Functional Integration of Ecological Networks through Pathway Proliferation

Large-scale structural patterns commonly occur in network models of complex systems including a skewed node degree distribution and small-world topology. These patterns suggest common organizational constraints and similar functional consequences. Here, we investigate a structural pattern termed pathway proliferation. Previous research enumerating pathways that link species determined that as pathway length increases, the number of pathways tends to increase without bound. We hypothesize that this pathway proliferation influences the flow of energy, matter, and information in ecosystems. In this paper, we clarify the pathway proliferation concept, introduce a measure of the node--node proliferation rate, describe factors influencing the rate, and characterize it in 17 large empirical food-webs. During this investigation, we uncovered a modular organization within these systems. Over half of the food-webs were composed of one or more subgroups that were strongly connected internally, but weakly connected to the rest of the system. Further, these modules had distinct proliferation rates. We conclude that pathway proliferation in ecological networks reveals subgroups of species that will be functionally integrated through cyclic indirect effects.Comment: 29 pages, 2 figures, 3 tables, Submitted to Journal of Theoretical Biolog

Parameterized Algorithms for Directed Maximum Leaf Problems

We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that includes all strong and acyclic digraphs. This settles completely an open question of Fellows and solves another one for digraphs in $\cal L$. Our algorithms are based on the following combinatorial result which can be viewed as a generalization of many results for a `spanning tree with many leaves' in the undirected case, and which is interesting on its own: If a digraph $D\in \cal L$ of order $n$ with minimum in-degree at least 3 contains a rooted spanning tree, then $D$ contains one with at least $(n/2)^{1/5}-1$ leaves

On the complexity of the chip-firing reachability problem

In this paper, we study the complexity of the chip-firing reachability problem. We show that for Eulerian digraphs, the reachability problem can be decided in strongly polynomial time, even if the digraph has multiple edges. We also show a special case when the reachability problem can be decided in polynomial time for general digraphs: if the target distribution is recurrent restricted to each strongly connected component. As a further positive result, we show that the chip-firing reachability problem is in co-NP for general digraphs. We also show that the chip-firing halting problem is in co-NP for Eulerian digraphs

Strong Connectivity in Directed Graphs under Failures, with Application

In this paper, we investigate some basic connectivity problems in directed graphs (digraphs). Let $G$ be a digraph with $m$ edges and $n$ vertices, and let $G\setminus e$ be the digraph obtained after deleting edge $e$ from $G$. As a first result, we show how to compute in $O(m+n)$ worst-case time: $(i)$ The total number of strongly connected components in $G\setminus e$, for all edges $e$ in $G$. $(ii)$ The size of the largest and of the smallest strongly connected components in $G\setminus e$, for all edges $e$ in $G$. Let $G$ be strongly connected. We say that edge $e$ separates two vertices $x$ and $y$, if $x$ and $y$ are no longer strongly connected in $G\setminus e$. As a second set of results, we show how to build in $O(m+n)$ time $O(n)$-space data structures that can answer in optimal time the following basic connectivity queries on digraphs: $(i)$ Report in $O(n)$ worst-case time all the strongly connected components of $G\setminus e$, for a query edge $e$. $(ii)$ Test whether an edge separates two query vertices in $O(1)$ worst-case time. $(iii)$ Report all edges that separate two query vertices in optimal worst-case time, i.e., in time $O(k)$, where $k$ is the number of separating edges. (For $k=0$, the time is $O(1)$). All of the above results extend to vertex failures. All our bounds are tight and are obtained with a common algorithmic framework, based on a novel compact representation of the decompositions induced by the $1$-connectivity (i.e., $1$-edge and $1$-vertex) cuts in digraphs, which might be of independent interest. With the help of our data structures we can design efficient algorithms for several other connectivity problems on digraphs and we can also obtain in linear time a strongly connected spanning subgraph of $G$ with $O(n)$ edges that maintains the $1$-connectivity cuts of $G$ and the decompositions induced by those cuts.Comment: An extended abstract of this work appeared in the SODA 201