High performance subgraph mining in molecular compounds

Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques particularly relevant. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiver-initiated, load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening dataset, where the approach attains close-to linear speedup in a network of workstations

A Universal Similarity Model for Transactional Data Clustering

Data mining methods are used to extract hidden knowledge from large database. Data partitioning methods are used to group up the relevant data values. Similar data values are grouped under the same cluster. K - means and Partitioning Around Medoids (PAM ) clustering algorithms are used to cluster numerical data. Distance measures are used to estimate the transaction similarity. Data partitioning solutions are identified using the cluster ensembl e models . The ensemble information matrix presents only cluster data point relations. Ensembles based clustering techniques produces final data partition based on incomplete information. Link - based approach improves the conventional matrix by discovering unknown entries through cluster similarity in an ensemble. Link - based algorithm is used for the underlying similarity assessment. Pairwise similarity and binary cluster association matrices summarize the underlying ensemble information. A weighted bipartite graph is formulated from the refined matrix. The graph partitioning technique is applied on the weighted bipartite graph. The Particle Swarm Optimization (PSO) clustering algorithm is a optimization based clustering scheme. It is integrated with the clu ster ensemble model. Binary , categorical and continuous data clustering is supported in the system. The attribute connectivity analysis is optimized for all attributes. Refined cluster - association matrix (RM) is updated with all attribute relationships

An effective multilevel tabu search approach for balanced graph partitioning

Graph partitioning is one of the fundamental NP-complete problems which is widely applied in many domains, such as VLSI design, image segmentation, data mining, etc. Given a graph G=(V,E), the balanced k-partitioning problem consists in partitioning the vertex set V into k disjoint subsets of about the same size, such that the number of cutting edges is minimized. In this paper, we present a multilevel algorithm for balanced partition, which integrates a powerful refinement procedure based on tabu search with periodic perturbations. Experimental evaluations on a wide collection of benchmark graphs show that the proposed approach not only competes very favorably with the two well-known partitioning packages METIS and CHACO, but also improves more than two thirds of the best balanced partitions ever reported in the literature

Structural Graph-based Metamodel Matching

Data integration has been, and still is, a challenge for applications processing multiple heterogeneous data sources. Across the domains of schemas, ontologies, and metamodels, this imposes the need for mapping specifications, i.e. the task of discovering semantic correspondences between elements. Support for the development of such mappings has been researched, producing matching systems that automatically propose mapping suggestions. However, especially in the context of metamodel matching the result quality of state of the art matching techniques leaves room for improvement. Although the traditional approach of pair-wise element comparison works on smaller data sets, its quadratic complexity leads to poor runtime and memory performance and eventually to the inability to match, when applied on real-world data. The work presented in this thesis seeks to address these shortcomings. Thereby, we take advantage of the graph structure of metamodels. Consequently, we derive a planar graph edit distance as metamodel similarity metric and mining-based matching to make use of redundant information. We also propose a planar graph-based partitioning to cope with large-scale matching. These techniques are then evaluated using real-world mappings from SAP business integration scenarios and the MDA community. The results demonstrate improvement in quality and managed runtime and memory consumption for large-scale metamodel matching

Exploiting Latent Features of Text and Graphs

As the size and scope of online data continues to grow, new machine learning techniques become necessary to best capitalize on the wealth of available information. However, the models that help convert data into knowledge require nontrivial processes to make sense of large collections of text and massive online graphs. In both scenarios, modern machine learning pipelines produce embeddings --- semantically rich vectors of latent features --- to convert human constructs for machine understanding. In this dissertation we focus on information available within biomedical science, including human-written abstracts of scientific papers, as well as machine-generated graphs of biomedical entity relationships. We present the Moliere system, and our method for identifying new discoveries through the use of natural language processing and graph mining algorithms. We propose heuristically-based ranking criteria to augment Moliere, and leverage this ranking to identify a new gene-treatment target for HIV-associated Neurodegenerative Disorders. We additionally focus on the latent features of graphs, and propose a new bipartite graph embedding technique. Using our graph embedding, we advance the state-of-the-art in hypergraph partitioning quality. Having newfound intuition of graph embeddings, we present Agatha, a deep-learning approach to hypothesis generation. This system learns a data-driven ranking criteria derived from the embeddings of our large proposed biomedical semantic graph. To produce human-readable results, we additionally propose CBAG, a technique for conditional biomedical abstract generation

Adaptive Partitioning for Large-Scale Dynamic Graphs

Abstract—In the last years, large-scale graph processing has gained increasing attention, with most recent systems placing particular emphasis on latency. One possible technique to improve runtime performance in a distributed graph processing system is to reduce network communication. The most notable way to achieve this goal is to partition the graph by minimizing the num-ber of edges that connect vertices assigned to different machines, while keeping the load balanced. However, real-world graphs are highly dynamic, with vertices and edges being constantly added and removed. Carefully updating the partitioning of the graph to reflect these changes is necessary to avoid the introduction of an extensive number of cut edges, which would gradually worsen computation performance. In this paper we show that performance degradation in dynamic graph processing systems can be avoided by adapting continuously the graph partitions as the graph changes. We present a novel highly scalable adaptive partitioning strategy, and show a number of refinements that make it work under the constraints of a large-scale distributed system. The partitioning strategy is based on iterative vertex migrations, relying only on local information. We have implemented the technique in a graph processing system, and we show through three real-world scenarios how adapting graph partitioning reduces execution time by over 50 % when compared to commonly used hash-partitioning. I

Efficient mining of discriminative molecular fragments

Frequent pattern discovery in structured data is receiving an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset