skip to main content

Title: The orbit-polynomial: a novel measure of symmetry in networks
Research on the structural complexity of networks has produced many useful results in graph theory and applied disciplines such as engineering and data analysis. This paper is intended as a further contribution to this area of research. Here we focus on measures designed to compare graphs with respect to symmetry. We do this by means of a novel characteristic of a graph G, namely an ``orbit polynomial.'' A typical term of this univariate polynomial is of the form czn, where c is the number of orbits of size n of the automorphism group of G. Subtracting the orbit polynomial from 1 results in another polynomial that has a unique positive root, which can serve as a relative measure of the symmetry of a graph. The magnitude of this root is indicative of symmetry and can thus be used to compare graphs with respect to that property. In what follows, we will prove several inequalities on the unique positive roots of orbit polynomials corresponding to different graphs, thus showing differences in symmetry. In addition, we present numerical results relating to several classes of graphs for the purpose of comparing the new symmetry measure with existing ones. Finally, it is applied to a set of isomers of the chemical compound adamantane C10H16. We more » believe that the measure can be quite useful for tackling applications in chemistry, bioinformatics, and structure-oriented drug design. « less
Authors:
; ; ; ; ; ; ; ;
Award ID(s):
1818884
Publication Date:
NSF-PAR ID:
10165215
Journal Name:
IEEE access
ISSN:
2169-3536
Sponsoring Org:
National Science Foundation
More Like this
  1. In this paper, we prove bounds for the unique, positive zero of O  G (z) := 1 −O G (z) , where O G ( z ) is the so-called orbit polynomial [1]. The orbit polynomial is based on the multiplic- ity and cardinalities of the vertex orbits of a graph. In [1] , we have shown that the unique, positive zero δ≤1 of O  G (z) can serve as a meaningful measure of graph symmetry. In this paper, we study special graph classes with a specified number of orbits and obtain bounds on the value of δ.
  2. In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these are used to index structures far more complex than a single string, as was originally done with the FM-index [Ferragina and Manzini, J. ACM 2005]. As such, there has been an increasing effort to better understand under which conditions such an indexing scheme is possible. This has led to the introduction of Wheeler graphs [Gagie et al., Theor. Comput. Sci., 2017]. Gagie et al. showed that de Bruijn graphs, generalized compressed suffix arrays, and several other BWT related structures can bemore »represented as Wheeler graphs and that Wheeler graphs can be indexed in a way which is space-efficient. Hence, being able to recognize whether a given graph is a Wheeler graph, or being able to approximate a given graph by a Wheeler graph, could have numerous applications in indexing. Here we resolve the open question of whether there exists an efficient algorithm for recognizing if a given graph is a Wheeler graph. We present - The problem of recognizing whether a given graph G=(V,E) is a Wheeler graph is NP-complete for any edge label alphabet of size sigma >= 2, even when G is a DAG. This holds even on a restricted, subset of graphs called d-NFA's for d >= 5. This is in contrast to recent results demonstrating the problem can be solved in polynomial time for d-NFA's where d <= 2. We also show the recognition problem can be solved in linear time for sigma =1; - There exists an 2^{e log sigma + O(n + e)} time exact algorithm where n = |V| and e = |E|. This algorithm relies on graph isomorphism being computable in strictly sub-exponential time; - We define an optimization variant of the problem called Wheeler Graph Violation, abbreviated WGV, where the aim is to remove the minimum number of edges in order to obtain a Wheeler graph. We show WGV is APX-hard, even when G is a DAG, implying there exists a constant C >= 1 for which there is no C-approximation algorithm (unless P = NP). Also, conditioned on the Unique Games Conjecture, for all C >= 1, it is NP-hard to find a C-approximation; - We define the Wheeler Subgraph problem, abbreviated WS, where the aim is to find the largest subgraph which is a Wheeler Graph (the dual of the WGV). In contrast to WGV, we prove that the WS problem is in APX for sigma=O(1); The above findings suggest that most problems under this theme are computationally difficult. However, we identify a class of graphs for which the recognition problem is polynomial-time solvable, raising the open question of which parameters determine this problem's difficulty.« less
