Parallel Algorithm for Frequent Itemset Mining on Intel Many-core Systems

Frequent itemset mining leads to the discovery of associations and correlations among items in large transactional databases. Apriori is a classical frequent itemset mining algorithm, which employs iterative passes over database combining with generation of candidate itemsets based on frequent itemsets found at the previous iteration, and pruning of clearly infrequent itemsets. The Dynamic Itemset Counting (DIC) algorithm is a variation of Apriori, which tries to reduce the number of passes made over a transactional database while keeping the number of itemsets counted in a pass relatively low. In this paper, we address the problem of accelerating DIC on the Intel Xeon Phi many-core system for the case when the transactional database fits in main memory. Intel Xeon Phi provides a large number of small compute cores with vector processing units. The paper presents a parallel implementation of DIC based on OpenMP technology and thread-level parallelism. We exploit the bit-based internal layout for transactions and itemsets. This technique reduces the memory space for storing the transactional database, simplifies the support count via logical bitwise operation, and allows for vectorization of such a step. Experimental evaluation on the platforms of the Intel Xeon CPU and the Intel Xeon Phi coprocessor with large synthetic and real databases showed good performance and scalability of the proposed algorithm.Comment: Accepted for publication in Journal of Computing and Information Technology (http://cit.fer.hr

Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This 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 receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids