Related papers: Unique perfect phylogeny is NP-hard
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…
Graph packing and partitioning problems have been studied in many contexts, including from the algorithmic complexity perspective. Consider the packing problem of determining whether a graph contains a spanning tree and a cycle that do not…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets in many practical problems due to the…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We investigate the complexity of the reachability problem for (deep) neural networks: does it compute valid output given some valid input? It was recently claimed that the problem is NP-complete for general neural networks and conjunctive…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
We consider a natural variant of the well-known Feedback Vertex Set problem, namely the problem of deleting a small subset of vertices or edges to a full binary tree. This version of the problem is motivated by real-world scenarios that are…
A graph class is hereditary if it is closed under vertex deletion. We give examples of NP-hard, PSPACE-complete and NEXPTIME-complete problems that become constant-time solvable for every hereditary graph class that is not equal to the…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
For complexity of the heterogeneous minimum spanning forest problem has not been determined, we reduce 3-SAT which is NP-complete to 2-heterogeneous minimum spanning forest problem to prove this problem is NP-hard and spread result to…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
Let $X$ be a finite set. We give criterion to say if a system of trees ${\cal P}=\{T_i\}_i$ with leaf sets $L(T_i) \in {X \choose 5}$ can be amalgamated into a supertree, that is, if there exists a tree $T$ with $L(T)=X$ such that $T$…
The purpose of this article is to examine and limit the conditions in which the P complexity class could be equivalent to the NP complexity class. Proof is provided by demonstrating that as the number of clauses in a NP-complete problem…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We classify rooted trees which have strictly unimodal q-polynomials (plucking polynomial). We also give criteria for a trapezoidal shape of a plucking polynomial. We generalize results of Pak and Panova on strict unimodality of q-binomial…
In this article, we study the complexity of the upgrading version of the maximal covering location problem with edge length modifications on networks. This problem is NP-hard on general networks. However, in some particular cases, we prove…
Graph isomorphism, subgraph isomorphism, and maximum common subgraphs are classical well-investigated objects. Their (parameterized) complexity and efficiently tractable cases have been studied. In the present paper, for a given set of…