Related papers: The Complexity of Rooted Phylogeny Problems
Background. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set $L$ is known to be solvable in linear time.…
The computational complexity of the partition, 0-1 subset sum, unbounded subset sum, 0-1 knapsack and unbounded knapsack problems and their multiple variants were studied in numerous papers in the past where all the weights and profits were…
This paper provides answers to questions regarding the almost sure limiting behavior of rooted, binary tree-structured rules for regression. Examples show that questions raised by Gordon and Olshen in 1984 have negative answers. For these…
The constraint satisfaction problem (CSP) can be formulated as a homomorphism problem between relational structures: given a structure $\mathcal{A}$, for any structure $\mathcal{X}$, whether there exists a homomorphism from $\mathcal{X}$ to…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
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…
For any particular class of graphs, algorithms for computational problems restricted to the class often rely on structural properties that depend on the specific problem at hand. This begs the question if a large set of such results can be…
Given a set of $n$ real numbers, the 3SUM problem is to decide whether there are three of them that sum to zero. Until a recent breakthrough by Gr{\o}nlund and Pettie [FOCS'14], a simple $\Theta(n^2)$-time deterministic algorithm for this…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
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…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Our concern is the problem of efficiently determining the data complexity of answering queries mediated by description logic ontologies and constructing their optimal rewritings to standard database queries. Originated in ontology-based…
We propose an exact polynomial algorithm for a resource allocation problem with convex costs and constraints on partial sums of resource consumptions, in the presence of either continuous or integer variables. No assumption of strict…
Satisfiability of Boolean circuits is among the most known and important problems in theoretical computer science. This problem is NP-complete in general but becomes polynomial time when restricted either to monotone gates or linear gates.…
We investigate the class of regular-ordered word equations. In such equations, each variable occurs at most once in each side and the order of the variables occurring in both sides is the preserved (the variables can be, however, separated…
We give a trichotomy theorem for the complexity of approximately counting the number of satisfying assignments of a Boolean CSP instance. Such problems are parameterised by a constraint language specifying the relations that may be used in…
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.…
In this work, we consider the satisfiability problem in a logic that combines word equations over string variables denoting words of unbounded lengths, regular languages to which words belong and Presburger constraints on the length of…
We study the phase diagram and the algorithmic hardness of the random `locked' constraint satisfaction problems, and compare them to the commonly studied 'non-locked' problems like satisfiability of boolean formulas or graph coloring. The…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…