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Fast Discovery of Sequential Patterns by Memory Indexing [chapter]

Ming-Yen Lin, Suh-Yin Lee
2002 Lecture Notes in Computer Science  
In this paper, we propose a memory indexing approach for fast sequential pattern mining, named MEMISP.  ...  As databases may fit into the ever-increasing main memory, efficient memory-based discovery of sequential patterns is becoming possible.  ...  Here, we propose a memory-indexing approach for fast discovery of sequential patterns, called MEMISP (MEMory Indexing for Sequential Pattern mining).  ... 
doi:10.1007/3-540-46145-0_15 fatcat:hgho7szk45fkfpegsmgjivnvpy

A New Algorithm for Fast Discovery of Maximal Sequential Patterns in a Document Collection [chapter]

René Arnulfo García-Hernández, José Francisco Martínez-Trinidad, Jesús Ariel Carrasco-Ochoa
2006 Lecture Notes in Computer Science  
Also, they are human readable patterns or descriptors of the text, which do not lose the sequential order of the words in the document.  ...  But the problem of discovering sequential patterns in a database of documents presents special characteristics which make it intractable for most of the apriori-like candidate-generationand-test approaches  ...  DIMASP: A New Algorithm for Fast Discovery of all Maximal Sequential Patterns The basic idea of DIMASP consists in finding all the sequential patterns in a data structure, built from the document database  ... 
doi:10.1007/11671299_53 fatcat:mryweza62veshgjqy65j3enfkm

Mining Sequential Patterns Using I-Prefixspan

Dhany Saputra, Dayang R. A. Rambli, Oi Mean Foong
2007 Zenodo  
Thus, with I-PrefixSpan there is no in-memory database stored after index set is constructed.  ...  In this paper, we propose an improvement of pattern growth-based PrefixSpan algorithm, called I-PrefixSpan.  ...  The problem of sequential patterns discovery was inspired by retailing industry problems.  ... 
doi:10.5281/zenodo.1083789 fatcat:3jtiupvr3ja6zijgjilnaxl4z4

MpBsmi: A new algorithm for the recognition of continuous biological sequence pattern based on index structure

Weina Li, Jiadong Ren, Xiangtao Li
2018 PLoS ONE  
Based on a connection strategy, the frequent patterns are expanded and the expanded table ST is updated by scanning the DB-Index.  ...  The existing algorithms of sequence pattern discovery, like MSPM and FBSB, suffice their low efficiency and accuracy.  ...  [22] proposed a fast sequence pattern algorithm named MEMISP based on memory index. This algorithm only needs scanning the sequence database once.  ... 
doi:10.1371/journal.pone.0195601 pmid:29684052 pmcid:PMC5912758 fatcat:4xzchjkcxrdt7gpwxt5c35j33y

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al-ouran, Lev Neiman, Lee J Nau, Joshua D Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank Drews (+2 others)
2010 BMC Bioinformatics  
An important focus of genomic science is the discovery and characterization of all functional elements within genomes.  ...  Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets.  ...  All of these problems require the discovery of patterns in genomic sequences. Several approaches have been developed for genomic pattern discovery.  ... 
doi:10.1186/1471-2105-11-s12-s6 pmid:21210985 pmcid:PMC3040532 fatcat:us24lb7pfjcyfcdazg2icg42j4

Incremental mining of sequential patterns: Progress and challenges

Bhawna Mallick, Deepak Garg, P.S. Grover
2013 Intelligent Data Analysis  
So, incremental mining of sequential patterns has become the norm. This article investigates the need for incremental mining of sequential patterns.  ...  Sequential pattern mining is a vital problem with broad applications.  ...  MEMISP (MEMory Indexing for Sequential Pattern mining) [16, 34] algorithm requires one pass over the database and at most two passes for very large database.  ... 
doi:10.3233/ida-130591 fatcat:ituubtk5ujca3bxmrxyl44zgdm

A Literature Survey on Association Rule Mining Algorithms

Pinar Yazgana, Ali Osman Kusakci
2016 Southeast Europe Journal of Soft Computing  
strong advantage over previous algorithms for discovery of frequent patterns.  ...  Sequential Pattern Discovery Using Equivalent Classes) Algorithm (SPADE) SPADE algorithm is an Apriori-Based Vertical Data Format algorithm represented by Zaki (2001) .The algorithm decomposes the original  ... 
doi:10.21533/scjournal.v5i1.102 fatcat:rghnonlu5vb2jazq3fso572ns4

