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Weka a tool_for_exploratory_data_mining

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The document discusses the machine learning toolkit WEKA. WEKA contains tools for data pre-processing, classification, regression, clustering, association rule mining, and attribute selection. It has a graphical user interface called the Explorer for loading and exploring data, applying these tools, and evaluating models. WEKA also contains interfaces for configuring experiments and visualizing data.

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 WEKA: A Machine Machine Learning with Learning Toolkit WEKA  The Explorer • Classification and Regression • Clustering Bernhard Pfahringer • Association Rules (based on material by Eibe Frank, Mark • Attribute Selection Hall, and Peter Reutemann) • Data Visualization Department of Computer Science,  The Experimenter University of Waikato, New Zealand  The Knowledge Flow GUI  Other Utilities  Conclusions
WEKA: the bird The Weka or woodhen (Gallirallus australis) is an endemic bird of New Zealand. (Source: WikiPedia) Copyright: Martin Kramer (mkramer@wxs.nl) 12/05/12 University of Waikato 2
WEKA: the software  Machine learning/data mining software written in Java (distributed under the GNU Public License)  Used for research, education, and applications  Complements “Data Mining” by Witten & Frank  Main features:  Comprehensive set of data pre-processing tools, learning algorithms and evaluation methods  Graphical user interfaces (incl. data visualization)  Environment for comparing learning algorithms 12/05/12 University of Waikato 3
History  Project funded by the NZ government since 1993  Develop state-of-the art workbench of data mining tools  Explore fielded applications  Develop new fundamental methods 12/05/12 University of Waikato 4
History (2)  Late 1992 - funding was applied for by Ian Witten  1993 - development of the interface and infrastructure  WEKA acronym coined by Geoff Holmes  WEKA’s file format “ARFF” was created by Andrew Donkin ARFF was rumored to stand for Andrew’s Ridiculous File Format  Sometime in 1994 - first internal release of WEKA  TCL/TK user interface + learning algorithms written mostly in C  Very much beta software  Changes for the b1 release included (among others): “Ambiguous and Unsupported menu commands removed.” “Crashing processes handled (in most cases :-)”  October 1996 - first public release: WEKA 2.1 12/05/12 University of Waikato 5
History (3)  July 1997 - WEKA 2.2  Schemes: 1R, T2, K*, M5, M5Class, IB1-4, FOIL, PEBLS, support for C5  Included a facility (based on Unix makefiles) for configuring and running large scale experiments  Early 1997 - decision was made to rewrite WEKA in Java  Originated from code written by Eibe Frank for his PhD  Originally codenamed JAWS (JAva Weka System) JA  May 1998 - WEKA 2.3  Last release of the TCL/TK-based system  Mid 1999 - WEKA 3 (100% Java) released  Version to complement the Data Mining book  Development version (including GUI) 12/05/12 University of Waikato 6
The GUI back then… TCL/TK interface of Weka 2.1 12/05/12 University of Waikato 7
WEKA: versions  There are several versions of WEKA:  WEKA 3.4: “book version” compatible with description in data mining book  WEKA 3.5.5: “development version” with lots of improvements  This talk is based on a nightly snapshot of WEKA 3.5.5 (12-Feb-2007) 12/05/12 University of Waikato 8
WEKA only deals with “flat” files @relation heart-disease-simplified @attribute age numeric @attribute sex { female, male} @attribute chest_pain_type { typ_angina, asympt, non_anginal, atyp_angina} @attribute cholesterol numeric @attribute exercise_induced_angina { no, yes} @attribute class { present, not_present} @data 63,male,typ_angina,233,no,not_present 67,male,asympt,286,yes,present 67,male,asympt,229,yes,present 38,female,non_anginal,?,no,not_present ... 12/05/12 University of Waikato 9
WEKA only deals with “flat” files @relation heart-disease-simplified @attribute age numeric @attribute sex { female, male} @attribute chest_pain_type { typ_angina, asympt, non_anginal, atyp_angina} @attribute cholesterol numeric @attribute exercise_induced_angina { no, yes} @attribute class { present, not_present} @data 63,male,typ_angina,233,no,not_present 67,male,asympt,286,yes,present 67,male,asympt,229,yes,present 38,female,non_anginal,?,no,not_present ... 12/05/12 University of Waikato 10
