On unique independent sets in graphs

J.Y.-T. Leung (J. Algorithms, no.5, (1984)) presented algorithms for generating all the maximal independent sets in interval graphs and circular-arc graphs. The algorithms take O(n/sup 2/+ beta ) steps, where beta is the sum of the number of nodes in all maximal independent sets. The authors use a new technique to give fast and efficient algorithms for finding all the maximum weight independent sets in interval graphs and circular-arc graphs. The algorithms take O(max(n/sup 2/, beta )) steps in O(n/sup 2/) space, where beta is the sum of the number of nodes in all maximum weight independent sets. The algorithms can be directly applied for finding a maximum weight independent set in these graphs in O(n/sup 2/) steps. Thus, the result is an improvement over the best known result of O(n/sup 2/ log n) for finding the maximum weight independent set in circular-arc graphs. >

A parallel algorithm for finding a near-maximum independent set in a circle graph is presented. An independent set in a graph is a set of vertices, no two of which are adjacent. A maximum independent set is an independent set whose cardinality is the largest among all independent sets of a graph. The algorithm is modified for predicting the secondary structure in ribonucleic acids (RNA). The proposed system, composed of an n neural network array (where n is the number of edges in the circle graph of the number of possible base pairs), not only generates a near-maximum independent set but also predicts the secondary structure of ribonucleic acids within several hundred iteration steps. The simulator discovered several solutions which are more stable structures, in a sequence of 359 bases from the potato spindle tuber viroid, than previously proposed structures.

A locally-optimal structure is a combinatorial structure that cannot be improved by certain (greedy) local moves, even though it may not be globally optimal. An example is a maximal independent set in a graph. It is trivial to construct an independent set in a graph. It is easy to (greedily) construct a maximal independent set. However, it is NP-hard to construct a globally-optimal (maximum) independent set.This situation is typical. Constructing a locally-optimal structure is somewhat more difficult than constructing an arbitrary structure, and constructing a globally-optimal structure is more difficult than constructing a locally-optimal structure. The same situation arises with listing. The differences between the problems become obscured when we move from listing to counting because nearly everything is \(\#\text {P} \)-complete. However, we highlight an interesting phenomenon that arises in approximate counting, where approximately counting locally-optimal structures is apparently more difficult than approximately counting globally-optimal structures. Specifically, we show that counting maximal independent sets is complete for \(\#\text {P} \) with respect to approximation-preserving reductions, whereas counting all independent sets, or counting maximum independent sets is complete for an apparently smaller class, #RH\(\varPi _1\) which has a prominent role in the complexity of approximate counting. Motivated by the difficulty of approximately counting maximal independent sets in bipartite graphs, we also study counting problems involving minimal separators and minimal edge separators (which are also locally-optimal structures). Minimal separators have applications via fixed-parameter-tractable algorithms for constructing triangulations and phylogenetic trees. Although exact (exponential-time) algorithms exist for listing these structures, we show that the counting problems are as hard as they could possibly be. All of the exact counting problems are \(\#\text {P} \)-complete, and all of the approximation problems are complete for \(\#\text {P} \) with respect to approximation-preserving reductions. A full version [14] containing detailed proofs is available at http://arxiv.org/abs/1411.6829. Theorem-numbering here matches the full version.

Maximal independent sets in bipartite graphs obtained from Boolean lattices

Parallel algorithms for fractional and maximal independent sets in planar graphs

Theminimum-degree greedy algorithm, or Greedy for short, is a simple and well-studied method for finding independent sets in graphs. We show that it achieves a performance ratio of (Δ+2)/3 for approximating independent sets in graphs with degree bounded by Δ. The analysis yields a precise characterization of the size of the independent sets found by the algorithm as a function of the independence number, as well as a generalization of Turan's bound. We also analyze the algorithm when run in combination with a known preprocessing technique, and obtain an improved $$(2\bar d + 3)/5$$ performance ratio on graphs with average degree $$\bar d$$ , improving on the previous best $$(\bar d + 1)/2$$ of Hochbaum. Finally, we present an efficient parallel and distributed algorithm attaining the performance guarantees of Greedy.

Counting independent sets in graphs

A number of modeling and simulation algorithms using internal coordinates rely on hierarchical representations of molecular systems. Given the potentially complex topologies of molecular systems, though, automatically generating such hierarchical decompositions may be difficult. In this article, we present a fast general algorithm for the complete construction of a hierarchical representation of a molecular system. This two-step algorithm treats the input molecular system as a graph in which vertices represent atoms or pseudo-atoms, and edges represent covalent bonds. The first step contracts all cycles in the input graph. The second step builds an assembly tree from the reduced graph. We analyze the complexity of this algorithm and show that the first step is linear in the number of edges in the input graph, whereas the second one is linear in the number of edges in the graph without cycles, but dependent on the branching factor of the molecular graph. We demonstrate the performance of our algorithm on a set of specifically tailored difficult cases as well as on a large subset of molecular graphs extracted from the protein data bank. In particular, we experimentally show that both steps behave linearly in the number of edges in the input graph (the branching factor is fixed for the second step). Finally, we demonstrate an application of our hierarchy construction algorithm to adaptive torsion-angle molecular mechanics.

