scholarly journals Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 110
Author(s):  
David Schaller ◽  
Manuela Geiß ◽  
Marc Hellmuth ◽  
Peter F. Stadler
Keyword(s):  
Phylogenetic Tree ◽  
Polynomial Time ◽  
Binary Tree ◽  
A Priori ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Minimum Cardinality ◽  
Mathematical Phylogenetics ◽  
Special Case

Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least resolved trees. We prove that the property of a rooted, leaf-colored tree to be least resolved for some BMG is preserved by the contraction of inner edges. For the special case of two-colored BMGs, this leads to a characterization of the least resolved trees (LRTs) of binary-explainable trees and a simple, polynomial-time algorithm for the minimum cardinality completion of the arc set of a BMG to reach a BMG that can be explained by a binary tree.

scholarly journals Tree Reconstruction from Triplet Cover Distances

10.37236/3388 ◽  
2014 ◽  
Vol 21 (2) ◽  
Author(s):  
Katharina T. Huber ◽  
Mike Steel
Keyword(s):  
Polynomial Time ◽  
Classical Result ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Interior Vertex ◽  
Evolutionary Genomics ◽  
Tree Reconstruction ◽  
Finite Tree ◽  
Path Distance ◽  
Special Case

It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict subset $\mathcal{L}$ of leaf pairs to suffice for reconstructing the tree and its edge weights, given just the distances between the leaf pairs in $\mathcal{L}$. It is known that any set ${\mathcal L}$ with this property for a tree in which all interior vertices have degree 3 must form a cover  for $T$ - that is, for each interior vertex $v$ of $T$, ${\mathcal L}$ must contain a pair of leaves from each pair of the three components of  $T-v$.  Here we provide a partial converse of this result by showing that if a set ${\mathcal L}$ of leaf pairs forms a cover  of a certain type for such a tree $T$ then $T$ and its edge weights can be uniquely determined from the distances between the pairs of leaves in ${\mathcal L}$. Moreover,  there is a polynomial-time algorithm for achieving this reconstruction. The result establishes a special case of a recent question concerning 'triplet covers', and is relevant to a problem arising in evolutionary genomics.

THE PROBLEM OF PARTITIONING WITH DUPLICATIONS AND ITS APPLICATIONS

1994 ◽  
Vol 03 (03) ◽  
pp. 395-405
Author(s):  
J. HARALAMBIDES ◽  
S. TRAGOUDAS
Keyword(s):  
Polynomial Time ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Vlsi Layout ◽  
Optimal Polynomial ◽  
Partitioning Problem ◽  
Polynomially Solvable ◽  
The Cost ◽  
Parallel Graph ◽  
Special Case

The problem of partitioning the elements of a graph G=(V, E) into two equal size sets A and B that share at most d elements such that the total number of edges (u, v), u∈A−B, v∈B−A is minimized, arises in the areas of Hypermedia Organization, Network Integrity, and VLSI Layout. We formulate the problem in terms of element duplication, where each element c∈A∩B is substituted by two copies c′∈A and c″∈B As a result, edges incident to c′ or c″ need not count in the cost of the partition. We show that this partitioning problem is NP-hard in general, and we present a solution which utilizes an optimal polynomial time algorithm for the special case where G is a series-parallel graph. We also discuss special other cases where the partitioning problem or variations are polynomially solvable.

NEAREST NEIGHBOR PROBLEMS

1992 ◽  
Vol 02 (04) ◽  
pp. 383-416 ◽  
Author(s):  
GORDON WILFONG
Keyword(s):  
Nearest Neighbor ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Minimum Size ◽  
Minimum Cardinality ◽  
Nearest Neighbor Rule ◽  
Np Complete ◽  
Cover Problem ◽  
Consistent Subset ◽  
Special Case

