Integrating Subdue With Analyst Notebook Users Manual 1.5

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SUBDUE Manual

The SUBDUE Project

SUBDUE Manual

Version 1.5

The SUBDUE Project

 2011

Copyright © 2011. The SUBDUE Project.
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
The Software is provided "as is", without warranty of any kind, express or
implied, including but not limited to the warranties of merchantability, fitness
for a particular purpose and noninfringement. In no event shall the authors,
copyright holders, or contributors be liable for any claim, damages or other
liability, whether in an action of contract, tort or otherwise, arising from,
out of or in connection with the Software or the use or other dealings in the
software.

SUBDUE Manual

The SUBDUE Project

Table of Contents
TABLE OF CONTENTS ........................................................................................... III
REVISION HISTORY ................................................................................................. V
PREFACE ................................................................................................................. VI
1.

INTRODUCTION............................................................................................... 1

1.1

Overview.................................................................................................................. 1

1.2

Reference Documents ........................................................................................... 1

2.

DOWNLOADING AND INSTALLING ............................................................... 2

2.1

Download................................................................................................................. 2

2.2

Files .......................................................................................................................... 2

2.3

Install ....................................................................................................................... 2

3.

DATA FORMAT ................................................................................................ 4

3.1 Input ......................................................................................................................... 4
3.1.1 Graph Format ..................................................................................................... 4
3.1.2 Samples ............................................................................................................... 5
3.2

Output ...................................................................................................................... 5

3.3

Example ................................................................................................................... 5

4.

EXECUTING ..................................................................................................... 9

4.1 Command................................................................................................................. 9
4.1.1 Options ................................................................................................................ 9
4.2 MPI Version .......................................................................................................... 14
4.2.1 build ...................................................................................................................14
4.2.2 run ......................................................................................................................14
4.3

Example Continued ............................................................................................. 15

4.4

More Examples ..................................................................................................... 18

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4.4.1
4.4.2
4.4.3
4.4.4

The SUBDUE Project

Supervised..........................................................................................................18
Overlap ...............................................................................................................23
Predefined Substructure ...................................................................................26
Recursion ...........................................................................................................31

4.5 Other Tools............................................................................................................ 35
4.5.1 cvtest ..................................................................................................................35
4.5.2 gm .......................................................................................................................36
4.5.3 gprune ................................................................................................................36
4.5.4 graph2dot ...........................................................................................................36
4.5.5 mdl .....................................................................................................................37
4.5.6 sgiso ....................................................................................................................37
4.5.7 subs2dot .............................................................................................................38
4.5.8 test......................................................................................................................38

5.

NOTES/ISSUES ............................................................................................. 39

5.1

Unix ........................................................................................................................ 39

A.

APPENDIX - TERMINOLOGY ........................................................................ 40

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Revision History
Release
Version
1.0
1.1
1.2
1.3
1.4
1.5

Preface

Date
April 27, 2005
January 27, 2006
April 22, 2006
May 29, 2006
January 11, 2007
June 6, 2011

Revisions
Initial release
Added –inc and –compress options; added MPI section.
Corrected typos and missing reference.
Updated SUBDUE references.
Corrected typos and minor formatting changes.
Minor updates to reflect changes in new Subdue version 5.2.2.

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The SUBDUE Project

Preface
Conventions
The following documentation conventions are followed within this document.
bold underlined text signifies notes or comments to the reader.
Italicized text signifies file names, directories or programs.
Bold italicized text signifies a reference to another document.

Preface

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SUBDUE Manual

The SUBDUE Project

1. Introduction
The following document provides a manual on how to use the SUBDUE system.

1.1 Overview
The SUBDUE graph-based pattern learning system finds relational patterns in data represented as a
graph. While the details of how SUBDUE works internally will not be discussed here (you can refer
to other documents on the SUBDUE web-site for more information), this document will provide you
with the specifics on how to install and run the application.

This document contains the following sections:
 Chapter 2: instructions on how to download and install SUBDUE
 Chapter 3: layout of the required graph input file
 Chapter 4: instructions on running SUBDUE
 Chapter 5: various notes and issues regarding the SUBDUE application
 Appendix A: terminology

1.2 Reference Documents
 SUBDUE Home Page: http://www.subdue.org/
 AT&T Labs GraphViz: http://www.graphviz.org/
 MPI: http://www.mcs.anl.gov/mpi/

1 Introduction

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SUBDUE Manual

The SUBDUE Project

2. Downloading and Installing
In order to build and run the SUBDUE application, you must first download the appropriate files.

2.1 Download
The SUBDUE system, including documentation, papers, and research, can be found on the SUBDUE
home page (http://www.subdue.org/).
In order to get the latest copy of the application, you must choose the Download option located on the
left-hand side of the SUBDUE home page. After clicking the Download link, you will be redirected
to the “Download” page, which contains a link to the latest source code for the SUBDUE application.
In order to pull a release of the SUBDUE application, you must click on the .zip file (where
 is the version of SUBDUE that you want) located under the “Source” heading. Depending
upon your browser and settings, you will either be able to just click on the link, which will then
prompt you to either open the file or save it to your local disk, or you will be able to right-click on the
link and either open or save the file.

2.2 Files
Once you have chosen a release, downloaded the archive, and unzipped the files, the following
directory/file structure is created:

./bin/ -- directory of executables (initially empty)
./copyright.txt-- file containing the SUBDUE copyright notice
./docs/ -- directory containing this manual
./graphs/ -- directory containing some sample graph input files
./readme.txt – file containing directions on how to build SUBDUE, as well as the version histories
./src/ - directory containing the source code and make files

(Note: All of this is actually created under another directory called subdue, where  is the
major release number.)

2.3 Install
After downloading and unzipping the files, you can now install the SUBDUE application. Installation
consists of actually building the application so that it is now native to your Unix system.
SUBDUE uses the standard make facility to build its application. In order to build the application,
you should perform the following steps:

2 Downloading and Installing

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SUBDUE Manual

The SUBDUE Project

1. Change directory to subdue-/src
2. At the command prompt, enter: make. This will compile the SUBDUE programs.
3. At the command prompt, enter: make install. This will copy the executables to the subdue/bin directory
4. At the command prompt, enter: make clean. This will clean up the src directory (removing object
files).

2 Downloading and Installing

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The SUBDUE Project

3. Data Format
The following section describes the format of the input graph that must be supplied in order to run the
SUBDUE application.

3.1 Input
The input to the SUBDUE application is comprised of a textual representation of a graph.

3.1.1 Graph Format
The input file can consist of one or more graphs. Each graph is prefaced (on a line by itself) by either
an "XP", indicating a positive example, or "XN" indicating a negative example. If the first (or only)
graph in the file is positive, then the "XP" can be omitted.

3.1.1.1 Vertices
Each graph is a sequence of vertices and edges. A vertex is defined as:
v <#> 

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Title                           : Integrating Subdue with Analyst Notebook
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