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Mining Sequential Patterns
, 1995
"... We are given a large database of customer transactions, where each transaction consists of customerid, transaction time, and the items bought in the transaction. We introduce the problem of mining sequential patterns over such databases. We present three algorithms to solve this problem, and empiri ..."
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Cited by 1178 (5 self)
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We are given a large database of customer transactions, where each transaction consists of customerid, transaction time, and the items bought in the transaction. We introduce the problem of mining sequential patterns over such databases. We present three algorithms to solve this problem, and empirically evaluate their performance using synthetic data. Two of the proposed algorithms, AprioriSome and AprioriAll, have comparable performance, albeit AprioriSome performs a little better when the minimum number of customers that must support a sequential pattern is low. Scaleup experiments show that both AprioriSome and AprioriAll scale linearly with the number of customer transactions. They also have excellent scaleup properties with respect to the number of transactions per customer and the number of items in a transaction. 1 Introduction Database mining is motivated by the decision support problem faced by most large retail organizations. Progress in barcode technology has made it po...
Database resources of the National Center for Biotechnology Information
 Nucleic Acids Res
, 2008
"... In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez, ..."
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Cited by 580 (11 self)
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In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez,
Mining Sequential Patterns: Generalizations and Performance Improvements
 Research Report RJ 9994, IBM Almaden Research
, 1995
"... Abstract. The problem of mining sequential patterns was recently introduced in [3]. We are given a database of sequences, where each sequence is a list of transactions ordered by transactiontime, and each transaction is a set of items. The problem is to discover all sequential patterns with a user ..."
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Cited by 551 (4 self)
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Abstract. The problem of mining sequential patterns was recently introduced in [3]. We are given a database of sequences, where each sequence is a list of transactions ordered by transactiontime, and each transaction is a set of items. The problem is to discover all sequential patterns with a userspeci ed minimum support, where the support of a pattern is the number of datasequences that contain the pattern. An example of a sequential pattern is \5 % of customers bought `Foundation' and `Ringworld ' in one transaction, followed by `Second Foundation ' in a later transaction". We generalize the problem as follows. First, we add time constraints that specify a minimum and/or maximum time period between adjacent elements in a pattern. Second, we relax the restriction that the items in an element of a sequential pattern must come from the same transaction, instead allowing the items to be present in a set of transactions whose transactiontimes are within a userspeci ed time window. Third, given a userde ned taxonomy (isa hierarchy) on items, we allow sequential patterns to include items across all levels of the taxonomy. We present GSP, a new algorithm that discovers these generalized sequential patterns. Empirical evaluation using synthetic and reallife data indicates that GSP is much faster than the AprioriAll algorithm presented in [3]. GSP scales linearly with the number of datasequences, and has very good scaleup properties with respect to the average datasequence size. 1
Fast Subsequence Matching in TimeSeries Databases
 SIGMOD 94
, 1994
"... We present an efficient indexing method to locate 1dimensional subsequences witbin a collection of sequences, such that the subsequences match a given (query) pattern within a specified tolerance. The idea is to map each data sequence into a small set of multidimensional rectangles in feature space ..."
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Cited by 426 (21 self)
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We present an efficient indexing method to locate 1dimensional subsequences witbin a collection of sequences, such that the subsequences match a given (query) pattern within a specified tolerance. The idea is to map each data sequence into a small set of multidimensional rectangles in feature space. Then, these rectangles can be readily indexed using traditional spatial access methods, like the R*tree [9]. In more deteil, we use a sliding window over the data sequence and extract its features; the result is a trail in feature space. We propose an efficient and effective algorithm to divide such trails into subtrails, which are subsequently represented by their Minimum Bounding Rectangles (MBRs). We also examine queries of varying lengths, and we show how to handle each case efficiently. We implemented our method and carried out experiments on synthetic and real data (stock price movements). We compared the method to sequential scanning, which is the only obvious competitor. The results were excellent: our method accelerated the search time from 3 times up to 100 times.
Efficient similarity search in sequence databases
, 1994
"... We propose an indexing method for time sequences for processing similarity queries. We use the Discrete Fourier Transform (DFT) to map time sequences to the frequency domain, the crucial observation being that, for most sequences of practical interest, only the first few frequencies are strong. Anot ..."
