Recognizing Generating Subgraphs Revisited

A graph [Formula: see text] is well-covered if all its maximal independent sets are of the same cardinality. Assume that a weight function [Formula: see text] is defined on its vertices. Then [Formula: see text] is [Formula: see text]well-covered if all maximal independent sets are of the same weight. For every graph [Formula: see text], the set of weight functions [Formula: see text] such that [Formula: see text] is [Formula: see text]-well-covered is a vector space, denoted as WCW(G). Deciding whether an input graph [Formula: see text] is well-covered is co-NP-complete. Therefore, finding WCW(G) is co-NP-hard. A generating subgraph of a graph [Formula: see text] is an induced complete bipartite subgraph [Formula: see text] of [Formula: see text] on vertex sets of bipartition [Formula: see text] and [Formula: see text], such that each of [Formula: see text] and [Formula: see text] is a maximal independent set of [Formula: see text], for some independent set [Formula: see text]. If [Formula: see text] is generating, then [Formula: see text] for every weight function [Formula: see text]. Therefore, generating subgraphs play an important role in finding WCW(G). The decision problem whether a subgraph of an input graph is generating is known to be NP-complete. In this article we prove NP- completeness of the problem for graphs without cycles of length 3 and 5, and for bipartite graphs with girth at least 6. On the other hand, we supply polynomial algorithms for recognizing generating subgraphs and finding WCW(G), when the input graph is bipartite without cycles of length 6. We also present a polynomial algorithm which finds WCW(G) when [Formula: see text] does not contain cycles of lengths 3, 4, 5, and 7.

Some Graphs Determined by their Signless Laplacian (Distance) Spectra

In literature, there are some results known about spectral determination of graphs with many edges. In [M.~C\'{a}mara and W.H.~Haemers. Spectral characterizations of almost complete graphs. {\em Discrete Appl. Math.}, 176:19--23, 2014.], C\'amara and Haemers studied complete graph with some edges deleted for spectral determination. In fact, they found that if the deleted edges form a matching, a complete graph $K_m$ provided $m \le n-2$, or a complete bipartite graph, then it is determined by its adjacency spectrum. In this paper, the graph $K_{n}\backslash K_{l,m}$ $(n>l+m)$ which is obtained from the complete graph $K_{n}$ by removing all the edges of a complete bipartite subgraph $K_{l,m}$ is studied. It is shown that the graph $K_{n}\backslash K_{1,m}$ with $m\ge4$ is determined by its signless Laplacian spectrum, and it is proved that the graph $K_{n}\backslash K_{l,m}$ is determined by its distance spectrum. The signless Laplacian spectral determination of the multicone graph $K_{n-2\alpha}\vee \alpha K_{2}$ was studied by Bu and Zhou in [C.~Bu and J.~Zhou. Signless Laplacian spectral characterization of the cones over some regular graphs. {\em Linear Algebra Appl.}, 436:3634--3641, 2012.] and Xu and He in [L. Xu and C. He. On the signless Laplacian spectral determination of the join of regular graphs. {\em Discrete Math. Algorithm. Appl.}, 6:1450050, 2014.] only for $n-2\alpha=1 ~\text{or}~ 2$. Here, this problem is completely solved for all positive integer $n-2\alpha$. The proposed approach is entirely different from those given by Bu and Zhou, and Xu and He.

Mining Pathway Associations from Networks of Mutual Exclusivity Interactions

Study of pairwise genetic interactions such as mutual exclusivity or synthetic lethality has led to the development of targeted anticancer therapies, and mining the network of such interactions is a common approach used to obtain deeper insights into the mechanism of cancer. A number of useful graph clustering-based tools exist to mine interaction networks. These tools find subgraphs or groups of genes wherein each gene belongs to a single subgraph. However, a gene may be present in multiple groups – for instance, a gene can be involved in multiple signalling pathways. We develop a new network mining algorithm, that does not impose this constraint and can provide a novel pathway-centric view. Our approach is based on finding edge-disjoint bipartite subgraphs of highest weights in an input network of genes, where edge weights indicate the significance of the interaction and each set of nodes in every bipartite subgraph is constrained to belong to a single pathway. This problem is NP-hard and we develop an Integer Linear Program to solve this problem. We evaluate our algorithm on breast and stomach cancer data. Our algorithm mines dense between-pathway interactions that are known to play important roles in cancer and are therapeutically actionable. Our algorithm complements existing network mining tools and can be useful to study the mutational landscape of cancer and inform therapy development.

