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

Hierarchy of neural organization in the embryonic spinal cord: Granger-causality graph analysis of in vivo calcium imaging data

The recent development of genetically encoded calcium indicators enables monitoring in vivo the activity of neuronal populations. Most analysis of these calcium transients relies on linear regression analysis based on the sensory stimulus applied or the behavior observed. To estimate the basic properties of the functional neural circuitry, we propose a network-based approach based on calcium imaging recorded at single cell resolution. Differently from previous analysis based on cross-correlation, we used Granger-causality estimates to infer activity propagation between the activities of different neurons. The resulting functional networks were then modeled as directed graphs and characterized in terms of connectivity and node centralities. We applied our approach to calcium transients recorded at low frequency (4 Hz) in ventral neurons of the zebrafish spinal cord at the embryonic stage when spontaneous coiling of the tail occurs. Our analysis on population calcium imaging data revealed a strong ipsilateral connectivity and a characteristic hierarchical organization of the network hubs that supported established propagation of activity from rostral to caudal spinal cord. Our method could be used for detecting functional defects in neuronal circuitry during development and pathological conditions

Theoretically Efficient Parallel Graph Algorithms Can Be Fast and Scalable

There has been significant recent interest in parallel graph processing due to the need to quickly analyze the large graphs available today. Many graph codes have been designed for distributed memory or external memory. However, today even the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) can fit in the memory of a single commodity multicore server. Nevertheless, most experimental work in the literature report results on much smaller graphs, and the ones for the Hyperlink graph use distributed or external memory. Therefore, it is natural to ask whether we can efficiently solve a broad class of graph problems on this graph in memory. This paper shows that theoretically-efficient parallel graph algorithms can scale to the largest publicly-available graphs using a single machine with a terabyte of RAM, processing them in minutes. We give implementations of theoretically-efficient parallel algorithms for 20 important graph problems. We also present the optimizations and techniques that we used in our implementations, which were crucial in enabling us to process these large graphs quickly. We show that the running times of our implementations outperform existing state-of-the-art implementations on the largest real-world graphs. For many of the problems that we consider, this is the first time they have been solved on graphs at this scale. We have made the implementations developed in this work publicly-available as the Graph-Based Benchmark Suite (GBBS).Comment: This is the full version of the paper appearing in the ACM Symposium on Parallelism in Algorithms and Architectures (SPAA), 201

Recognizing Planar Laman Graphs

Laman graphs are the minimally rigid graphs in the plane. We present two algorithms for recognizing planar Laman graphs. A simple algorithm with running time O(n^(3/2)) and a more complicated algorithm with running time O(n log^3 n) based on involved planar network flow algorithms. Both improve upon the previously fastest algorithm for general graphs by Gabow and Westermann [Algorithmica, 7(5-6):465 - 497, 1992] with running time O(n sqrt{n log n}). To solve this problem we introduce two algorithms (with the running times stated above) that check whether for a directed planar graph G, disjoint sets S, T subseteq V(G), and a fixed k the following connectivity condition holds: for each vertex s in S there are k directed paths from s to T pairwise having only vertex s in common. This variant of connectivity seems interesting on its own

Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time

We present faster algorithms for computing the 2-edge and 2-vertex strongly connected components of a directed graph, which are straightforward generalizations of strongly connected components. While in undirected graphs the 2-edge and 2-vertex connected components can be found in linear time, in directed graphs only rather simple $O(m n)$-time algorithms were known. We use a hierarchical sparsification technique to obtain algorithms that run in time $O(n^2)$. For 2-edge strongly connected components our algorithm gives the first running time improvement in 20 years. Additionally we present an $O(m^2 / \log{n})$-time algorithm for 2-edge strongly connected components, and thus improve over the $O(m n)$ running time also when $m = O(n)$. Our approach extends to k-edge and k-vertex strongly connected components for any constant k with a running time of $O(n^2 \log^2 n)$ for edges and $O(n^3)$ for vertices

Algorithms of causal inference for the analysis of effective connectivity among brain regions

In recent years, powerful general algorithms of causal inference have been developed. In particular, in the framework of Pearl’s causality, algorithms of inductive causation (IC and IC*) provide a procedure to determine which causal connections among nodes in a network can be inferred from empirical observations even in the presence of latent variables, indicating the limits of what can be learned without active manipulation of the system. These algorithms can in principle become important complements to established techniques such as Granger causality and Dynamic Causal Modeling (DCM) to analyze causal influences (effective connectivity) among brain regions. However, their application to dynamic processes has not been yet examined. Here we study how to apply these algorithms to time-varying signals such as electrophysiological or neuroimaging signals. We propose a new algorithm which combines the basic principles of the previous algorithms with Granger causality to obtain a representation of the causal relations suited to dynamic processes. Furthermore, we use graphical criteria to predict dynamic statistical dependencies between the signals from the causal structure. We show how some problems for causal inference from neural signals (e.g., measurement noise, hemodynamic responses, and time aggregation) can be understood in a general graphical approach. Focusing on the effect of spatial aggregation, we show that when causal inference is performed at a coarser scale than the one at which the neural sources interact, results strongly depend on the degree of integration of the neural sources aggregated in the signals, and thus characterize more the intra-areal properties than the interactions among regions. We finally discuss how the explicit consideration of latent processes contributes to understand Granger causality and DCM as well as to distinguish functional and effective connectivity