Let G = (V;E) be a simple undirected graph. Define G n , the n-th power of G, as the graph on the vertex set V n in which two vertices (u1;:::;un) and (v1;:::;vn) are adjacent if and only if ui is adjacent to vi in G for every i. We give a characterization of all independent sets in such graphs whenever G is connected and non-bipartite. Consider the stationary measure of the simple random walk on G n . We show that every independent set is almost contained with respect to this measure in a junta, a cylinder of constant co-dimension. Moreover we show that the projection of that junta defines a nearly independent set, i.e., it spans few edges (this also guarantees that it is not trivially the entire vertex-set). Our approach is based on an analog of Fourier analysis for product spaces combined with spectral techniques and on a powerful invariance principle presented in [18]. This principle has already been shown in [11] to imply that independent sets in such graph products have an influential coordinate. In this work we prove that in fact there is a set of few coordinates and a junta on them that capture the independent set almost completely.

Computing the maximum size of an independent set in a graph is a famously hard combinatorial problem that has been well studied for various classes of graphs. When it comes to random graphs, the classic Erdős–Rényi–Gilbert random graph [Formula: see text] has been analyzed and shown to have the largest independent sets of size [Formula: see text] with high probability (w.h.p.) This classic model does not capture any dependency structure between edges that can appear in real-world networks. We define random graphs [Formula: see text] whose existence of edges is determined by a Markov process that is also governed by a decay parameter [Formula: see text]. We prove that w.h.p. [Formula: see text] has independent sets of size [Formula: see text] for arbitrary [Formula: see text]. This is derived using bounds on the terms of a harmonic series, a Turán bound on a stability number, and a concentration analysis for a certain sequence of dependent Bernoulli variables that may also be of independent interest. Because [Formula: see text] collapses to [Formula: see text] when there is no decay, it follows that having even the slightest bit of dependency (any [Formula: see text]) in the random graph construction leads to the presence of large independent sets, and thus, our random model has a phase transition at its boundary value of r = 1. This implies that there are large matchings in the line graph of [Formula: see text], which is a Markov random field. For the maximal independent set output by a greedy algorithm, we deduce that it has a performance ratio of at most [Formula: see text] w.h.p. when the lowest degree vertex is picked at each iteration and also show that, under any other permutation of vertices, the algorithm outputs a set of size [Formula: see text], where [Formula: see text] and, hence, has a performance ratio of [Formula: see text]. Funding: The initial phase of this research was supported by the National Science Foundation [Grant DMS-1913294].

We show that a simple Markov chain, the Glauber dynamics, can efficiently sample independent sets almost uniformly at random in polynomial time for graphs in a certain class. The class is determined by boundedness of a new graph parameter called bipartite pathwidth. This result, which we prove for the more general hardcore distribution with fugacity , can be viewed as a strong generalization of Jerrum and Sinclair's work on approximately counting matchings, that is, independent sets in line graphs. The class of graphs with bounded bipartite pathwidth includes claw‐free graphs, which generalize line graphs. We consider two further generalizations of claw‐free graphs and prove that these classes have bounded bipartite pathwidth. We also show how to extend all our results to polynomially bounded vertex weights.

Independent sets in quasi-regular graphs

We study the task of estimating the number of edges in a graph, where the access to the graph is provided via an independent set oracle. Independent set queries draw motivation from group testing and have applications to the complexity of decision versus counting problems. We give two algorithms to estimate the number of edges in an n -vertex graph, using (i) polylog( n ) bipartite independent set queries or (ii) n 2/3 polylog( n ) independent set queries.

Extremal graphs for blow-ups of stars and paths

It is well known [9] that finding a maximal independent set in a graph is in class NC and [10] that finding a maximal independent set in a hypergraph with fixed dimension is in RNC. It is not known whether this latter problem remains in NC when the dimension is part of the input. We will study the problem when the problem instances are randomly chosen. It was shown in [6] that the expected running time of a simple parallel algorithm for finding the lexicographically first maximal independent set (Ifmis) in a random simple graph is logarithmic in the input size. In this paper, we will prove a generalization of this result. We show that if a random k-uniform hypergraph has vertex set {1, 2, …, n} and its edges are chosen independently with probability p from the set of (nk) possible edges, then our algorithm finds the Ifmis in O() expected time. The hidden constant is independent of k, p. © 1996 John Wiley & Sons, Inc. Random Struct. Alg., 9, 359–377 (1996)