Finding Near-Optimal Independent Sets at Scale

The independent set problem is NP-hard and particularly difficult to solve in large sparse graphs. In this work, we develop an advanced evolutionary algorithm, which incorporates kernelization techniques to compute large independent sets in huge sparse networks. A recent exact algorithm has shown that large networks can be solved exactly by employing a branch-and-reduce technique that recursively kernelizes the graph and performs branching. However, one major drawback of their algorithm is that, for huge graphs, branching still can take exponential time. To avoid this problem, we recursively choose vertices that are likely to be in a large independent set (using an evolutionary approach), then further kernelize the graph. We show that identifying and removing vertices likely to be in large independent sets opens up the reduction space---which not only speeds up the computation of large independent sets drastically, but also enables us to compute high-quality independent sets on much larger instances than previously reported in the literature.Comment: 17 pages, 1 figure, 8 tables. arXiv admin note: text overlap with arXiv:1502.0168

Fine-grained dichotomies for the Tutte plane and Boolean #CSP

Jaeger, Vertigan, and Welsh [15] proved a dichotomy for the complexity of evaluating the Tutte polynomial at fixed points: The evaluation is #P-hard almost everywhere, and the remaining points admit polynomial-time algorithms. Dell, Husfeldt, and Wahl\'en [9] and Husfeldt and Taslaman [12], in combination with Curticapean [7], extended the #P-hardness results to tight lower bounds under the counting exponential time hypothesis #ETH, with the exception of the line $y=1$, which was left open. We complete the dichotomy theorem for the Tutte polynomial under #ETH by proving that the number of all acyclic subgraphs of a given $n$-vertex graph cannot be determined in time $exp(o(n))$ unless #ETH fails. Another dichotomy theorem we strengthen is the one of Creignou and Hermann [6] for counting the number of satisfying assignments to a constraint satisfaction problem instance over the Boolean domain. We prove that all #P-hard cases are also hard under #ETH. The main ingredient is to prove that the number of independent sets in bipartite graphs with $n$ vertices cannot be computed in time $exp(o(n))$ unless #ETH fails. In order to prove our results, we use the block interpolation idea by Curticapean [7] and transfer it to systems of linear equations that might not directly correspond to interpolation.Comment: 16 pages, 1 figur

JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

Scalable Kernelization for Maximum Independent Sets

The most efficient algorithms for finding maximum independent sets in both theory and practice use reduction rules to obtain a much smaller problem instance called a kernel. The kernel can then be solved quickly using exact or heuristic algorithms---or by repeatedly kernelizing recursively in the branch-and-reduce paradigm. It is of critical importance for these algorithms that kernelization is fast and returns a small kernel. Current algorithms are either slow but produce a small kernel, or fast and give a large kernel. We attempt to accomplish both of these goals simultaneously, by giving an efficient parallel kernelization algorithm based on graph partitioning and parallel bipartite maximum matching. We combine our parallelization techniques with two techniques to accelerate kernelization further: dependency checking that prunes reductions that cannot be applied, and reduction tracking that allows us to stop kernelization when reductions become less fruitful. Our algorithm produces kernels that are orders of magnitude smaller than the fastest kernelization methods, while having a similar execution time. Furthermore, our algorithm is able to compute kernels with size comparable to the smallest known kernels, but up to two orders of magnitude faster than previously possible. Finally, we show that our kernelization algorithm can be used to accelerate existing state-of-the-art heuristic algorithms, allowing us to find larger independent sets faster on large real-world networks and synthetic instances.Comment: Extended versio

All Maximal Independent Sets and Dynamic Dominance for Sparse Graphs

We describe algorithms, based on Avis and Fukuda's reverse search paradigm, for listing all maximal independent sets in a sparse graph in polynomial time and delay per output. For bounded degree graphs, our algorithms take constant time per set generated; for minor-closed graph families, the time is O(n) per set, and for more general sparse graph families we achieve subquadratic time per set. We also describe new data structures for maintaining a dynamic vertex set S in a sparse or minor-closed graph family, and querying the number of vertices not dominated by S; for minor-closed graph families the time per update is constant, while it is sublinear for any sparse graph family. We can also maintain a dynamic vertex set in an arbitrary m-edge graph and test the independence of the maintained set in time O(sqrt m) per update. We use the domination data structures as part of our enumeration algorithms.Comment: 10 page

Markov models for fMRI correlation structure: is brain functional connectivity small world, or decomposable into networks?

Correlations in the signal observed via functional Magnetic Resonance Imaging (fMRI), are expected to reveal the interactions in the underlying neural populations through hemodynamic response. In particular, they highlight distributed set of mutually correlated regions that correspond to brain networks related to different cognitive functions. Yet graph-theoretical studies of neural connections give a different picture: that of a highly integrated system with small-world properties: local clustering but with short pathways across the complete structure. We examine the conditional independence properties of the fMRI signal, i.e. its Markov structure, to find realistic assumptions on the connectivity structure that are required to explain the observed functional connectivity. In particular we seek a decomposition of the Markov structure into segregated functional networks using decomposable graphs: a set of strongly-connected and partially overlapping cliques. We introduce a new method to efficiently extract such cliques on a large, strongly-connected graph. We compare methods learning different graph structures from functional connectivity by testing the goodness of fit of the model they learn on new data. We find that summarizing the structure as strongly-connected networks can give a good description only for very large and overlapping networks. These results highlight that Markov models are good tools to identify the structure of brain connectivity from fMRI signals, but for this purpose they must reflect the small-world properties of the underlying neural systems