Subgraph Complementation

A subgraph complement of the graph G is a graph obtained from G by complementing all the edges in one of its induced subgraphs. We study the following algorithmic question: for a given graph G and graph class G, is there a subgraph complement of G which is in G? We show that this problem can be solved in polynomial time for various choices of the graphs class G, such as bipartite, d-degenerate, or cographs. We complement these results by proving that the problem is NP-complete when G is the class of regular graphs.publishedVersio

Linear rank-width of distance-hereditary graphs II. Vertex-minor obstructions

In the companion paper [Linear rank-width of distance-hereditary graphs I. A polynomial-time algorithm, Algorithmica 78(1):342--377, 2017], we presented a characterization of the linear rank-width of distance-hereditary graphs, from which we derived an algorithm to compute it in polynomial time. In this paper, we investigate structural properties of distance-hereditary graphs based on this characterization. First, we prove that for a fixed tree $T$, every distance-hereditary graph of sufficiently large linear rank-width contains a vertex-minor isomorphic to $T$. We extend this property to bigger graph classes, namely, classes of graphs whose prime induced subgraphs have bounded linear rank-width. Here, prime graphs are graphs containing no splits. We conjecture that for every tree $T$, every graph of sufficiently large linear rank-width contains a vertex-minor isomorphic to $T$. Our result implies that it is sufficient to prove this conjecture for prime graphs. For a class $\Phi$ of graphs closed under taking vertex-minors, a graph $G$ is called a vertex-minor obstruction for $\Phi$ if $G\notin \Phi$ but all of its proper vertex-minors are contained in $\Phi$. Secondly, we provide, for each $k\ge 2$, a set of distance-hereditary graphs that contains all distance-hereditary vertex-minor obstructions for graphs of linear rank-width at most $k$. Also, we give a simpler way to obtain the known vertex-minor obstructions for graphs of linear rank-width at most $1$.Comment: 38 pages, 13 figures, 1 table, revised journal version. A preliminary version of Section 5 appeared in the proceedings of WG1

Graph Concatenation for Quantum Codes

Graphs are closely related to quantum error-correcting codes: every stabilizer code is locally equivalent to a graph code, and every codeword stabilized code can be described by a graph and a classical code. For the construction of good quantum codes of relatively large block length, concatenated quantum codes and their generalizations play an important role. We develop a systematic method for constructing concatenated quantum codes based on "graph concatenation", where graphs representing the inner and outer codes are concatenated via a simple graph operation called "generalized local complementation." Our method applies to both binary and non-binary concatenated quantum codes as well as their generalizations.Comment: 26 pages, 12 figures. Figures of concatenated [[5,1,3]] and [[7,1,3]] are added. Submitted to JM

Inferring Network Mechanisms: The Drosophila melanogaster Protein Interaction Network

Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as degree distributions or clustering coefficients. We present a method for inferring the mechanism most accurately capturing a given network topology, exploiting discriminative tools from machine learning. The Drosophila melanogaster protein network is confidently and robustly (to noise and training data subsampling) classified as a duplication-mutation-complementation network over preferential attachment, small-world, and other duplication-mutation mechanisms. Systematic classification, rather than statistical study of specific properties, provides a discriminative approach to understand the design of complex networks.Comment: 19 pages, 5 figure

Subgraph complementation and minimum rank

Any finite simple graph $G = (V,E)$ can be represented by a collection $\mathscr{C}$ of subsets of $V$ such that $uv\in E$ if and only if $u$ and $v$ appear together in an odd number of sets in $\mathscr{C}$. Let $c_2(G)$ denote the minimum cardinality of such a collection. This invariant is equivalent to the minimum dimension of a faithful orthogonal representation of $G$ over $\mathbb{F}_2$ and is closely connected to the minimum rank of $G$. We show that $c_2(G) = \operatorname{mr}(G,\mathbb{F}_2)$ when $\operatorname{mr}(G,\mathbb{F}_2)$ is odd, or when $G$ is a forest. Otherwise, $\operatorname{mr}(G,\mathbb{F}_2)\leq c_2(G)\leq \operatorname{mr}(G,\mathbb{F}_2)+1$. Furthermore, we show that the following are equivalent for any graph $G$ with at least one edge: i. $c_2(G)=\operatorname{mr}(G,\mathbb{F}_2)+1$; ii. the adjacency matrix of $G$ is the unique matrix of rank $\operatorname{mr}(G,\mathbb{F}_2)$ which fits $G$ over $\mathbb{F}_2$; iii. there is a minimum collection $\mathscr{C}$ as described in which every vertex appears an even number of times; and iv. for every component $G'$ of $G$, $c_2(G') = \operatorname{mr}(G',\mathbb{F}_2) + 1$. We also show that, for these graphs, $\operatorname{mr}(G,\mathbb{F}_2)$ is twice the minimum number of tricliques whose symmetric difference of edge sets is $E$. Additionally, we provide a set of upper bounds on $c_2(G)$ in terms of the order, size, and vertex cover number of $G$. Finally, we show that the class of graphs with $c_2(G)\leq k$ is hereditary and finitely defined. For odd $k$, the sets of minimal forbidden induced subgraphs are the same as those for the property $\operatorname{mr}(G,\mathbb{F}_2)\leq k$, and we exhibit this set for $c_2(G)\leq2$