer $\ell$, decide…
Given a text $T$ and a pattern $P$ over alphabet $\Sigma$, the classic exact matching problem searches for all occurrences of pattern $P$ in text $T$. Unlike exact matching problem, order-preserving pattern matching (OPPM) considers the…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
$k$-defective cliques relax cliques by allowing up-to $k$ missing edges from being a complete graph. This relaxation enables us to find larger near-cliques and has applications in link prediction, cluster detection, social network analysis…
We study the problem of clustering networks whose nodes have imputed or physical positions in a single dimension, for example prestige hierarchies or the similarity dimension of hyperbolic embeddings. Existing algorithms, such as the…
We study the internal dictionary matching (IDM) problem where a dictionary $\mathcal{D}$ containing $d$ substrings of a text $T$ is given, and each query concerns the occurrences of patterns in $\mathcal{D}$ in another substring of $T$. We…
Subset selection is central to many wireless communication problems, including link scheduling, power allocation, and spectrum management. However, these problems are often NP-complete, because of which heuristic algorithms applied to solve…
We present a quantum algorithm in bioinformatics for solving the Binary Near-Perfect Phylogeny Problem (BNPP) with a complexity bound of $O(8.926^q + 8^q nm2)$, where n is the number of input taxa and m is the sequence length for each taxon…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Disjoint paths problems are among the most prominent problems in combinatorial optimization. The edge- as well as vertex-disjoint paths problem, are NP-complete on directed and undirected graphs. But on undirected graphs, Robertson and…
Unstructured neural network pruning algorithms have achieved impressive compression rates. However, the resulting - typically irregular - sparse matrices hamper efficient hardware implementations, leading to additional memory usage and…
Semi-directed networks are partially directed graphs that model evolution where the directed edges represent reticulate evolutionary events. We present an algorithm that reconstructs binary $n$-leaf semi-directed level-1 networks in $O(…
The problem of designing connectivity oracles supporting vertex failures is one of the basic data structures problems for undirected graphs. It is already well understood: previous works [Duan--Pettie STOC'10; Long--Saranurak FOCS'22]…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Population protocols are a well-studied model of distributed computation in which a group of anonymous finite-state agents communicates via pairwise interactions. Together they decide whether their initial configuration, that is, the…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
We study a delay-sensitive information flow problem where a source streams information to a sink over a directed graph G(V,E) at a fixed rate R possibly using multiple paths to minimize the maximum end-to-end delay, denoted as the…