Efficiently answering reachability and path queries on temporal bipartite graphs

Bipartite graphs are naturally used to model relationships between two different types of entities, such as people-location, authorpaper, and customer-product. When modeling real-world applications like disease outbreaks, edges are often enriched with temporal information, leading to temporal bipartite graphs. While reachability has been extensively studied on (temporal) unipartite graphs, it remains largely unexplored on temporal bipartite graphs. To fill this research gap, in this paper, we study the reachability problem on temporal bipartite graphs. Specifically, a vertex u reaches a vertex w in a temporal bipartite graph G if u and w are connected through a series of consecutive wedges with time constraints. Towards efficiently answering if a vertex can reach the other vertex, we propose an index-based method by adapting the idea of 2-hop labeling. Effective optimization strategies and parallelization techniques are devised to accelerate the index construction process. To better support real-life scenarios, we further show how the index is leveraged to efficiently answer other types of queries, e.g., singlesource reachability query and earliest-arrival path query. Extensive experiments on 16 real-world graphs demonstrate the effectiveness and efficiency of our proposed techniques

Temporal Graph Traversals: Definitions, Algorithms, and Applications

A temporal graph is a graph in which connections between vertices are active at specific times, and such temporal information leads to completely new patterns and knowledge that are not present in a non-temporal graph. In this paper, we study traversal problems in a temporal graph. Graph traversals, such as DFS and BFS, are basic operations for processing and studying a graph. While both DFS and BFS are well-known simple concepts, it is non-trivial to adopt the same notions from a non-temporal graph to a temporal graph. We analyze the difficulties of defining temporal graph traversals and propose new definitions of DFS and BFS for a temporal graph. We investigate the properties of temporal DFS and BFS, and propose efficient algorithms with optimal complexity. In particular, we also study important applications of temporal DFS and BFS. We verify the efficiency and importance of our graph traversal algorithms in real world temporal graphs

Verifying Recursive Active Documents with Positive Data Tree Rewriting

This paper proposes a data tree-rewriting framework for modeling evolving documents. The framework is close to Guarded Active XML, a platform used for handling XML repositories evolving through web services. We focus on automatic verification of properties of evolving documents that can contain data from an infinite domain. We establish the boundaries of decidability, and show that verification of a {\em positive} fragment that can handle recursive service calls is decidable. We also consider bounded model-checking in our data tree-rewriting framework and show that it is \nexptime-complete

Basins of Attraction, Commitment Sets and Phenotypes of Boolean Networks

The attractors of Boolean networks and their basins have been shown to be highly relevant for model validation and predictive modelling, e.g., in systems biology. Yet there are currently very few tools available that are able to compute and visualise not only attractors but also their basins. In the realm of asynchronous, non-deterministic modeling not only is the repertoire of software even more limited, but also the formal notions for basins of attraction are often lacking. In this setting, the difficulty both for theory and computation arises from the fact that states may be ele- ments of several distinct basins. In this paper we address this topic by partitioning the state space into sets that are committed to the same attractors. These commitment sets can easily be generalised to sets that are equivalent w.r.t. the long-term behaviours of pre-selected nodes which leads us to the notions of markers and phenotypes which we illustrate in a case study on bladder tumorigenesis. For every concept we propose equivalent CTL model checking queries and an extension of the state of the art model checking software NuSMV is made available that is capa- ble of computing the respective sets. All notions are fully integrated as three new modules in our Python package PyBoolNet, including functions for visualising the basins, commitment sets and phenotypes as quotient graphs and pie charts