java weka.gui.GUIChooser 12/05/12 University of Waikato 11
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java -jar weka.jar 12/05/12 University of Waikato 14
Explorer: pre-processing the data  Data can be imported from a file in various formats: ARFF, CSV, C4.5, binary  Data can also be read from a URL or from an SQL database (using JDBC)  Pre-processing tools in WEKA are called “filters”  WEKA contains filters for:  Discretization, normalization, resampling, attribute selection, transforming and combining attributes, … 12/05/12 University of Waikato 15
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Explorer: building “classifiers”  Classifiers in WEKA are models for predicting nominal or numeric quantities  Implemented learning schemes include:  Decision trees and lists, instance-based classifiers, support vector machines, multi-layer perceptrons, logistic regression, Bayes’ nets, …  “Meta”-classifiers include:  Bagging, boosting, stacking, error-correcting output codes, locally weighted learning, … 12/05/12 University of Waikato 37
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12/05/12 QuickTime™ and a T IFF (LZW) decompressor are needed to see this picture. University of Waikato 72
12/05/12 QuickTime™ and a T IFF (LZW) decompressor are needed to see this picture. University of Waikato 73
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Qui c k Ti m e ™ a nd a TIFF (LZW) d ec om pre s s o r a re n e ed e d to s e e th i s p i c tu re . 12/05/12 University of Waikato 78
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Explorer: clustering data  WEKA contains “clusterers” for finding groups of similar instances in a dataset  Some implemented schemes are:  k-Means, EM, Cobweb, X-means, FarthestFirst  Clusters can be visualized and compared to “true” clusters (if given)  Evaluation based on loglikelihood if clustering scheme produces a probability distribution 12/05/12 University of Waikato 93
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Explorer: finding associations  WEKA contains the Apriori algorithm (among others) for learning association rules  Works only with discrete data  Can identify statistical dependencies between groups of attributes:  milk, butter ⇒ bread, eggs (with confidence 0.9 and support 2000)  Apriori can compute all rules that have a given minimum support and exceed a given confidence 12/05/12 University of Waikato 103
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Explorer: attribute selection  Panel that can be used to investigate which (subsets of) attributes are the most predictive ones  Attribute selection methods contain two parts:  A search method: best-first, forward selection, random, exhaustive, genetic algorithm, ranking  An evaluation method: correlation-based, wrapper, information gain, chi-squared, …  Very flexible: WEKA allows (almost) arbitrary combinations of these two 12/05/12 University of Waikato 107
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Explorer: data visualization  Visualization very useful in practice: e.g. helps to determine difficulty of the learning problem  WEKA can visualize single attributes (1-d) and pairs of attributes (2-d)  To do: rotating 3-d visualizations (Xgobi-style)  Color-coded class values  “Jitter” option to deal with nominal attributes (and to detect “hidden” data points)  “Zoom-in” function 12/05/12 University of Waikato 114
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Performing experiments  Experimenter makes it easy to compare the performance of different learning schemes  For classification and regression problems  Results can be written into file or database  Evaluation options: cross-validation, learning curve, hold-out  Can also iterate over different parameter settings  Significance-testing built in! 12/05/12 University of Waikato 125
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The Knowledge Flow GUI  Java-Beans-based interface for setting up and running machine learning experiments  Data sources, classifiers, etc. are beans and can be connected graphically  Data “flows” through components: e.g., “data source” -> “filter” -> “classifier” -> “evaluator”  Layouts can be saved and loaded again later  cf. Clementine ™ 12/05/12 University of Waikato 136
