High Performance Frequent Subgraph Mining on Transactional Datasets

Graph data mining has been a crucial as well as inevitable area of research. Large amounts of graph data are produced in many areas, such as Bioinformatics, Cheminformatics, Social Networks, and Web etc. Scalable graph data mining methods are getting increasingly popular and necessary due to increased graph complexities. Frequent subgraph mining is one such area where the task is to find overly recurring patterns/subgraphs. To tackle this problem, many main memory-based methods were proposed, which proved to be inefficient as the data size grew exponentially over time. In the past few years several research groups have attempted to handle the frequent subgraph mining (FSM) problem in multiple ways. Many authors have tried to achieve better performance using Graphic Processing Units (GPUs) which has multi-fold improvement over in-memory while dealing with large datasets. Later, Google\u27s MapReduce model with the Hadoop framework proved to be a major breakthrough in high performance large batch processing. Although MapReduce came with many benefits, its disk I/O and non-iterative style model could not help much for FSM domain since subgraph mining process is an iterative approach. In recent years, Spark has emerged to be the De Facto industry standard with its distributed in-memory computing capability. This is a right fit solution for iterative style of programming as well. In this work, we cover how high-performance computing has helped in improving the performance tremendously in the transactional directed and undirected aspect of graphs and performance comparisons of various FSM techniques are done based on experimental results

Predictive analysis of real-time strategy games using graph mining

Machine learning and computational intelligence have facilitated the development of recommendation systems for a broad range of domains. Such recommendations are based on contextual information that is explicitly provided or pervasively collected. Recommendation systems often improve decision-making or increase the efficacy of a task. Real-Time Strategy (RTS) video games are not only a popular entertainment medium, they also are an abstraction of many real-world applications where the aim is to increase your resources and decrease those of your opponent. Using predictive analytics, which examines past examples of success and failure, we can learn how to predict positive outcomes for such scenarios. To do this, one way to represent this type of data in order to model relationships between entities is by using graphs. The vast amount of data has resulting in complex and large graphs that are difficult to process. Hence, researchers frequently employ parallelized or distributed processing. But first, the graph data must be partitioned and assigned to multiple processors in such a way that the workload will be balanced, and inter-processor communication will be minimized. The latter problem may be complicated by the existence of edges between vertices in a graph that have been assigned to different processors. One objective of this research is to develop an accurate predictive recommendation system for multiplayer strategic games to determine recommendations for moves that a player should, and should not, make which can provide a competitive advantage. Another objective is to determine how to partition a single undirected graph in order to optimize multiprocessor load balancing and reduce the number of edges between split subgraphs --Abstract, page iv

Graph Pattern Mining Techniques to Identify Potential Model Organisms

Recent advances in high throughput technologies have led to an increasing amount of rich and diverse biological data and related literature. Model organisms are classically selected as subjects for studying human disease based on their genotypic and phenotypic features. A significant problem with model organism identification is the determination of characteristic features related to biological processes that can provide insights into the mechanisms underlying diseases. These insights could have a positive impact on the diagnosis and management of diseases and the development of therapeutic drugs. The increased availability of biological data presents an opportunity to develop data mining methods that can address these challenges and help scientists formulate and test data-driven hypotheses. In this dissertation, data mining methods were developed to provide a quantitative approach for the identification of potential model organisms based on underlying features that may be correlated with disease manifestation in humans. The work encompassed three major types of contributions that aimed to address challenges related to inferring information from biological data available from a range of sources. First, new statistical models and algorithms for graph pattern mining were developed and tested on diverse genres of data (biological networks, drug chemical compounds, and text documents). Second, data mining techniques were developed and shown to identify characteristic disease patterns (disease fingerprints), predict potentially new genetic pathways, and facilitate the assessment of organisms as potential disease models. Third, a methodology was developed that combined the application of graph-based models with information derived from natural language processing methods to identify statistically significant patterns in biomedical text. Together, the approaches developed for this dissertation show promise for summarizing the information about biological processes and phenomena associated with organisms broadly and for the potential assessment of their suitability to study human diseases

Multipartite Graph Algorithms for the Analysis of Heterogeneous Data

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of biomolecules within an organism. This dissertation describes the design, implementation and application of graph algorithms, with the goal of seeking dense structure in data derived from omics experiments in order to detect latent associations between often heterogeneous entities, such as genes, diseases and phenotypes. Exact combinatorial solutions are developed and implemented, rather than relying on approximations or heuristics, even when problems are exceedingly large and/or difficult. Datasets on which the algorithms are applied include time series transcriptomic data from an experiment on the developing mouse cerebellum, gene expression data measuring acute ethanol response in the prefrontal cortex, and the analysis of a predicted protein-protein interaction network. A bipartite graph model is used to integrate heterogeneous data types, such as genes with phenotypes and microbes with mouse strains. The techniques are then extended to a multipartite algorithm to enumerate dense substructure in multipartite graphs, constructed using data from three or more heterogeneous sources, with applications to functional genomics. Several new theoretical results are given regarding multipartite graphs and the multipartite enumeration algorithm. In all cases, practical implementations are demonstrated to expand the frontier of computational feasibility

GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics

Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call “pattern diffusion” to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs