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The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an…
We consider a matrix completion problem that exploits social or item similarity graphs as side information. We develop a universal, parameter-free, and computationally efficient algorithm that starts with hierarchical graph clustering and…
Given a similarity graph between items, correlation clustering (CC) groups similar items together and dissimilar ones apart. One of the most popular CC algorithms is KwikCluster: an algorithm that serially clusters neighborhoods of…
This paper proposes a new algorithm for simultaneous graph matching and clustering. For the first time in the literature, these two problems are solved jointly and synergetically without relying on any training data, which brings advantages…
Maximal biclique enumeration is a fundamental problem in bipartite graph data analysis. Existing biclique enumeration methods mainly focus on non-attributed bipartite graphs and also ignore the \emph{fairness} of graph attributes. In this…
In this paper, we introduce a \textit{Bi-level OPTimization} (BiOPT) framework for minimizing the sum of two convex functions, where both can be nonsmooth. The BiOPT framework involves two levels of methodologies. At the upper level of…
Reconfiguring two shortest paths in a graph means modifying one shortest path to the other by changing one vertex at a time so that all the intermediate paths are also shortest paths. This problem has several natural applications, namely:…
Given integers $k,j$ with $1\le j \le k-1$, we consider the length of the longest $j$-tight path in the binomial random $k$-uniform hypergraph $H^k(n,p)$. We show that this length undergoes a phase transition from logarithmic length to…
Cutwidth is one of the classic layout parameters for graphs. It measures how well one can order the vertices of a graph in a linear manner, so that the maximum number of edges between any prefix and its complement suffix is minimized. As…
For a connected graph $G=(V,E)$, a matching $M\subseteq E$ is a matching cut of $G$ if $G-M$ is disconnected. It is known that for an integer $d$, the corresponding decision problem Matching Cut is polynomial-time solvable for graphs of…
We consider the structure of $H$-free subgraphs of graphs with high minimal degree. We prove that for every $k>m$ there exists an $\epsilon:=\epsilon(k,m)>0$ so that the following holds. For every graph $H$ with chromatic number $k$ from…
Given a graph, a $k$-plex is a set of vertices in which each vertex is not adjacent to at most $k-1$ other vertices in the set. The maximum $k$-plex problem, which asks for the largest $k$-plex from the given graph, is an important but…
The $k$-cover of a point cloud $X$ in $\mathbb{R}^{d}$ at radius $r$ is the set of all points within distance $r$ of at least $k$ points of $X$. By varying $r$ and $k$ we obtain a two-parameter filtration known as the multicover…
Center-based clustering techniques are fundamental in some areas of machine learning such as data summarization. Generic $k$-center algorithms can produce biased cluster representatives so there has been a recent interest in fair $k$-center…
The $k$-cut problem asks, given a connected graph $G$ and a positive integer $k$, to find a minimum-weight set of edges whose removal splits $G$ into $k$ connected components. We give the first polynomial-time algorithm with approximation…
A graph is $H$-free if it does not contain an induced subgraph isomorphic to $H$. We denote by $P_k$ and $C_k$ the path and the cycle on $k$ vertices, respectively. In this paper, we prove that 4-COLORING is NP-complete for $P_7$-free…
We propose an improved algorithm for counting the number of Hamiltonian cycles in a directed graph. The basic idea of the method is sequential acceptance/rejection, which is successfully used in approximating the number of perfect matchings…
We consider the problem of enumerating optimal solutions for two hypergraph $k$-partitioning problems -- namely, Hypergraph-$k$-Cut and Minmax-Hypergraph-$k$-Partition. The input in hypergraph $k$-partitioning problems is a hypergraph…
The monography considers the problem of constructing a Hamiltonian cycle in a complete graph. A rule for constructing a Hamiltonian cycle based on isometric cycles of a graph is established. An algorithm for constructing a Hamiltonian cycle…
Motivated by hybrid graph representations, we introduce and study the following beyond-planarity problem, which we call $h$-Clique2Path Planarity: Given a graph $G$, whose vertices are partitioned into subsets of size at most $h$, each…