  3. A graph G is called {\em self-ordered} (a.k.a asymmetric) if the identity permutation is its only automorphism. Equivalently, there is a unique isomorphism from G to any graph that is isomorphic to G. We say that G=(VE) is {\em robustly self-ordered}if the size of the symmetric difference between E and the edge-set of the graph obtained by permuting V using any permutation :VV is proportional to the number of non-fixed-points of . In this work, we initiate the study of the structure, construction and utility of robustly self-ordered graphs. We show that robustly self-ordered bounded-degree graphs exist (in abundance), andmore »that they can be constructed efficiently, in a strong sense. Specifically, given the index of a vertex in such a graph, it is possible to find all its neighbors in polynomial-time (i.e., in time that is poly-logarithmic in the size of the graph). We provide two very different constructions, in tools and structure. The first, a direct construction, is based on proving a sufficient condition for robust self-ordering, which requires that an auxiliary graph, on {\em pairs} of vertices of the original graph, is expanding. In this case the original graph is (not only robustly self-ordered but) also expanding. The second construction proceeds in three steps: It boosts the mere existence of robustly self-ordered graphs, which provides explicit graphs of sublogarithmic size, to an efficient construction of polynomial-size graphs, and then, repeating it again, to exponential-size(robustly self-ordered) graphs that are locally constructible. This construction can yield robustly self-ordered graphs that are either expanders or highly disconnected, having logarithmic size connected components. We also consider graphs of unbounded degree, seeking correspondingly unbounded robustness parameters. We again demonstrate that such graphs (of linear degree)exist (in abundance), and that they can be constructed efficiently, in a strong sense. This turns out to require very different tools. Specifically, we show that the construction of such graphs reduces to the construction of non-malleable two-source extractors with very weak parameters but with some additional natural features. We actually show two reductions, one simpler than the other but yielding a less efficient construction when combined with the known constructions of extractors. We demonstrate that robustly self-ordered bounded-degree graphs are useful towards obtaining lower bounds on the query complexity of testing graph properties both in the bounded-degree and the dense graph models. Indeed, their robustness offers efficient, local and distance preserving reductions from testing problems on ordered structures (like sequences) to the unordered (effectively unlabeled) graphs. One of the results that we obtain, via such a reduction, is a subexponential separation between the query complexities of testing and tolerant testing of graph properties in the bounded-degree graph model. Changes to previous version: We retract the claims made in our initial posting regarding the construction of non-malleable two-source extractors (which are quasi-orthogonal) as well as the claims about the construction of relocation-detecting codes (see Theorems 1.5 and 1.6 in the original version). The source of trouble is a fundamental flaw in the proof of Lemma 9.7 (in the original version), which may as well be wrong. Hence, the original Section 9 was omitted, except that the original Section 9.3 was retained as a new Section 8.3. The original Section 8 appears as Section 8.0 and 8.1, and Section 8.2 is new.« less
  4. Abstract
    Excessive phosphorus (P) applications to croplands can contribute to eutrophication of surface waters through surface runoff and subsurface (leaching) losses. We analyzed leaching losses of total dissolved P (TDP) from no-till corn, hybrid poplar (Populus nigra X P. maximowiczii), switchgrass (Panicum virgatum), miscanthus (Miscanthus giganteus), native grasses, and restored prairie, all planted in 2008 on former cropland in Michigan, USA. All crops except corn (13 kg P ha−1 year−1) were grown without P fertilization. Biomass was harvested at the end of each growing season except for poplar. Soil water at 1.2 m depth was sampled weekly to biweekly for TDP determination during March–November 2009–2016More>>
  5. An automorphism of a graph is a mapping of the vertices onto themselves such that connections between respective edges are preserved. A vertex v in a graph G is fixed if it is mapped to itself under every automorphism of G. The fixing number of a graph G is the minimum number of vertices, when fixed, fixes all of the vertices in G. The determination of fixing numbers is important as it can be useful in determining the group of automorphisms of a graph-a famous and difficult problem. Fixing numbers were introduced and initially studied by Gibbons and Laison, Erwinmore »and Harary and Boutin. In this paper, we investigate fixing numbers for graphs with an underlying cyclic structure, which provides an inherent presence of symmetry. We first determine fixing numbers for circulant graphs, showing in many cases the fixing number is 2. However, we also show that circulant graphs with twins, which are pairs of vertices with the same neighbourhoods, have considerably higher fixing numbers. This is the first paper that investigates fixing numbers of point-block incidence graphs, which lie at the intersection of graph theory and combinatorial design theory. We also present a surprising result-identifying infinite families of graphs in which fixing any vertex fixes every vertex, thus removing all symmetries from the graph.« less