Improving suffix array locality for fast pattern matching on disk

Ranjan Sinha, Simon Puglisi, Alistair Moffat, Andrew Turpin
2008 Proceedings of the 2008 ACM SIGMOD international conference on Management of data - SIGMOD '08  
Here we address the problem of arranging a suffix array on disk so that querying is fast in practice.  ...  The suffix tree (or equivalently, the enhanced suffix array) provides efficient solutions to many problems involving pattern matching and pattern discovery in large strings, such as those arising in computational  ...  We thank the authors of TDD [27] and TREL-LIS [23] for making their code available. This work was supported by the Australian Research Council.  ... 
doi:10.1145/1376616.1376683 dblp:conf/sigmod/SinhaPMT08 fatcat:ij5tit5dibdrpnmcsvamv62c3e

The Pharmit backend: A computer systems approach to enabling interactive online drug discovery

D. R. Koes
2018 IBM Journal of Research and Development  
The key concepts are to maximize parallelism while minimizing intra-thread communication, optimize data layout for sequential processing, and efficiently manage memory allocation.  ...  Pharmit (http://pharmit.csb.pitt.edu) is an open-source online resource that allows users to interactively search libraries of millions compounds as part of a structure-based drug discovery workflow.  ...  This work was supported in part by a grant from R01GM108340 from the National Institute of General Medical Sciences.  ... 
doi:10.1147/jrd.2018.2883977 pmid:33871478 pmcid:PMC8049614 fatcat:pztjsbig75d2jdsca7z6xped2y

Advances in Engineering Software for Multicore Systems [chapter]

Ali Jannesari
2018 Dependability Engineering  
The vast amounts of data to be processed by today's applications demand higher computational power.  ...  A contribution of this work is an efficient profiling method to determine the control and data dependences for performing parallelism discovery or other types of code analysis.  ...  However, if a loop index variable (loop indexing) had been used in the sequential code, we would have detected a doall loop pattern based on our pattern detection algorithm (template matching).  ... 
doi:10.5772/intechopen.72784 fatcat:rxkrgppehndvrnqzdafew3vfte

DSM-PLW: Single-pass mining of path traversal patterns over streaming Web click-sequences

Hua-Fu Li, Suh-Yin Lee, Man-Kwan Shan
2006 Computer Networks  
patterns over a continuous stream of maximal forward references generated at a rapid rate.  ...  The set of all maximal reference sequences is determined from the SP-forest by a depth-first-search mechanism, called MRS-mining (Maximal Reference Sequence mining).  ...  The research is supported in part by the National Science Council, Project No. NSC 93-2213-E-009-043, Taiwan, Republic of China.  ... 
doi:10.1016/j.comnet.2005.10.018 fatcat:cn2aghozazfwnibdvhveigc5yy

Enhance similarity searching algorithm with optimized fast population count method based on parallel design

SeyedVahid Dianat, Yasaman Eftekharypour, Nurul Hashimah Ahamed Hassain Malim, Nur'Aini Abdul Rashid
2013 IOSR Journal of Computer Engineering  
We achieved significant results in terms of performance and execution time in both CUDA and OPENMP designs of fast population count method with data conversion when compared to the sequential code.  ...  Here the aim is to minimize hardware memory allocation by proposed data conversion method and improve data transmission speed.  ...  So we can do drug discovery based on similarity searching with the single reference by applying CUDA design with fast population count method.  ... 
doi:10.9790/0661-1464352 fatcat:swiextx76nhupdkakgvr6moc5u

A Comprehensive Survey of Pattern Mining: Challenges and Opportunities

Pragati Upadhyay, M. K., Narendra Kohli
2018 International Journal of Computer Applications  
It is the improved version of SPADE algorithm. Another approach of indexed sparse list IDs is introduced by Fast [19] method.  ...  By weakening the conditions of the original constraints, this mechanism allows the discovery of unknown information.  ... 
doi:10.5120/ijca2018916573 fatcat:dktrnmfvhzadzm5rhutwijfkvy

Efficient Mining of Interesting Patterns in Large Biological Sequences

Md. Mamunur Rashid, Md. Rezaul Karim, Byeong-Soo Jeong, Ho-Jin Choi
2012 Genomics & Informatics  
Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics.  ...  So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not.  ...  Sequential patterns are grown by exploring length-1 frequent patterns in each projected database.  ... 
doi:10.5808/gi.2012.10.1.44 pmid:23105928 pmcid:PMC3475482 fatcat:sstsa2moqvgvnhmh5ss5yfhrva

Survey on Mining High Utility Patterns in One Phase

Harshita Taran, Shilpa Ghode
2017 International Journal of Engineering Research and  
Look ahead strategy is to identify high utility patterns without enumeration by a closure property and a singleton property.  ...  Concretely, pattern growth approach is to search a reverse set enumeration tree and to prune search space by utility upper bounding.  ...  The algorithms utilize the structural properties of frequent itemsets to facilitate fast discovery.  ... 
doi:10.17577/ijertv6is070111 fatcat:yn6s4mfwvzacvh5hep5k2hxn6y
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