On the subtree isomorphism problem for ordered trees

1989 ◽  
Vol 32 (5) ◽  
pp. 271-273 ◽  
Author(s):  
Erkki Mäkinen
2012 ◽  
Vol 217 ◽  
pp. 1-11 ◽  
Author(s):  
V. Arvind ◽  
Bireswar Das ◽  
Johannes Köbler ◽  
Sebastian Kuhnert
Keyword(s):  

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Jördis-Ann Schüler ◽  
Steffen Rechner ◽  
Matthias Müller-Hannemann

AbstractAn important task in cheminformatics is to test whether two molecules are equivalent with respect to their 2D structure. Mathematically, this amounts to solving the graph isomorphism problem for labelled graphs. In this paper, we present an approach which exploits chemical properties and the local neighbourhood of atoms to define highly distinctive node labels. These characteristic labels are the key for clever partitioning molecules into molecule equivalence classes and an effective equivalence test. Based on extensive computational experiments, we show that our algorithm is significantly faster than existing implementations within , and . We provide our Java implementation as an easy-to-use, open-source package (via GitHub) which is compatible with . It fully supports the distinction of different isotopes and molecules with radicals.


Author(s):  
Mareike Fischer

AbstractTree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are more likely than balanced ones. Also, concerning ordered search trees, more balanced ones allow for more efficient data structuring than imbalanced ones. Therefore, different methods to measure the balance of trees were introduced. The Sackin index is one of the most frequently used measures for this purpose. In many contexts, statements about the minimal and maximal values of this index have been discussed, but formal proofs have only been provided for some of them, and only in the context of ordered binary (search) trees, not for general rooted trees. Moreover, while the number of trees with maximal Sackin index as well as the number of trees with minimal Sackin index when the number of leaves is a power of 2 are relatively easy to understand, the number of trees with minimal Sackin index for all other numbers of leaves has been completely unknown. In this manuscript, we extend the findings on trees with minimal and maximal Sackin indices from the literature on ordered trees and subsequently use our results to provide formulas to explicitly calculate the numbers of such trees. We also extend previous studies by analyzing the case when the underlying trees need not be binary. Finally, we use our results to contribute both to the phylogenetic as well as the computer scientific literature using the new findings on Sackin minimal and maximal trees to derive formulas to calculate the number of both minimal and maximal phylogenetic trees as well as minimal and maximal ordered trees both in the binary and non-binary settings. All our results have been implemented in the Mathematica package SackinMinimizer, which has been made publicly available.


2021 ◽  
Vol 64 (5) ◽  
pp. 98-105
Author(s):  
Martin Grohe ◽  
Daniel Neuen

We investigate the interplay between the graph isomorphism problem, logical definability, and structural graph theory on a rich family of dense graph classes: graph classes of bounded rank width. We prove that the combinatorial Weisfeiler-Leman algorithm of dimension (3 k + 4) is a complete isomorphism test for the class of all graphs of rank width at most k. A consequence of our result is the first polynomial time canonization algorithm for graphs of bounded rank width. Our second main result addresses an open problem in descriptive complexity theory: we show that fixed-point logic with counting expresses precisely the polynomial time properties of graphs of bounded rank width.


2021 ◽  
Vol 178 (3) ◽  
pp. 173-185
Author(s):  
Arthur Adinayev ◽  
Itamar Stein

In this paper, we study a certain case of a subgraph isomorphism problem. We consider the Hasse diagram of the lattice Mk (the unique lattice with k + 2 elements and one anti-chain of length k) and find the maximal k for which it is isomorphic to a subgraph of the reduction graph of a given one-rule string rewriting system. We obtain a complete characterization for this problem and show that there is a dichotomy. There are one-rule string rewriting systems for which the maximal such k is 2 and there are cases where there is no maximum. No other intermediate option is possible.


Sign in / Sign up

Export Citation Format

Share Document