On subgraphs of C2k-free graphs and a problem of Kühn and Osthus

Let c denote the largest constant such that every C6-free graph G contains a bipartite and C4-free subgraph having a fraction c of edges of G. Győri, Kensell and Tompkins showed that 3/8 ⩽ c ⩽ 2/5. We prove that c = 38. More generally, we show that for any ε > 0, and any integer k ⩾ 2, there is a C2k-free graph $G'$ which does not contain a bipartite subgraph of girth greater than 2k with more than a fraction $$\Bigl(1-\frac{1}{2^{2k-2}}\Bigr)\frac{2}{2k-1}(1+\varepsilon)$$ of the edges of $G'$ . There also exists a C2k-free graph $G''$ which does not contain a bipartite and C4-free subgraph with more than a fraction $$\Bigl(1-\frac{1}{2^{k-1}}\Bigr)\frac{1}{k-1}(1+\varepsilon)$$ of the edges of $G''$ .One of our proofs uses the following statement, which we prove using probabilistic ideas, generalizing a theorem of Erdős. For any ε > 0, and any integers a, b, k ⩾ 2, there exists an a-uniform hypergraph H of girth greater than k which does not contain any b-colourable subhypergraph with more than a fraction $$\Bigl(1-\frac{1}{b^{a-1}}\Bigr)(1+\varepsilon)$$ of the hyperedges of H. We also prove further generalizations of this theorem.In addition, we give a new and very short proof of a result of Kühn and Osthus, which states that every bipartite C2k-free graph G contains a C4-free subgraph with at least a fraction 1/(k−1) of the edges of G. We also answer a question of Kühn and Osthus about C2k-free graphs obtained by pasting together C2l’s (with k >l ⩾ 3).

The Largest Complete Bipartite Subgraph in Point-Hyperplane Incidence Graphs

Given $m$ points and $n$ hyperplanes in $\mathbb{R}^d$ ($d\geqslant 3)$, if there are many incidences, we expect to find a big cluster $K_{r,s}$ in their incidence graph. Apfelbaum and Sharir found lower and upper bounds for the largest size of $rs$, which match (up to a constant) only in three dimensions. In this paper we close the gap in four and five dimensions, up to some polylogarithmic factors.

MAXIMUM CUTS IN GRAPHS WITHOUT WHEELS

For a graph $G$, let $f(G)$ denote the maximum number of edges in a bipartite subgraph of $G$. Given a fixed graph $H$ and a positive integer $m$, let $f(m,H)$ denote the minimum possible cardinality of $f(G)$, as $G$ ranges over all graphs on $m$ edges that contain no copy of $H$. Alon et al. [‘Maximum cuts and judicious partitions in graphs without short cycles’, J. Combin. Theory Ser. B 88 (2003), 329–346] conjectured that, for any fixed graph $H$, there exists an $\unicode[STIX]{x1D716}(H)>0$ such that $f(m,H)\geq m/2+\unicode[STIX]{x1D6FA}(m^{3/4+\unicode[STIX]{x1D716}})$. We show that, for any wheel graph $W_{2k}$ of $2k$ spokes, there exists $c(k)>0$ such that $f(m,W_{2k})\geq m/2+c(k)m^{(2k-1)/(3k-1)}\log m$. In particular, we confirm the conjecture asymptotically for $W_{4}$ and give general lower bounds for $W_{2k+1}$.

A Note on Chromatic Number and Induced Odd Cycles

An odd hole is an induced odd cycle of length at least 5. Scott and Seymour confirmed a conjecture of Gyárfás and proved that if a graph $G$ has no odd holes then $\chi(G)\le 2^{2^{\omega(G)+2}}$. Chudnovsky, Robertson, Seymour and Thomas showed that if $G$ has neither $K_4$ nor odd holes then $\chi(G)\le 4$. In this note, we show that if a graph $G$ has neither triangles nor quadrilaterals, and has no odd holes of length at least 7, then $\chi(G)\le 4$ and $\chi(G)\le 3$ if $G$ has radius at most $3$, and for each vertex $u$ of $G$, the set of vertices of the same distance to $u$ induces a bipartite subgraph. This answers some questions in Plummer and Zha (2014).

Large Cuts with Local Algorithms on Triangle-Free Graphs

Let $G$ be a $d$-regular triangle-free graph with $m$ edges. We present an algorithm which finds a cut in $G$ with at least $(1/2 + 0.28125/\sqrt{d})m$ edges in expectation, improving upon Shearer's classic result. In particular, this implies that any $d$-regular triangle-free graph has a cut of at least this size, and thus, we obtain a new lower bound for the maximum number of edges in a bipartite subgraph of $G$.Our algorithm is simpler than Shearer's classic algorithm and it can be interpreted as a very efficient randomised distributed (local) algorithm: each node needs to produce only one random bit, and the algorithm runs in one round. The randomised algorithm itself was discovered using computational techniques. We show that for any fixed $d$, there exists a weighted neighbourhood graph $\mathcal{N}_d$ such that there is a one-to-one correspondence between heavy cuts of $\mathcal{N}_d$ and randomised local algorithms that find large cuts in any $d$-regular input graph. This turns out to be a useful tool for analysing the existence of cuts in $d$-regular graphs: we can compute the optimal cut of $\mathcal{N}_d$ to attain a lower bound on the maximum cut size of any $d$-regular triangle-free graph.