Suppose E is a set of labeled points (examples) in some metric space. A subset C of E is said to be a consistent subset ofE if it has the property that for any example e∈E, the label of the closest example in C to e is the same as the label of e. We consider the problem of computing a minimum cardinality consistent subset. Consistent subsets have applications in pattern classification schemes that are based on the nearest neighbor rule. The idea is to replace the training set of examples with as small a consistent subset as possible so as to improve the efficiency of the system while not significantly affecting its accuracy. The problem of finding a minimum size consistent subset of a set of examples is shown to be NP-complete. A special case is described and is shown to be equivalent to an optimal disc cover problem. A polynomial time algorithm for this optimal disc cover problem is then given.

scholarly journals Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

2021 ◽  
Vol 82 (3) ◽  
Author(s):  
David Schaller ◽  
Manuela Geiß ◽  
Peter F. Stadler ◽  
Marc Hellmuth
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
A Priori ◽  
Gene Tree ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Complete Characterization ◽  
Species Trees ◽  
Genome Scale

AbstractGenome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least $$75\%$$ 75 % of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.

scholarly journals Liveness in broadcast networks

Computing ◽  
2021 ◽  
Author(s):  
Peter Chini ◽  
Roland Meyer ◽  
Prakash Saivasan
Keyword(s):  
Model Checking ◽  
Polynomial Time ◽  
Message Passing ◽  
Linear Time ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Final State ◽  
Broadcast Network ◽  
Broadcast Networks

AbstractWe study liveness and model checking problems for broadcast networks, a system model of identical clients communicating via message passing. The first problem that we consider is Liveness Verification. It asks whether there is a computation such that one clients visits a final state infinitely often. The complexity of the problem has been open. It was shown to be $$\texttt {P}$$ P -hard but in $$\texttt {EXPSPACE}$$ EXPSPACE . We close the gap by a polynomial-time algorithm. The latter relies on a characterization of live computations in terms of paths in a suitable graph, combined with a fixed-point iteration to efficiently check the existence of such paths. The second problem is Fair Liveness Verification. It asks for a computation where all participating clients visit a final state infinitely often. We adjust the algorithm to also solve fair liveness in polynomial time. Both problems can be instrumented to answer model checking questions for broadcast networks against linear time temporal logic specifications. The first problem in this context is Fair Model Checking. It demands that for all computations of a broadcast network, all participating clients satisfy the specification. We solve the problem via the Vardi–Wolper construction and a reduction to Liveness Verification. The second problem is Sparse Model Checking. It asks whether each computation has a participating client that satisfies the specification. We reduce the problem to Fair Liveness Verification.

A Pseudo-Polynomial Time Algorithm for a Special Multiobjective Order Picking Problem

2015 ◽  
Vol 14 (05) ◽  
pp. 1111-1128 ◽  
Author(s):  
Özgür Özpeynirci ◽  
Cansu Kandemir
Keyword(s):  
Polynomial Time ◽  
Exact Algorithm ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Order Picking ◽  
Special Design ◽  
Nondominated Points ◽  
Polynomially Solvable ◽  
Nondominated Point ◽  
Special Case

In this study, we work on the order picking problem (OPP) in a specially designed warehouse with a single picker. Ratliff and Rosenthal [Operations Research31(3) (1983) 507–521] show that the special design of the warehouse and use of one picker lead to a polynomially solvable case. We address the multiobjective version of this special case and investigate the properties of the nondominated points. We develop an exact algorithm that finds any nondominated point and present an illustrative example. Finally we conduct a computational test and report the results.

MULTI-TERMINAL NETWORK CONNECTEDNESS ON SERIES-PARALLEL NETWORKS

2009 ◽  
Vol 01 (02) ◽  
pp. 253-265 ◽  
Author(s):  
TONI R. FARLEY ◽  
CHARLES J. COLBOURN
Keyword(s):  
Polynomial Time ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Polynomial Time Algorithms ◽  
Parallel Networks ◽  
Network Connectedness ◽  
Network Operation ◽  
Terminal Reliability ◽  
Special Case ◽  
General Networks

Network operation may require that a specified number k of nodes be able to communicate via paths consisting of operating edges and nodes. In an environment of node and edge failure, this leads to associated reliability measures. When the k nodes are known in advance, this has been widely studied as k-terminal reliability; when the k nodes are chosen uniformly at random, this has been studied as k-resilience. A third notion, when it suffices to have anyk nodes communicate, is related to the expected size of the largest component in the network. We generalize these three measures to the probability that given h nodes chosen in advance and i nodes chosen at random, they appear in a component of size at least k = h + i + j. As expected, for general networks, for most choices of (h, i, j) the computation is #P-complete and hence unlikely to admit a polynomial time algorithm. We develop polynomial time algorithms in the special case that the network is series-parallel, which subsume and generalize earlier methods for k-terminal reliability and k-resilience.

