Today

• 6 hours ago

  ImplementedAlgorithms (A list of the currently implemented and supported algorithms...) Wiki page edited by David.Jurgens   -   Revision r707 Added ISA and ESA to the list

  Revision r707 Added ISA and ESA to the list

Yesterday

• 32 hours ago

  r706 (M test/edu/ucla/sspace/vector/VectorsTest.java - Add a ...) committed by FozzietheBeat   -   M test/edu/ucla/sspace/vector/VectorsTest.java - Add a simple test for integer copyOf for generics M src/edu/ucla/sspace/hermit/FlyingHermit.java - fix some null pointer exceptions - change the saved split senses to generic vectors M src/edu/ucla/sspace/vector/Vectors.java - fix some javadoc - fix a copyOf bug when copying a view vector.

  M test/edu/ucla/sspace/vector/VectorsTest.java - Add a simple test for integer copyOf for generics M src/edu/ucla/sspace/hermit/FlyingHermit.java - fix some null pointer exceptions - change the saved split senses to generic vectors M src/edu/ucla/sspace/vector/Vectors.java - fix some javadoc - fix a copyOf bug when copying a view vector.
• 38 hours ago

  RelevantPublications (A listing of relevant publications to the algorithms impleme...) Wiki page added by David.Jurgens   -   Revision r705 Created wiki page through web user interface.

  Revision r705 Created wiki page through web user interface.
• 38 hours ago

  ImplementedAlgorithms (A list of the currently implemented and supported algorithms...) Wiki page added by David.Jurgens   -   Revision r704 Created wiki page through web user interface.

  Revision r704 Created wiki page through web user interface.

Last 7 days

• Dec 11, 2009

  r703 (Added more unit tests, fixed bugs and added equals() M t...) committed by David.Jurgens   -   Added more unit tests, fixed bugs and added equals() M test/edu/ucla/sspace/vector/VectorsTest.java - Added unit tests for basic subview functionality M src/edu/ucla/sspace/vector/Vectors.java - Added overloaded equals() methods for comparing vectors M src/edu/ucla/sspace/vector/VectorView.java - Fixed bug where the offset was subtracted, rather than added

  Added more unit tests, fixed bugs and added equals() M test/edu/ucla/sspace/vector/VectorsTest.java - Added unit tests for basic subview functionality M src/edu/ucla/sspace/vector/Vectors.java - Added overloaded equals() methods for comparing vectors M src/edu/ucla/sspace/vector/VectorView.java - Fixed bug where the offset was subtracted, rather than added
• Dec 11, 2009

  r702 (M vector/VectorMath.java - remove debug output ) committed by FozzietheBeat   -   M vector/VectorMath.java - remove debug output

  M vector/VectorMath.java - remove debug output
• Dec 11, 2009

  r701 (M test/edu/ucla/sspace/vector/VectorsTest.java - add te...) committed by FozzietheBeat   -   M test/edu/ucla/sspace/vector/VectorsTest.java - add test cases for copyOf A test/edu/ucla/sspace/vector/VectorMathTest.java - add test cases for both addition functions M src/edu/ucla/sspace/hermit/FlyingHermit.java - Changed to use a hash integer vector M src/edu/ucla/sspace/vector/VectorMath.java - Update bugs found in unit tests M src/edu/ucla/sspace/vector/Vectors.java - Update bugs found in unit tests M build.xml - Added a comment block for ignoring test caes.

  M test/edu/ucla/sspace/vector/VectorsTest.java - add test cases for copyOf A test/edu/ucla/sspace/vector/VectorMathTest.java - add test cases for both addition functions M src/edu/ucla/sspace/hermit/FlyingHermit.java - Changed to use a hash integer vector M src/edu/ucla/sspace/vector/VectorMath.java - Update bugs found in unit tests M src/edu/ucla/sspace/vector/Vectors.java - Update bugs found in unit tests M build.xml - Added a comment block for ignoring test caes.
• Dec 10, 2009

  r700 (M src/edu/ucla/sspace/tools/WikipediaCleaner.java - add...) committed by FozzietheBeat   -   M src/edu/ucla/sspace/tools/WikipediaCleaner.java - add in use of the pre processor

  M src/edu/ucla/sspace/tools/WikipediaCleaner.java - add in use of the pre processor
• Dec 10, 2009

  r699 (M src/edu/ucla/sspace/tools/WikipediaCleaner.java - han...) committed by FozzietheBeat   -   M src/edu/ucla/sspace/tools/WikipediaCleaner.java - handle the case where {{ is used as part of a latex equation. wiki tags after this may not be handled properly.

