SPMF documentation > Mining Frequent Sequential Patterns Using the PrefixSpan Algorithm

This example explains how to run the PrefixSpan algorithm using the SPMF open-source data mining library.

How to run this example?

To run the implementation of PrefixSpan implemented by P. Fournier-Viger (PFV):

To run the version the implementation of PrefixSpan by A. Gomariz Peñalver (AGP):

What is PrefixSpan?

PrefixSpan is an algorithm for discovering sequential patterns in sequence databases, proposed by Pei et al. (2001).

What is the input of PrefixSpan?

The input of PrefixSpan is a sequence database and a user-specified threshold named minsup (a value in [0,1] representing a percentage).

A sequence database is a set of sequences where each sequence is a list of itemsets. An itemset is an unordered set of distinct items. For example, the table shown below contains four sequences. The first sequence, named S1, contains 5 itemsets. It means that item 1 was followed by items 1 2 and 3 at the same time, which were followed by 1 and 3, followed by 4, and followed by 3 and 6. It is assumed that items in an itemset are sorted in lexicographical order. This database is provided in the file "contextPrefixSpan.txt" of the SPMF distribution. Note that it is assumed that no items appear twice in the same itemset and that items in an itemset are lexically ordered.

ID Sequences
S1 (1), (1 2 3), (1 3), (4), (3 6)
S2 (1 4), (3), (2 3), (1 5)
S3 (5 6), (1 2), (4 6), (3), (2)
S4 (5), (7), (1 6), (3), (2), (3)

What is the output of PrefixSpan?

PrefixSpan discovers all frequent sequential patterns occurring in a sequence database (subsequences that occurs in more than minsup sequences of the database.

To explain more formally what is a sequential pattern, it is necessary to review some definition.

A sequential pattern is a sequence. A sequence SA = X1, X2, ... Xk, where X1, X2... Xk are itemsets is said to occur in another sequence SB = Y1, Y2, ... Ym, where Y1, Y2... Ym are itemsets, if and only if there exists integers 1 <= i1 < i2... < ik <= m such that X1 ⊆ Yi1, X2 ⊆ Yi2, ... Xk ⊆ Yik.

The support of a sequential pattern is the number of sequences where the pattern occurs divided by the total number of sequences in the database.

A frequent sequential pattern is a sequential pattern having a support no less than the minsup parameter provided by the user.

For example, if we run PrefixSpan with minsup= 50 % and with a maximum pattern length of 100 items, 53 sequential patterns are found. The list is too long to be presented here. An example of pattern found is "(1,2),(6)" which appears in the first and the third sequences (it has therefore a support of 50%). This pattern has a length of 3 because it contains three items. Another pattern is "(4), (3), (2)". It appears in the second and third sequence (it has thus a support of 50 %). It also has a length of 3 because it contains 3 items.

Optional parameter(s)

The PrefixSpan implementation allows to specify additional optional parameter(s) :

These parameter(s) are available in the GUI of SPMF and also in the example(s) "MainTestPrefixSpan ... .java" provided in the source code of SPMF.

The parameter(s) can be also used in the command line with the Jar file. If you want to use these optional parameter(s) in the command line, it can be done as follows. Consider this example:
java -jar spmf.jar run PrefixSpan contextPrefixSpan.txt output.txt 50% 5 true
This command means to apply the algorithm on the file "contextPrefixSpan.txt" and output the results to "output.txt". Moreover, it specifies that the user wants to find patterns for minsup = 50%, and patterns must have a maximum length of 5 items, and sequence ids should be output for each pattern found.

Input file format

The input file format is defined as follows. It is a text file where each line represents a sequence from a sequence database. Each item from a sequence is a positive integer and items from the same itemset within a sequence are separated by single space. Note that it is assumed that items within a same itemset are sorted according to a total order and that no item can appear twice in the same itemset. The value "-1" indicates the end of an itemset. The value "-2" indicates the end of a sequence (it appears at the end of each line). For example, the input file "contextPrefixSpan.txt" contains the following four lines (four sequences).

1 -1 1 2 3 -1 1 3 -1 4 -1 3 6 -1 -2
1 4 -1 3 -1 2 3 -1 1 5 -1 -2
5 6 -1 1 2 -1 4 6 -1 3 -1 2 -1 -2
5 -1 7 -1 1 6 -1 3 -1 2 -1 3 -1 -2

The first line represents a sequence where the itemset {1} is followed by the itemset {1, 2, 3}, followed by the itemset {1, 3}, followed by the itemset {4}, followed by the itemset {3, 6}. The next lines follow the same format.

Note that it is also possible to use a text file containing a text (several sentences) if the text file has the ".text" extension, as an alternative to the default input format. If the algorithm is applied on a text file from the graphical interface or command line interface, the text file will be automatically converted to the SPMF format, by dividing the text into sentences separated by ".", "?" and "!", where each word is considered as an item. Note that when a text file is used as input of a data mining algorithm, the performance will be slightly less than if the native SPMF file format is used because a conversion of the input file will be automatically performed before launching the algorithm and the result will also have to be converted. This cost however should be small.

Output file format

The output file format is defined as follows. It is a text file. Each line is a frequent sequential pattern. Each item from a sequential pattern is a positive integer and items from the same itemset within a sequence are separated by single spaces. The value "-1" indicates the end of an itemset. On each line, the sequential pattern is first indicated. Then, the keyword "#SUP:" appears followed by an integer indicating the support of the pattern as a number of sequences. For example, a few lines from the output file from the previous example are shown below:

2 3 -1 1 -1 #SUP: 2
6 -1 2 -1 #SUP: 2
6 -1 2 -1 3 -1 #SUP: 2

The first line indicates that the frequent sequential pattern consisting of the itemset {2, 3}, followed by the itemset {1} has a support of 2 sequences.


PrefixSpan is one of the fastest sequential pattern mining algorithm. However, the SPAM and SPADE implementation in SPMF can be faster than PrefixSpan (see the "performance" section of the website for a performance comparison).

Optional feature: giving names to items

Some users have requested the feature of given names to items instead of using numbers. This feature is offered in the user interface of SPMF and in the command line of SPMF. To use this feature, your file must include @CONVERTED_FROM_TEXT as first line and then several lines to define the names of items in your file. For example, consider the example database "contextPrefixSpan.txt". Here we have modified the file to give names to the items:

1 -1 1 2 3 -1 1 3 -1 4 -1 3 6 -1 -2
1 4 -1 3 -1 2 3 -1 1 5 -1 -2
5 6 -1 1 2 -1 4 6 -1 3 -1 2 -1 -2
5 -1 7 -1 1 6 -1 3 -1 2 -1 3 -1 -2

In this file, the first line indicates, that it is a file where names are given to items. Then, the second line indicates that the item 1 is called "apple". The third line indicates that the item 2 is called "orange". The 9th line indicates that the symbol "-1" must be replaced by "|". Then the following lines define four sequences in the SPMF format.

Then, if we apply a sequential pattern mining algorithm using this file using the user interface of SPMF or the command line, the output file contains several patterns, including the following ones:

apple | #SUP: 4 
orange | #SUP: 4 
tomato | #SUP: 4 
apple | orange | #SUP: 4 

Note that this feature could be also used from the source code of SPMF using the ResultConverter class. However, there is currently no example provided.

Implementation details

Note that in the source code, we also provide examples of how to keep the result into memory instead of saving it to a file. This can be useful if the algorithms are integrated into another Java software.

Note also that in the source code, there is a version of PrefixSpan based on the PFV version that takes as input a dataset with strings instead of integers. It can be run by using the files MainTestPrefixSpan_WithStrings_saveToMemory.java and MainTestPrefixSpanWithStrings_saveToFile.java. For the graphical user interface version of SPMF, it is possible to use the version of PrefixSpan that uses Strings instead of integer by selecting "PrefixSpan with strings" and to test it with the input file contextPrefixSpanStrings.txt. The version of PrefixSpan with Strings was made to temporarily accommodate the needs of some users of SPMF. In the future, it may be replaced by a more general mechanism for using files with strings for all algorithms.

Where can I get more information about PrefixSpan?

The PrefixSpan algorithm is described in this article:

J. Pei, J. Han, B. Mortazavi-Asl, J. Wang, H. Pinto, Q. Chen, U. Dayal, M. Hsu: Mining Sequential Patterns by Pattern-Growth: The PrefixSpan Approach. IEEE Trans. Knowl. Data Eng. 16(11): 1424-1440 (2004)

Besides, you may read this survey of sequential pattern mining, which gives an overview of sequential pattern mining algorithms.

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