Related papers: Potential Maximal Clique Algorithms for Perfect Ph…
In this paper, we study the Planted Clique problem in a semi-random model. Our model is inspired from the Feige-Kilian model [16] which has been studied in many other works [8,11,17,26,35,38] for a variety of graph problems. Our algorithm…
We study the perfect phylogeny problem and establish a generalization of the four gamete condition (also called the Splits Equivalence Theorem) for sequences over three state characters. Our main result is that a set of input sequences over…
We study a planted clique model introduced by Feige where a complete graph of size $c\cdot n$ is planted uniformly at random in an arbitrary $n$-vertex graph. We give a simple deterministic algorithm that, in almost linear time, recovers a…
The Maximum Common Subgraph (MCS) problem plays a crucial role across various domains, bridging theoretical exploration and practical applications in fields like bioinformatics and social network analysis. Despite its wide applicability,…
A perfect matching cut is a perfect matching that is also a cutset, or equivalently a perfect matching containing an even number of edges on every cycle. The corresponding algorithmic problem, Perfect Matching Cut, is known to be…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
We study the complexity of Maximum Clique in intersection graphs of convex objects in the plane. On the algorithmic side, we extend the polynomial-time algorithm for unit disks [Clark '90, Raghavan and Spinrad '03] to translates of any…
In this paper, we apply the Rank-Sparsity Matrix Decomposition to the planted Maximum Quasi-Clique Problem (MQCP). This problem has the planted Maximum Clique Problem (MCP) as a special case. The maximum clique problem is NP-hard. A…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We consider the NP-complete problem of tracking paths in a graph, first introduced by Banik et. al. [3]. Given an undirected graph with a source $s$ and a destination $t$, find the smallest subset of vertices whose intersection with any…
We consider the problem of finding a local optimum for Max-Cut with FLIP-neighborhood, in which exactly one node changes the partition. Schaeffer and Yannakakis (SICOMP, 1991) showed PLS-completeness of this problem on graphs with unbounded…
We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…
The problem of minimizing a polynomial over the standard simplex is one of the basic NP-hard nonlinear optimization problems --- it contains the maximum clique problem in graphs as a special case. It is known that the problem allows a…
A geometric intersection graph is constructed over a set of geometric objects, where each vertex represents a distinct object and an edge connects two vertices if and only if the corresponding objects intersect. We examine the problem of…
We are given a graph $G$ with $n$ vertices, where a random subset of $k$ vertices has been made into a clique, and the remaining edges are chosen independently with probability $\tfrac12$. This random graph model is denoted…
The $k$-defective clique model relaxes the strict completeness constraint of the traditional clique by allowing up to $k$ missing edges, providing a robust formulation for detecting cohesive structures in noisy graphs. Consequently, the…
A complete graph is the graph in which every two vertices are adjacent. For a graph $G=(V,E)$, the complete width of $G$ is the minimum $k$ such that there exist $k$ independent sets $\mathtt{N}_i\subseteq V$, $1\le i\le k$, such that the…
Many natural computational problems, including e.g. Max Weight Independent Set, Feedback Vertex Set, or Vertex Planarization, can be unified under an umbrella of finding the largest sparse induced subgraph, that satisfies some property…
Bir\'{o} et al. (1992) introduced $H$-graphs, intersection graphs of connected subgraphs of a subdivision of a graph $H$. They are related to many classes of geometric intersection graphs, e.g., interval graphs, circular-arc graphs, split…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…