Fully dynamic cycle-equivalence in graphs

Two edges e_1 and e_2 of an undirected graph are cycle-equivalent iff all cycles that contain e_1 also contain e_2, i.e., iff e_1 and e_2 are a cut-edge pair. The cycle-equivalence classes of the control-flow graph are used in optimizing compilers to speed up existing control-flow and data-flow algorithms. While the cycle-equivalence classes can be computed in linear time, we present the first fully dynamic algorithm for maintaining the cycle-equivalence relation. In an n-node graph our data structure executes an edge insertion or deletion in O(sqrt(n.log n)) time and answers the query whether two given edges are cycle-equivalent in O(pow2(log(n))) time. We also present an algorithm for plane graphs with O(log n) update and query time and for planar graphs with O(log n) insertion time and O(log2 n) query and deletion time. Additionally, we show a lower bound of Ω(log n/log log n) for the amortized time per operation for the dynamic cycle-equivalence problem in the cell probe mode

A unified view on bipartite species-reaction and interaction graphs for chemical reaction networks

The Jacobian matrix of a dynamic system and its principal minors play a prominent role in the study of qualitative dynamics and bifurcation analysis. When interpreting the Jacobian as an adjacency matrix of an interaction graph, its principal minors correspond to sets of disjoint cycles in this graph and conditions for various dynamic behaviors can be inferred from its cycle structure. For chemical reaction systems, more fine-grained analyses are possible by studying a bipartite species-reaction graph. Several results on injectivity, multistationarity, and bifurcations of a chemical reaction system have been derived by using various definitions of such bipartite graph. Here, we present a new definition of the species-reaction graph that more directly connects the cycle structure with determinant expansion terms, principal minors, and the coefficients of the characteristic polynomial and encompasses previous graph constructions as special cases. This graph has a direct relation to the interaction graph, and properties of cycles and sub-graphs can be translated in both directions. A simple equivalence relation enables to decompose determinant expansions more directly and allows simpler and more direct proofs of previous results.Comment: 27 pages. submitted to J. Math. Bio

Minimum Equivalent Precedence Relation Systems

In this paper two related simplification problems for systems of linear inequalities describing precedence relation systems are considered. Given a precedence relation system, the first problem seeks a minimum subset of the precedence relations (i.e., inequalities) which has the same solution set as that of the original system. The second problem is the same as the first one except that the ``subset restriction'' in the first problem is removed. This paper establishes that the first problem is NP-hard. However, a sufficient condition is provided under which the first problem is solvable in polynomial-time. In addition, a decomposition of the first problem into independent tractable and intractable subproblems is derived. The second problem is shown to be solvable in polynomial-time, with a full parameterization of all solutions described. The results in this paper generalize those in [Moyles and Thompson 1969, Aho, Garey, and Ullman 1972] for the minimum equivalent graph problem and transitive reduction problem, which are applicable to unweighted directed graphs

Solving weighted and counting variants of connectivity problems parameterized by treewidth deterministically in single exponential time

It is well known that many local graph problems, like Vertex Cover and Dominating Set, can be solved in 2^{O(tw)}|V|^{O(1)} time for graphs G=(V,E) with a given tree decomposition of width tw. However, for nonlocal problems, like the fundamental class of connectivity problems, for a long time we did not know how to do this faster than tw^{O(tw)}|V|^{O(1)}. Recently, Cygan et al. (FOCS 2011) presented Monte Carlo algorithms for a wide range of connectivity problems running in time $c^{tw}|V|^{O(1)} for a small constant c, e.g., for Hamiltonian Cycle and Steiner tree. Naturally, this raises the question whether randomization is necessary to achieve this runtime; furthermore, it is desirable to also solve counting and weighted versions (the latter without incurring a pseudo-polynomial cost in terms of the weights). We present two new approaches rooted in linear algebra, based on matrix rank and determinants, which provide deterministic c^{tw}|V|^{O(1)} time algorithms, also for weighted and counting versions. For example, in this time we can solve the traveling salesman problem or count the number of Hamiltonian cycles. The rank-based ideas provide a rather general approach for speeding up even straightforward dynamic programming formulations by identifying "small" sets of representative partial solutions; we focus on the case of expressing connectivity via sets of partitions, but the essential ideas should have further applications. The determinant-based approach uses the matrix tree theorem for deriving closed formulas for counting versions of connectivity problems; we show how to evaluate those formulas via dynamic programming.Comment: 36 page

Network Sparsification for Steiner Problems on Planar and Bounded-Genus Graphs

We propose polynomial-time algorithms that sparsify planar and bounded-genus graphs while preserving optimal or near-optimal solutions to Steiner problems. Our main contribution is a polynomial-time algorithm that, given an unweighted graph $G$ embedded on a surface of genus $g$ and a designated face $f$ bounded by a simple cycle of length $k$, uncovers a set $F \subseteq E(G)$ of size polynomial in $g$ and $k$ that contains an optimal Steiner tree for any set of terminals that is a subset of the vertices of $f$. We apply this general theorem to prove that: * given an unweighted graph $G$ embedded on a surface of genus $g$ and a terminal set $S \subseteq V(G)$, one can in polynomial time find a set $F \subseteq E(G)$ that contains an optimal Steiner tree $T$ for $S$ and that has size polynomial in $g$ and $|E(T)|$; * an analogous result holds for an optimal Steiner forest for a set $S$ of terminal pairs; * given an unweighted planar graph $G$ and a terminal set $S \subseteq V(G)$, one can in polynomial time find a set $F \subseteq E(G)$ that contains an optimal (edge) multiway cut $C$ separating $S$ and that has size polynomial in $|C|$. In the language of parameterized complexity, these results imply the first polynomial kernels for Steiner Tree and Steiner Forest on planar and bounded-genus graphs (parameterized by the size of the tree and forest, respectively) and for (Edge) Multiway Cut on planar graphs (parameterized by the size of the cutset). Additionally, we obtain a weighted variant of our main contribution