Partitioning Wide Area Graphs Using a Space Filling Curve

Graph structure is a very powerful tool to model system and represent their actual shape. For instance, modelling an infrastructure or social network naturally leads to graph. Yet, graphs can be very different from one another as they do not share the same properties (size, connectivity, communities, etc.) and building a system able to manage graphs should take into account this diversity. A big challenge concerning graph management is to design a system providing a scalable persistent storage and allowing efficient browsing. Mainly to study social graphs, the most recent developments in graph partitioning research often consider scale-free graphs. As we are interested in modelling connected objects and their context, we focus on partitioning geometric graphs. Consequently our strategy differs, we consider geometry as our main partitioning tool. In fact, we rely on Inverse Space-filling Partitioning, a technique which relies on a space filling curve to partition a graph and was previously applied to graphs essentially generated from Meshes. Furthermore, we extend Inverse Space-Filling Partitioning toward a new target we define as Wide Area Graphs. We provide an extended comparison with two state-of-the-art graph partitioning streaming strategies, namely LDG and FENNEL. We also propose customized metrics to better understand and identify the use cases for which the ISP partitioning solution is best suited. Experimentations show that in favourable contexts, edge-cuts can be drastically reduced, going from more 34% using FENNEL to less than 1% using ISP.

Phasertng: directed acyclic graphs for crystallographic phasing

Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies.

Historical Graph Management in Dynamic Environments

Since dynamic graph data continuously change over time, it is necessary to manage historical data for accessing a snapshot graph at a specific time. In this paper, we propose a new historical graph management scheme that consists of an intersection snapshot and a delta snapshot to enhance storage utilization and historical graph accessibility. The proposed scheme constantly detects graph changes and calculates a common subgraph ratio between historical graphs over time. If the common subgraph ratio is lower than a threshold value, the intersection snapshot stores the common subgraphs within a time interval. A delta snapshot stores the subgraphs that are not contained in the intersection snapshot. Several delta snapshots are connected to the intersection snapshot to maintain the modified subgraph over time. The efficiency of storage space is improved by managing common subgraphs stored in the intersection snapshot. Furthermore, the intersection and delta snapshots can be connected to search a graph at a specific time. We show the superiority of the proposed scheme through various performance evaluations.

Graph Management Systems: A Qualitative Survey

In the recent years many real-world applications have been modeled by graph structures (e.g., social networks, mobile phone networks, web graphs, etc.), and many systems have been developed to manage, query, and analyze these datasets. These systems could be divided into specialized graph database systems and large-scale graph analytics systems. The first ones consider end-to-end data management issues including storage representations, transactions, and query languages, whereas the second ones focus on processing specific tasks over large data graphs. In this paper we provide an overview of several graph database systems and graph processing systems, with the aim of assisting the reader in identifying the best-suited solution for her application scenario.