ToPoMine: A graph miner for analysis of atom-dynamics simulation data in material science
In materials science, micro-level (atomic-scale) activities are considered to be the key to understanding various macro-level (bulk) properties of a material. Molecular dynamics simulations are widely used to obtain atom dynamics. However, researchers are often too overwhelmed by the amount of simulation data to discover relevant atomic activities. Furthermore, mining the structure graph of a material (the graph where the constituent atoms form nodes and the bonds between the atoms form edges) offers little help in this scenario. It is the patterns among the atomic dynamics that may reveal the mechanisms underlying a particular material property. Discovery of such patterns can lead to a better model and better predictions of the properties and behaviors of the materials. We propose an event graph to model the atomic dynamics and propose a graph mining algorithm to discover popular subgraphs in the event graph. Because the event graph is a directed acyclic graph, our mining algorithm uses a new graph encoding scheme that is based on topological-sorting. This encoding scheme ensures that our algorithm enumerates candidate subgraphs without any duplication. Experiments with simulation data of silica liquid demonstrate the effectiveness of our mining system which we call ''ToPoMine''.
Publication Source (Journal or Book title)
Intelligent Data Analysis
Shakya, S., Zhang, J., & Karki, B. (2016). ToPoMine: A graph miner for analysis of atom-dynamics simulation data in material science. Intelligent Data Analysis, 20 (5), 1181-1198. https://doi.org/10.3233/IDA-160862