Related papers: The Complexity of Rooted Phylogeny Problems
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…
We prove a complexity dichotomy theorem for all non-negative weighted counting Constraint Satisfaction Problems (CSP). This caps a long series of important results on counting problems including unweighted and weighted graph homomorphisms…
This paper is concerned with exact real solving of well-constrained, bivariate polynomial systems. The main problem is to isolate all common real roots in rational rectangles, and to determine their intersection multiplicities. We present…
We consider combinatorial problems that can be solved in polynomial time for graphs of bounded treewidth but where the order of the polynomial that bounds the running time is expected to depend on the treewidth bound. First we review some…
We present three new complexity results for classes of planning problems with simple causal graphs. First, we describe a polynomial-time algorithm that uses macros to generate plans for the class 3S of planning problems with binary state…
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…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
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…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
The Feder-Vardi dichotomy conjecture for Constraint Satisfaction Problems (CSPs) with finite templates, confirmed independently by Bulatov and Zhuk, has an extension to certain well-behaved infinite templates due to Bodirsky and Pinsker…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…
Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an $n\times n$ matrix $M$ and will receive $n$ column-vectors of size $n$, denoted by $v_1,\ldots,v_n$, one by one. After seeing each vector $v_i$, we…
This work explores the relationship between solution space and time complexity in the context of the $\textbf{P}$ vs. $\textbf{NP}$ problem, particularly through the lens of the sliding tile puzzle and root finding algorithms. We focus on…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
A computational problem exhibits a "gap property" when there is no tractable boundary between two disjoint sets of instances. We establish a Gap Trichotomy Theorem for a family of constraint problem variants, completely classifying the…
This paper depicts algorithms for solving the decision Boolean Satisfiability Problem. An extreme problem is formulated to analyze the complexity of algorithms and the complexity for solving it. A novel and easy reformulation as a lottery…
Query evaluation over probabilistic databases is known to be intractable in many cases, even in data complexity, i.e., when the query is fixed. Although some restrictions of the queries [19] and instances [4] have been proposed to lower the…