Sequential Patterns Post-processing for Structural Relation Patterns Mining

Sequential patterns mining is an important data-mining technique used to identify frequently observed sequential occurrence of items across ordered transactions over time. It has been extensively studied in the literature, and there exists a diversity of algorithms. However, more complex structural patterns are often hidden behind sequences. This article begins with the introduction of a model for the representation of sequential patterns—Sequential Patterns Graph—which motivates the search for new structural relation patterns. An integrative framework for the discovery of these patterns–Postsequential Patterns Mining–is then described which underpins the postprocessing of sequential patterns. A corresponding data-mining method based on sequential patterns postprocessing is proposed and shown to be effective in the search for concurrent patterns. From experiments conducted on three component algorithms, it is demonstrated that sequential patterns-based concurrent patterns mining provides an efficient method for structural knowledge discover

From sequential patterns to concurrent branch patterns: a new post sequential patterns mining approach

A thesis submitted for the degree of Doctor ofPhilosophy of the University of BedfordshireSequential patterns mining is an important pattern discovery technique used to identify frequently observed sequential occurrence of items across ordered transactions over time. It has been intensively studied and there exists a great diversity of algorithms. However, there is a major problem associated with the conventional sequential patterns mining in that patterns derived are often large and not very easy to understand or use. In addition, more complex relations among events are often hidden behind sequences. A novel model for sequential patterns called Sequential Patterns Graph (SPG) is proposed. The construction algorithm of SPG is presented with experimental results to substantiate the concept. The thesis then sets out to define some new structural patterns such as concurrent branch patterns, exclusive patterns and iterative patterns which are generally hidden behind sequential patterns. Finally, an integrative framework, named Post Sequential Patterns Mining (PSPM), which is based on sequential patterns mining, is also proposed for the discovery and visualisation of structural patterns. This thesis is intended to prove that discrete sequential patterns derived from traditional sequential patterns mining can be modelled graphically using SPG. It is concluded from experiments and theoretical studies that SPG is not only a minimal representation of sequential patterns mining, but it also represents the interrelation among patterns and establishes further the foundation for mining structural knowledge (i.e. concurrent branch patterns, exclusive patterns and iterative patterns). from experiments conducted on both synthetic and real datasets, it is shown that Concurrent Branch Patterns (CBP) mining is an effective and efficient mining algorithm suitable for concurrent branch patterns

WildSpan: mining structured motifs from protein sequences

<p>Abstract</p> <p>Background</p> <p>Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards) are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions) that incorporates several pruning strategies to largely reduce the mining cost.</p> <p>Results</p> <p>WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode of WildSpan is developed for discovering functional regions of a single protein by referring to a set of related sequences (e.g. its homologues). The discovered W-patterns are used to characterize the protein sequence and the results are compared with the conserved positions identified by multiple sequence alignment (MSA). The family-based mining mode of WildSpan is developed for extracting sequence signatures for a group of related proteins (e.g. a protein family) for protein function classification. In this situation, the discovered W-patterns are compared with PROSITE patterns as well as the patterns generated by three existing methods performing the similar task. Finally, analysis on execution time of running WildSpan reveals that the proposed pruning strategy is effective in improving the scalability of the proposed algorithm.</p> <p>Conclusions</p> <p>The mining results conducted in this study reveal that WildSpan is efficient and effective in discovering functional signatures of proteins directly from sequences. The proposed pruning strategy is effective in improving the scalability of WildSpan. It is demonstrated in this study that the W-patterns discovered by WildSpan provides useful information in characterizing protein sequences. The WildSpan executable and open source codes are available on the web (<url>http://biominer.csie.cyu.edu.tw/wildspan</url>).</p

Applications of concurrent access patterns in web usage mining

This paper builds on the original data mining and modelling research which has proposed the discovery of novel structural relation patterns, applying the approach in web usage mining. The focus of attention here is on concurrent access patterns (CAP), where an overarching framework illuminates the methodology for web access patterns post-processing. Data pre-processing, pattern discovery and patterns analysis all proceed in association with access patterns mining, CAP mining and CAP modelling. Pruning and selection of access pat-terns takes place as necessary, allowing further CAP mining and modelling to be pursued in the search for the most interesting concurrent access patterns. It is shown that higher level CAPs can be modelled in a way which brings greater structure to bear on the process of knowledge discovery. Experiments with real-world datasets highlight the applicability of the approach in web navigation