Related papers: The Complexity of Phylogeny Constraint Satisfactio…
In this paper we explore fundamental concepts in computational complexity theory and the boundaries of algorithmic decidability. We examine the relationship between complexity classes \textbf{P} and \textbf{NP}, where $L \in \textbf{P}$…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
A kernelization algorithm for a computational problem is a procedure which compresses an instance into an equivalent instance whose size is bounded with respect to a complexity parameter. For the Boolean satisfiability problem (SAT), and…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
The goal of this paper is to set a constraint programming framework to solve lot-sizing problems. More specifically, we consider a single-item lot-sizing problem with time-varying lower and upper bounds for production and inventory. The…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
Today's propositional satisfiability (SAT) solvers are extremely powerful and can be used as an efficient back-end for solving NP-complete problems. However, many fundamental problems in knowledge representation and reasoning are located at…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
This paper investigates concurrency-constrained scheduling problems, where the objective is to construct a schedule for a set of jobs subject to concurrency restrictions. Formally, we are given a conflict graph $G$ defined over a set of $n$…
The rooted tree is an important data structure, and the subtree size, height, and depth are naturally defined attributes of every node. We consider the problem of the existence of a k-ary tree given a list of attribute sequences. We give…
We show that any submodular minimization (SM) problem defined on a linear constraint set with constraints having up to two variables per inequality, are 2-approximable in polynomial time. If the constraints are monotone (the two variables…
Ordered matchings, defined as graphs with linearly ordered vertices, where each vertex is connected to exactly one edge, play a crucial role in the area of ordered graphs and their homomorphisms. Therefore, we consider related problems from…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
Constraint satisfaction problem (CSP) is a well-studied combinatorial search problem, in which we are asked to find an assignment of values to given variables so as to satisfy all of given constraints. We study a reconfiguration variant of…
There has been great interest in identifying tractable subclasses of NP complete problems and designing efficient algorithms for these tractable classes. Constraint satisfaction and Bayesian network inference are two examples of such…
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
Genetic Programming (GP) has found various applications. Understanding this type of algorithm from a theoretical point of view is a challenging task. The first results on the computational complexity of GP have been obtained for problems…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…