Covering Small Independent Sets and Separators with Applications to Parameterized Algorithms

We present two new combinatorial tools for the design of parameterized algorithms. The first is a simple linear time randomized algorithm that given as input a $d$-degenerate graph $G$ and an integer $k$, outputs an independent set $Y$, such that for every independent set $X$ in $G$ of size at most $k$, the probability that $X$ is a subset of $Y$ is at least $\left({(d+1)k \choose k} \cdot k(d+1)\right)^{-1}$.The second is a new (deterministic) polynomial time graph sparsification procedure that given a graph $G$, a set $T = \{\{s_1, t_1\}, \{s_2, t_2\}, \ldots, \{s_\ell, t_\ell\}\}$ of terminal pairs and an integer $k$, returns an induced subgraph $G^\star$ of $G$ that maintains all the inclusion minimal multicuts of $G$ of size at most $k$, and does not contain any $(k+2)$-vertex connected set of size $2^{{\cal O}(k)}$. In particular, $G^\star$ excludes a clique of size $2^{{\cal O}(k)}$ as a topological minor. Put together, our new tools yield new randomized fixed parameter tractable (FPT) algorithms for Stable $s$-$t$ Separator, Stable Odd Cycle Transversal and Stable Multicut on general graphs, and for Stable Directed Feedback Vertex Set on $d$-degenerate graphs, resolving two problems left open by Marx et al. [ACM Transactions on Algorithms, 2013]. All of our algorithms can be derandomized at the cost of a small overhead in the running time.Comment: 35 page

An algebraic formulation of the graph reconstruction conjecture

The graph reconstruction conjecture asserts that every finite simple graph on at least three vertices can be reconstructed up to isomorphism from its deck - the collection of its vertex-deleted subgraphs. Kocay's Lemma is an important tool in graph reconstruction. Roughly speaking, given the deck of a graph $G$ and any finite sequence of graphs, it gives a linear constraint that every reconstruction of $G$ must satisfy. Let $\psi(n)$ be the number of distinct (mutually non-isomorphic) graphs on $n$ vertices, and let $d(n)$ be the number of distinct decks that can be constructed from these graphs. Then the difference $\psi(n) - d(n)$ measures how many graphs cannot be reconstructed from their decks. In particular, the graph reconstruction conjecture is true for $n$-vertex graphs if and only if $\psi(n) = d(n)$. We give a framework based on Kocay's lemma to study this discrepancy. We prove that if $M$ is a matrix of covering numbers of graphs by sequences of graphs, then $d(n) \geq \mathsf{rank}_\mathbb{R}(M)$. In particular, all $n$-vertex graphs are reconstructible if one such matrix has rank $\psi(n)$. To complement this result, we prove that it is possible to choose a family of sequences of graphs such that the corresponding matrix $M$ of covering numbers satisfies $d(n) = \mathsf{rank}_\mathbb{R}(M)$.Comment: 12 pages, 2 figure

Disproving the normal graph conjecture

A graph $G$ is called normal if there exist two coverings, $\mathbb{C}$ and $\mathbb{S}$ of its vertex set such that every member of $\mathbb{C}$ induces a clique in $G$, every member of $\mathbb{S}$ induces an independent set in $G$ and $C \cap S \neq \emptyset$ for every $C \in \mathbb{C}$ and $S \in \mathbb{S}$. It has been conjectured by De Simone and K\"orner in 1999 that a graph $G$ is normal if $G$ does not contain $C_5$, $C_7$ and $\overline{C_7}$ as an induced subgraph. We disprove this conjecture

Symmetry adapted Assur decompositions

Assur graphs are a tool originally developed by mechanical engineers to decompose mechanisms for simpler analysis and synthesis. Recent work has connected these graphs to strongly directed graphs, and decompositions of the pinned rigidity matrix. Many mechanisms have initial configurations which are symmetric, and other recent work has exploited the orbit matrix as a symmetry adapted form of the rigidity matrix. This paper explores how the decomposition and analysis of symmetric frameworks and their symmetric motions can be supported by the new symmetry adapted tools.Comment: 40 pages, 22 figure

The Relativized Second Eigenvalue Conjecture of Alon

We prove a relativization of the Alon Second Eigenvalue Conjecture for all $d$-regular base graphs, $B$, with $d\ge 3$: for any $\epsilon>0$, we show that a random covering map of degree $n$ to $B$ has a new eigenvalue greater than $2\sqrt{d-1}+\epsilon$ in absolute value with probability $O(1/n)$. Furthermore, if $B$ is a Ramanujan graph, we show that this probability is proportional to $n^{-{\eta_{\rm \,fund}}(B)}$, where ${\eta_{\rm \,fund}}(B)$ is an integer depending on $B$, which can be computed by a finite algorithm for any fixed $B$. For any $d$-regular graph, $B$, ${\eta_{\rm \,fund}}(B)$ is greater than $\sqrt{d-1}$. Our proof introduces a number of ideas that simplify and strengthen the methods of Friedman's proof of the original conjecture of Alon. The most significant new idea is that of a ``certified trace,'' which is not only greatly simplifies our trace methods, but is the reason we can obtain the $n^{-{\eta_{\rm \,fund}}(B)}$ estimate above. This estimate represents an improvement over Friedman's results of the original Alon conjecture for random $d$-regular graphs, for certain values of $d$

Covering Pairs in Directed Acyclic Graphs

The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In this paper, we study the computational complexity of two constrained variants of Minimum Path Cover motivated by the recent introduction of next-generation sequencing technologies in bioinformatics. The first problem (MinPCRP), given a DAG and a set of pairs of vertices, asks for a minimum cardinality set of paths "covering" all the vertices such that both vertices of each pair belong to the same path. For this problem, we show that, while it is NP-hard to compute if there exists a solution consisting of at most three paths, it is possible to decide in polynomial time whether a solution consisting of at most two paths exists. The second problem (MaxRPSP), given a DAG and a set of pairs of vertices, asks for a path containing the maximum number of the given pairs of vertices. We show its NP-hardness and also its W[1]-hardness when parametrized by the number of covered pairs. On the positive side, we give a fixed-parameter algorithm when the parameter is the maximum overlapping degree, a natural parameter in the bioinformatics applications of the problem