Related papers: Potential Maximal Clique Algorithms for Perfect Ph…
The planted clique problem is a paradigmatic model of statistical-to-computational gaps: the planted clique is information-theoretically detectable if its size $k\ge 2\log_2 n$ but polynomial-time algorithms only exist for the recovery task…
This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…
Combinatorial optimization problems arise in a wide range of applications from diverse domains. Many of these problems are NP-hard and designing efficient heuristics for them requires considerable time and experimentation. On the other…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
The $k$-Maximum Dispersion Problem with Cardinality Constraints ($k$-MDCC) asks for a partition of a given item set with pairwise dissimilarities into $k$ cardinality-constrained groups such that the minimum pairwise intra-group…
We study the polyhedral properties of three problems of constructing an optimal complete bipartite subgraph (a biclique) in a bipartite graph. In the first problem we consider a balanced biclique with the same number of vertices in both…
We propose improved exact and heuristic algorithms for solving the maximum weight clique problem, a well-known problem in graph theory with many applications. Our algorithms interleave successful techniques from related work with novel data…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Reconstructing the evolutionary history of a set of species is a central task in computational biology. In real data, it is often the case that some information is missing: the Incomplete Directed Perfect Phylogeny (IDPP) problem asks,…
Chordal decomposition techniques are used to reduce large structured positive semidefinite matrix constraints in semidefinite programs (SDPs). The resulting equivalent problem contains multiple smaller constraints on the nonzero blocks (or…
We consider problems of finding a maximum size/weight $t$-matching without forbidden subgraphs in an undirected graph $G$ with the maximum degree bounded by $t+1$, where $t$ is an integer greater than $2$. Depending on the variant forbidden…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
In the 90's Clark, Colbourn and Johnson wrote a seminal paper where they proved that maximum clique can be solved in polynomial time in unit disk graphs. Since then, the complexity of maximum clique in intersection graphs of d-dimensional…
I present a single algorithm which solves the clique problems, "What is the largest size clique?", "What are all the maximal cliques?" and the decision problem, "Does a clique of size k exist?" for any given graph in polynomial time. The…
Given simple undirected graph G = (V, E), the Maximum Clique Problem(MCP) is that of finding a maximum-cardinality subset Q of V such that any two vertices in Q are adjacent. We present a modified local search algorithm for this problem.…
A $k$-defective clique of an undirected graph $G$ is a subset of its vertices that induces a nearly complete graph with a maximum of $k$ missing edges. The maximum $k$-defective clique problem, which asks for the largest $k$-defective…
The maximum clique (MC) problem is a challenging graph mining problem which, due to its NP-hard nature, can take a substantial amount of execution time. The MC problem is dominated by set intersection operations similar to Maximal Clique…
We study reconfiguration problems for cliques in a graph, which determine whether there exists a sequence of cliques that transforms a given clique into another one in a step-by-step fashion. As one step of a transformation, we consider…
We establish the expressibility in fixed-point logic with counting (FPC) of a number of natural polynomial-time problems. In particular, we show that the size of a maximum matching in a graph is definable in FPC. This settles an open…
The maximum labelled clique problem is a variant of the maximum clique problem where edges in the graph are given labels, and we are not allowed to use more than a certain number of distinct labels in a solution. We introduce a new…