Efficient enumeration of solutions produced by closure operations

In this paper we address the problem of generating all elements obtained by the saturation of an initial set by some operations. More precisely, we prove that we can generate the closure of a boolean relation (a set of boolean vectors) by polymorphisms with a polynomial delay. Therefore we can compute with polynomial delay the closure of a family of sets by any set of "set operations": union, intersection, symmetric difference, subsets, supersets $\dots$). To do so, we study the $Membership_{\mathcal{F}}$ problem: for a set of operations $\mathcal{F}$, decide whether an element belongs to the closure by $\mathcal{F}$ of a family of elements. In the boolean case, we prove that $Membership_{\mathcal{F}}$ is in P for any set of boolean operations $\mathcal{F}$. When the input vectors are over a domain larger than two elements, we prove that the generic enumeration method fails, since $Membership_{\mathcal{F}}$ is NP-hard for some $\mathcal{F}$. We also study the problem of generating minimal or maximal elements of closures and prove that some of them are related to well known enumeration problems such as the enumeration of the circuits of a matroid or the enumeration of maximal independent sets of a hypergraph. This article improves on previous works of the same authors.Comment: 30 pages, 1 figure. Long version of the article arXiv:1509.05623 of the same name which appeared in STACS 2016. Final version for DMTCS journa

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

Optimizing the double description method for normal surface enumeration

Many key algorithms in 3-manifold topology involve the enumeration of normal surfaces, which is based upon the double description method for finding the vertices of a convex polytope. Typically we are only interested in a small subset of these vertices, thus opening the way for substantial optimization. Here we give an account of the vertex enumeration problem as it applies to normal surfaces, and present new optimizations that yield strong improvements in both running time and memory consumption. The resulting algorithms are tested using the freely available software package Regina.Comment: 27 pages, 12 figures; v2: Removed the 3^n bound from Section 3.3, fixed the projective equation in Lemma 4.4, clarified "most triangulations" in the introduction to section 5; v3: replace -ise with -ize for Mathematics of Computation (note that this changes the title of the paper

Converting between quadrilateral and standard solution sets in normal surface theory

The enumeration of normal surfaces is a crucial but very slow operation in algorithmic 3-manifold topology. At the heart of this operation is a polytope vertex enumeration in a high-dimensional space (standard coordinates). Tollefson's Q-theory speeds up this operation by using a much smaller space (quadrilateral coordinates), at the cost of a reduced solution set that might not always be sufficient for our needs. In this paper we present algorithms for converting between solution sets in quadrilateral and standard coordinates. As a consequence we obtain a new algorithm for enumerating all standard vertex normal surfaces, yielding both the speed of quadrilateral coordinates and the wider applicability of standard coordinates. Experimentation with the software package Regina shows this new algorithm to be extremely fast in practice, improving speed for large cases by factors from thousands up to millions.Comment: 55 pages, 10 figures; v2: minor fixes only, plus a reformat for the journal styl

Simultaneous Representation of Proper and Unit Interval Graphs

In a confluence of combinatorics and geometry, simultaneous representations provide a way to realize combinatorial objects that share common structure. A standard case in the study of simultaneous representations is the sunflower case where all objects share the same common structure. While the recognition problem for general simultaneous interval graphs - the simultaneous version of arguably one of the most well-studied graph classes - is NP-complete, the complexity of the sunflower case for three or more simultaneous interval graphs is currently open. In this work we settle this question for proper interval graphs. We give an algorithm to recognize simultaneous proper interval graphs in linear time in the sunflower case where we allow any number of simultaneous graphs. Simultaneous unit interval graphs are much more "rigid" and therefore have less freedom in their representation. We show they can be recognized in time O(|V|*|E|) for any number of simultaneous graphs in the sunflower case where G=(V,E) is the union of the simultaneous graphs. We further show that both recognition problems are in general NP-complete if the number of simultaneous graphs is not fixed. The restriction to the sunflower case is in this sense necessary