A polynomial time algorithm for big data in a special case of minimum constraint removal problem

2019 ◽  
Vol 13 (2) ◽  
pp. 247-254
Author(s):  
Bahram Sadeghi Bigham ◽  
Fariba Noorizadeh ◽  
Salman Khodayifar
Keyword(s):  
Big Data ◽  
Polynomial Time ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Special Case

OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION

2004 ◽  
Vol 02 (01) ◽  
pp. 173-213 ◽  
Author(s):  
DAN GUSFIELD ◽  
SATISH EDDHU ◽  
CHARLES LANGLEY
Keyword(s):  
Phylogenetic Tree ◽  
Polynomial Time ◽  
Phylogenetic Network ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Phylogenetic Networks ◽  
Seminal Paper ◽  
Back Mutation ◽  
True Tree ◽  
The One

A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.1 studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galled-tree". They gave a polynomial-time algorithm that was intended to determine whether or not a set of sequences could be generated on galled-tree. Unfortunately, the algorithm by Wang et al.1 is incomplete and does not constitute a necessary test for the existence of a galled-tree for the data. In this paper, we completely solve the problem. Moreover, we prove that if there is a galled-tree, then the one produced by our algorithm minimizes the number of recombinations over all phylogenetic networks for the data, even allowing multiple-crossover recombinations. We also prove that when there is a galled-tree for the data, the galled-tree minimizing the number of recombinations is "essentially unique". We also note two additional results: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation per site is allowed; second, the site compatibility problem (which is NP-hard in general) can be solved in polynomial time for any set of sequences that can be derived on a galled tree. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in general phylogenetic networks. This paper greatly extends the conference version that appears in an earlier work.8 PowerPoint slides of the conference talk can be found at our website.7

Algorithmic aspects of k-part degree restricted domination in graphs

2020 ◽  
Vol 12 (05) ◽  
pp. 2050057
Author(s):  
S. S. Kamath ◽  
A. Senthil Thilak ◽  
M. Rashmi
Keyword(s):  
Communication Networks ◽  
Polynomial Time ◽  
Dominating Set ◽  
Domination Number ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Bipartite Graphs ◽  
Chordal Graphs ◽  
Circle Graphs ◽  
Minimum Cardinality

The concept of network is predominantly used in several applications of computer communication networks. It is also a fact that the dominating set acts as a virtual backbone in a communication network. These networks are vulnerable to breakdown due to various causes, including traffic congestion. In such an environment, it is necessary to regulate the traffic so that these vulnerabilities could be reasonably controlled. Motivated by this, [Formula: see text]-part degree restricted domination is defined as follows. For a positive integer [Formula: see text], a dominating set [Formula: see text] of a graph [Formula: see text] is said to be a [Formula: see text]-part degree restricted dominating set ([Formula: see text]-DRD set) if for all [Formula: see text], there exists a set [Formula: see text] such that [Formula: see text] and [Formula: see text]. The minimum cardinality of a [Formula: see text]-DRD set of a graph [Formula: see text] is called the [Formula: see text]-part degree restricted domination number of [Formula: see text] and is denoted by [Formula: see text]. In this paper, we present a polynomial time reduction that proves the NP -completeness of the [Formula: see text]-part degree restricted domination problem for bipartite graphs, chordal graphs, undirected path graphs, chordal bipartite graphs, circle graphs, planar graphs and split graphs. We propose a polynomial time algorithm to compute a minimum [Formula: see text]-DRD set of a tree and minimal [Formula: see text]-DRD set of a graph.

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