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Sourceforge.net – Downloads 12/05/12 University of Waikato 152
Sourceforge.net – Web Traffic WekaDoc Wiki introduced – 12/2005 WekaWiki launched – 05/2005 12/05/12 University of Waikato 153
Projects based on WEKA  45 projects currently (30/01/07) listed on the WekaWiki  Incorporate/wrap WEKA  GRB Tool Shed - a tool to aid gamma ray burst research  YALE - facility for large scale ML experiments  GATE - NLP workbench with a WEKA interface  Judge - document clustering and classification  RWeka - an R interface to Weka  Extend/modify WEKA  BioWeka - extension library for knowledge discovery in biology  WekaMetal - meta learning extension to WEKA  Weka-Parallel - parallel processing for W EKA  Grid Weka - grid computing using WEKA  Weka-CG - computational genetics tool library 12/05/12 University of Waikato 154
WEKA and PENTAHO  Pentaho – The leader in Open Source Business Intelligence (BI)  September 2006 – Pentaho acquires the Weka project (exclusive license and SF.net page)  Weka will be used/integrated as data mining component in their BI suite  Weka will be still available as GPL open source software  Most likely to evolve 2 editions:  Community edition  BI oriented edition 12/05/12 University of Waikato 155
Limitations of WEKA  Traditional algorithms need to have all data in main memory  ==> big datasets are an issue  Solution:  Incremental schemes  Stream algorithms MOA “Massive Online Analysis” (not only a flightless bird, but also extinct!) 12/05/12 University of Waikato 156
Conclusion: try it yourself!  WEKA is available at http://www.cs.waikato.ac.nz/ml/weka  Also has a list of projects based on WEKA  (probably incomplete list of) WEKA contributors: Abdelaziz Mahoui, Alexander K. Seewald, Ashraf M. Kibriya, Bernhard Pfahringer, Brent Martin, Peter Flach, Eibe Frank, Gabi Schmidberger, Ian H. Witten, J. Lindgren, Janice Boughton, Jason Wells, Len Trigg, Lucio de Souza Coelho, Malcolm Ware, Mark Hall, Remco Bouckaert, Richard Kirkby, Shane Butler, Shane Legg, Stuart Inglis, Sylvain Roy, Tony Voyle, Xin Xu, Yong Wang, Zhihai Wang 12/05/12 University of Waikato 157

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Weka a tool_for_exploratory_data_mining

  • 1. WEKA: A Machine Machine Learning with Learning Toolkit WEKA  The Explorer • Classification and Regression • Clustering Bernhard Pfahringer • Association Rules (based on material by Eibe Frank, Mark • Attribute Selection Hall, and Peter Reutemann) • Data Visualization Department of Computer Science,  The Experimenter University of Waikato, New Zealand  The Knowledge Flow GUI  Other Utilities  Conclusions
  • 2. WEKA: the bird The Weka or woodhen (Gallirallus australis) is an endemic bird of New Zealand. (Source: WikiPedia) Copyright: Martin Kramer (mkramer@wxs.nl) 12/05/12 University of Waikato 2
  • 3. WEKA: the software  Machine learning/data mining software written in Java (distributed under the GNU Public License)  Used for research, education, and applications  Complements “Data Mining” by Witten & Frank  Main features:  Comprehensive set of data pre-processing tools, learning algorithms and evaluation methods  Graphical user interfaces (incl. data visualization)  Environment for comparing learning algorithms 12/05/12 University of Waikato 3
  • 4. History  Project funded by the NZ government since 1993  Develop state-of-the art workbench of data mining tools  Explore fielded applications  Develop new fundamental methods 12/05/12 University of Waikato 4
  • 5. History (2)  Late 1992 - funding was applied for by Ian Witten  1993 - development of the interface and infrastructure  WEKA acronym coined by Geoff Holmes  WEKA’s file format “ARFF” was created by Andrew Donkin ARFF was rumored to stand for Andrew’s Ridiculous File Format  Sometime in 1994 - first internal release of WEKA  TCL/TK user interface + learning algorithms written mostly in C  Very much beta software  Changes for the b1 release included (among others): “Ambiguous and Unsupported menu commands removed.” “Crashing processes handled (in most cases :-)”  October 1996 - first public release: WEKA 2.1 12/05/12 University of Waikato 5
  • 6. History (3)  July 1997 - WEKA 2.2  Schemes: 1R, T2, K*, M5, M5Class, IB1-4, FOIL, PEBLS, support for C5  Included a facility (based on Unix makefiles) for configuring and running large scale experiments  Early 1997 - decision was made to rewrite WEKA in Java  Originated from code written by Eibe Frank for his PhD  Originally codenamed JAWS (JAva Weka System) JA  May 1998 - WEKA 2.3  Last release of the TCL/TK-based system  Mid 1999 - WEKA 3 (100% Java) released  Version to complement the Data Mining book  Development version (including GUI) 12/05/12 University of Waikato 6
  • 7. The GUI back then… TCL/TK interface of Weka 2.1 12/05/12 University of Waikato 7
  • 8. WEKA: versions  There are several versions of WEKA:  WEKA 3.4: “book version” compatible with description in data mining book  WEKA 3.5.5: “development version” with lots of improvements  This talk is based on a nightly snapshot of WEKA 3.5.5 (12-Feb-2007) 12/05/12 University of Waikato 8
  • 9. WEKA only deals with “flat” files @relation heart-disease-simplified @attribute age numeric @attribute sex { female, male} @attribute chest_pain_type { typ_angina, asympt, non_anginal, atyp_angina} @attribute cholesterol numeric @attribute exercise_induced_angina { no, yes} @attribute class { present, not_present} @data 63,male,typ_angina,233,no,not_present 67,male,asympt,286,yes,present 67,male,asympt,229,yes,present 38,female,non_anginal,?,no,not_present ... 12/05/12 University of Waikato 9
  • 10. WEKA only deals with “flat” files @relation heart-disease-simplified @attribute age numeric @attribute sex { female, male} @attribute chest_pain_type { typ_angina, asympt, non_anginal, atyp_angina} @attribute cholesterol numeric @attribute exercise_induced_angina { no, yes} @attribute class { present, not_present} @data 63,male,typ_angina,233,no,not_present 67,male,asympt,286,yes,present 67,male,asympt,229,yes,present 38,female,non_anginal,?,no,not_present ... 12/05/12 University of Waikato 10
  • 11. java weka.gui.GUIChooser 12/05/12 University of Waikato 11
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  • 14. java -jar weka.jar 12/05/12 University of Waikato 14
  • 15. Explorer: pre-processing the data  Data can be imported from a file in various formats: ARFF, CSV, C4.5, binary  Data can also be read from a URL or from an SQL database (using JDBC)  Pre-processing tools in WEKA are called “filters”  WEKA contains filters for:  Discretization, normalization, resampling, attribute selection, transforming and combining attributes, … 12/05/12 University of Waikato 15
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  • 37. Explorer: building “classifiers”  Classifiers in WEKA are models for predicting nominal or numeric quantities  Implemented learning schemes include:  Decision trees and lists, instance-based classifiers, support vector machines, multi-layer perceptrons, logistic regression, Bayes’ nets, …  “Meta”-classifiers include:  Bagging, boosting, stacking, error-correcting output codes, locally weighted learning, … 12/05/12 University of Waikato 37
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  • 72. 12/05/12 QuickTime™ and a T IFF (LZW) decompressor are needed to see this picture. University of Waikato 72
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  • 78. Qui c k Ti m e ™ a nd a TIFF (LZW) d ec om pre s s o r a re n e ed e d to s e e th i s p i c tu re . 12/05/12 University of Waikato 78
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  • 93. Explorer: clustering data  WEKA contains “clusterers” for finding groups of similar instances in a dataset  Some implemented schemes are:  k-Means, EM, Cobweb, X-means, FarthestFirst  Clusters can be visualized and compared to “true” clusters (if given)  Evaluation based on loglikelihood if clustering scheme produces a probability distribution 12/05/12 University of Waikato 93
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  • 103. Explorer: finding associations  WEKA contains the Apriori algorithm (among others) for learning association rules  Works only with discrete data  Can identify statistical dependencies between groups of attributes:  milk, butter ⇒ bread, eggs (with confidence 0.9 and support 2000)  Apriori can compute all rules that have a given minimum support and exceed a given confidence 12/05/12 University of Waikato 103
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  • 107. Explorer: attribute selection  Panel that can be used to investigate which (subsets of) attributes are the most predictive ones  Attribute selection methods contain two parts:  A search method: best-first, forward selection, random, exhaustive, genetic algorithm, ranking  An evaluation method: correlation-based, wrapper, information gain, chi-squared, …  Very flexible: WEKA allows (almost) arbitrary combinations of these two 12/05/12 University of Waikato 107
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  • 114. Explorer: data visualization  Visualization very useful in practice: e.g. helps to determine difficulty of the learning problem  WEKA can visualize single attributes (1-d) and pairs of attributes (2-d)  To do: rotating 3-d visualizations (Xgobi-style)  Color-coded class values  “Jitter” option to deal with nominal attributes (and to detect “hidden” data points)  “Zoom-in” function 12/05/12 University of Waikato 114
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  • 125. Performing experiments  Experimenter makes it easy to compare the performance of different learning schemes  For classification and regression problems  Results can be written into file or database  Evaluation options: cross-validation, learning curve, hold-out  Can also iterate over different parameter settings  Significance-testing built in! 12/05/12 University of Waikato 125
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  • 136. The Knowledge Flow GUI  Java-Beans-based interface for setting up and running machine learning experiments  Data sources, classifiers, etc. are beans and can be connected graphically  Data “flows” through components: e.g., “data source” -> “filter” -> “classifier” -> “evaluator”  Layouts can be saved and loaded again later  cf. Clementine ™ 12/05/12 University of Waikato 136
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  • 152. Sourceforge.net – Downloads 12/05/12 University of Waikato 152
  • 153. Sourceforge.net – Web Traffic WekaDoc Wiki introduced – 12/2005 WekaWiki launched – 05/2005 12/05/12 University of Waikato 153
  • 154. Projects based on WEKA  45 projects currently (30/01/07) listed on the WekaWiki  Incorporate/wrap WEKA  GRB Tool Shed - a tool to aid gamma ray burst research  YALE - facility for large scale ML experiments  GATE - NLP workbench with a WEKA interface  Judge - document clustering and classification  RWeka - an R interface to Weka  Extend/modify WEKA  BioWeka - extension library for knowledge discovery in biology  WekaMetal - meta learning extension to WEKA  Weka-Parallel - parallel processing for W EKA  Grid Weka - grid computing using WEKA  Weka-CG - computational genetics tool library 12/05/12 University of Waikato 154
  • 155. WEKA and PENTAHO  Pentaho – The leader in Open Source Business Intelligence (BI)  September 2006 – Pentaho acquires the Weka project (exclusive license and SF.net page)  Weka will be used/integrated as data mining component in their BI suite  Weka will be still available as GPL open source software  Most likely to evolve 2 editions:  Community edition  BI oriented edition 12/05/12 University of Waikato 155
  • 156. Limitations of WEKA  Traditional algorithms need to have all data in main memory  ==> big datasets are an issue  Solution:  Incremental schemes  Stream algorithms MOA “Massive Online Analysis” (not only a flightless bird, but also extinct!) 12/05/12 University of Waikato 156
  • 157. Conclusion: try it yourself!  WEKA is available at http://www.cs.waikato.ac.nz/ml/weka  Also has a list of projects based on WEKA  (probably incomplete list of) WEKA contributors: Abdelaziz Mahoui, Alexander K. Seewald, Ashraf M. Kibriya, Bernhard Pfahringer, Brent Martin, Peter Flach, Eibe Frank, Gabi Schmidberger, Ian H. Witten, J. Lindgren, Janice Boughton, Jason Wells, Len Trigg, Lucio de Souza Coelho, Malcolm Ware, Mark Hall, Remco Bouckaert, Richard Kirkby, Shane Butler, Shane Legg, Stuart Inglis, Sylvain Roy, Tony Voyle, Xin Xu, Yong Wang, Zhihai Wang 12/05/12 University of Waikato 157