Efficient Generation of Stable Planar Cages for Chemistry

In this paper we describe an algorithm which generates all colored planar maps with a good minimum sparsity from simple motifs and rules to connect them. An implementation of this algorithm is available and is used by chemists who want to quickly generate all sound molecules they can obtain by mixing some basic components.Comment: 17 pages, 7 figures. Accepted at the 14th International Symposium on Experimental Algorithms (SEA 2015

Isomorph-free generation of 2-connected graphs with applications

Many interesting graph families contain only 2-connected graphs, which have ear decompositions. We develop a technique to generate families of unlabeled 2-connected graphs using ear augmentations and apply this technique to two problems. In the first application, we search for uniquely K_r-saturated graphs and find the list of uniquely K_4-saturated graphs on at most 12 vertices, supporting current conjectures for this problem. In the second application, we verifying the Edge Reconstruction Conjecture for all 2-connected graphs on at most 12 vertices. This technique can be easily extended to more problems concerning 2-connected graphs.Comment: 15 pages, 3 figures, 4 table

Saturation in the Hypercube and Bootstrap Percolation

Let $Q_d$ denote the hypercube of dimension $d$. Given $d\geq m$, a spanning subgraph $G$ of $Q_d$ is said to be $(Q_d,Q_m)$-saturated if it does not contain $Q_m$ as a subgraph but adding any edge of $E(Q_d)\setminus E(G)$ creates a copy of $Q_m$ in $G$. Answering a question of Johnson and Pinto, we show that for every fixed $m\geq2$ the minimum number of edges in a $(Q_d,Q_m)$-saturated graph is $\Theta(2^d)$. We also study weak saturation, which is a form of bootstrap percolation. A spanning subgraph of $Q_d$ is said to be weakly $(Q_d,Q_m)$-saturated if the edges of $E(Q_d)\setminus E(G)$ can be added to $G$ one at a time so that each added edge creates a new copy of $Q_m$. Answering another question of Johnson and Pinto, we determine the minimum number of edges in a weakly $(Q_d,Q_m)$-saturated graph for all $d\geq m\geq1$. More generally, we determine the minimum number of edges in a subgraph of the $d$-dimensional grid $P_k^d$ which is weakly saturated with respect to `axis aligned' copies of a smaller grid $P_r^m$. We also study weak saturation of cycles in the grid.Comment: 21 pages, 2 figures. To appear in Combinatorics, Probability and Computin

All-Pairs Minimum Cuts in Near-Linear Time for Surface-Embedded Graphs

For an undirected $n$-vertex graph $G$ with non-negative edge-weights, we consider the following type of query: given two vertices $s$ and $t$ in $G$, what is the weight of a minimum $st$-cut in $G$? We solve this problem in preprocessing time $O(n\log^3 n)$ for graphs of bounded genus, giving the first sub-quadratic time algorithm for this class of graphs. Our result also improves by a logarithmic factor a previous algorithm by Borradaile, Sankowski and Wulff-Nilsen (FOCS 2010) that applied only to planar graphs. Our algorithm constructs a Gomory-Hu tree for the given graph, providing a data structure with space $O(n)$ that can answer minimum-cut queries in constant time. The dependence on the genus of the input graph in our preprocessing time is $2^{O(g^2)}$