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Cited by 415 (20 self)
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We propose an indexing method for time sequences for processing similarity queries. We use the Discrete Fourier Transform (DFT) to map time sequences to the frequency domain, the crucial observation being that, for most sequences of practical interest, only the first few frequencies are strong. Another important observation is Parseval's theorem, which specifies that the Fourier transform preserves the Euclidean distance in the time or frequency domain. Having thus mapped sequences to a lowerdimensionality space by using only the first few Fourier coe cients, we use Rtrees to index the sequences and e ciently answer similarity queries. We provide experimental results which show that our method is superior to search based on sequential scanning. Our experiments show that a few coefficients (13) are adequate to provide good performance. The performance gain of our method increases with the number and length of sequences.
A Guided Tour to Approximate String Matching
 ACM Computing Surveys
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
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Cited by 409 (38 self)
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We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices according to each case. We conclude with some future work directions and open problems. 1
Hidden Markov models for detecting remote protein homologies
 Bioinformatics
, 1998
"... A new hidden Markov model method (SAMT98) for nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (hmm) from the sequence and homologs found using the hmm for database search. SAMT98 is ..."
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Cited by 308 (12 self)
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A new hidden Markov model method (SAMT98) for nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (hmm) from the sequence and homologs found using the hmm for database search. SAMT98 is also used to construct model libraries automatically from sequences in structural databases. We evaluate the SAMT98 method with four datasets. Three of the test sets are foldrecognition tests, where the correct answers are determined by structural similarity. The fourth uses a curated database. The method is compared against wublastp and against doubleblast, a twostep method similar to ISS, but using blast instead of fasta. Results SAMT98 had the fewest errors in all tests dramatically so for the foldrecognition tests. At the minimumerror point on the SCOPdomains test, SAMT98 got 880 true positives and 68 false positives, doubleblast got 533 true positives with 71 false positives, and wublastp got 353 true positives with 24 false positives. The method is optimized to recognize superfamilies, and would require parameter adjustment to be used to nd family or fold relationships. One key to the performance of the hmm method is a new scorenormalization technique that compares the score to the score with a reversed model rather than to a uniform null model. Availability A World Wide Web server, as well as information on obtaining the Sequence Alignment and PREPRINT to appear in Bioinformatics, 1999
Taverna: A tool for the composition and enactment of bioinformatics workflows
 Bioinformatics
, 2004
"... *To whom correspondence should be addressed. Running head: Composing and enacting workflows using Taverna Motivation: In silico experiments in bioinformatics involve the coordinated use of computational tools and information repositories. A growing number of these resources are being made available ..."
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Cited by 296 (8 self)
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*To whom correspondence should be addressed. Running head: Composing and enacting workflows using Taverna Motivation: In silico experiments in bioinformatics involve the coordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the Simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by with which in silico experiments can be represented as Scufl workflows using the workbench application. Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from
When Is "Nearest Neighbor" Meaningful?
 In Int. Conf. on Database Theory
, 1999
"... . We explore the effect of dimensionality on the "nearest neighbor " problem. We show that under a broad set of conditions (much broader than independent and identically distributed dimensions), as dimensionality increases, the distance to the nearest data point approaches the distance to the fa ..."
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Cited by 295 (1 self)
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. We explore the effect of dimensionality on the "nearest neighbor " problem. We show that under a broad set of conditions (much broader than independent and identically distributed dimensions), as dimensionality increases, the distance to the nearest data point approaches the distance to the farthest data point. To provide a practical perspective, we present empirical results on both real and synthetic data sets that demonstrate that this effect can occur for as few as 1015 dimensions. These results should not be interpreted to mean that highdimensional indexing is never meaningful; we illustrate this point by identifying some highdimensional workloads for which this effect does not occur. However, our results do emphasize that the methodology used almost universally in the database literature to evaluate highdimensional indexing techniques is flawed, and should be modified. In particular, most such techniques proposed in the literature are not evaluated versus simple...
The Landscape of Parallel Computing Research: A View from Berkeley
 TECHNICAL REPORT, UC BERKELEY
, 2006
"... All rights reserved. ..."