  M src/edu/ucla/sspace/tools/WikipediaCleaner.java - handle the case where {{ is used as part of a latex equation. wiki tags after this may not be handled properly.
• Dec 10, 2009

  r698 (M tools/WikipediaCleaner.java - maybe fix for wiki clea...) committed by FozzietheBeat   -   M tools/WikipediaCleaner.java - maybe fix for wiki cleaner?

  M tools/WikipediaCleaner.java - maybe fix for wiki cleaner?
• Dec 10, 2009

  r697 (Updates to Vectors API, bug fixes M test/edu/ucla/sspace...) committed by David.Jurgens   -   Updates to Vectors API, bug fixes M test/edu/ucla/sspace/vector/VectorsTest.java M test/edu/ucla/sspace/common/SimilarityTest.java M src/edu/ucla/sspace/index/IntegerVectorGeneratorMap.java - SparseIntVector -> CompactSparseIntegerVector M src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java M src/edu/ucla/sspace/beagle/Beagle.java M src/edu/ucla/sspace/hermit/FlyingHermit.java M src/edu/ucla/sspace/common/CachingOnDiskSemanticSpace.java M src/edu/ucla/sspace/coals/Coals.java M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java M src/edu/ucla/sspace/matrix/SparseMatrix.java M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java - Use new Vectors API A src/edu/ucla/sspace/vector/SparseDoubleVector.java A src/edu/ucla/sspace/vector/SparseIntegerVector.java - Added new interfaces that combine the sparse interface with type-specific vectors. D src/edu/ucla/sspace/vector/SparseIntVector.java A + src/edu/ucla/sspace/vector/CompactSparseIntegerVector.java - Renamed to mirror the Double classes and to avoid confusion with the SIV interface - Updated to implement SparseIntegerVector A src/edu/ucla/sspace/vector/IntegerVectorView.java - Added a view for IntegerVector instances to support overloaded immutable() and subview() methods M src/edu/ucla/sspace/vector/Vectors.java - Renamed methods to be consistent with the current version on the trunk - Added NullPointerExceptions back - overloaded immutable() and subview() methods with IntegerVector equivalents M src/edu/ucla/sspace/vector/SparseHashIntegerVector.java - Updated to implement SparseIntegerVector

  Updates to Vectors API, bug fixes M test/edu/ucla/sspace/vector/VectorsTest.java M test/edu/ucla/sspace/common/SimilarityTest.java M src/edu/ucla/sspace/index/IntegerVectorGeneratorMap.java - SparseIntVector -> CompactSparseIntegerVector M src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java M src/edu/ucla/sspace/beagle/Beagle.java M src/edu/ucla/sspace/hermit/FlyingHermit.java M src/edu/ucla/sspace/common/CachingOnDiskSemanticSpace.java M src/edu/ucla/sspace/coals/Coals.java M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java M src/edu/ucla/sspace/matrix/SparseMatrix.java M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java - Use new Vectors API A src/edu/ucla/sspace/vector/SparseDoubleVector.java A src/edu/ucla/sspace/vector/SparseIntegerVector.java - Added new interfaces that combine the sparse interface with type-specific vectors. D src/edu/ucla/sspace/vector/SparseIntVector.java A + src/edu/ucla/sspace/vector/CompactSparseIntegerVector.java - Renamed to mirror the Double classes and to avoid confusion with the SIV interface - Updated to implement SparseIntegerVector A src/edu/ucla/sspace/vector/IntegerVectorView.java - Added a view for IntegerVector instances to support overloaded immutable() and subview() methods M src/edu/ucla/sspace/vector/Vectors.java - Renamed methods to be consistent with the current version on the trunk - Added NullPointerExceptions back - overloaded immutable() and subview() methods with IntegerVector equivalents M src/edu/ucla/sspace/vector/SparseHashIntegerVector.java - Updated to implement SparseIntegerVector
• Dec 10, 2009

  r696 (M test/edu/ucla/sspace/common/SimilarityTest.java - add...) committed by FozzietheBeat   -   M test/edu/ucla/sspace/common/SimilarityTest.java - adding a simple test case for cosinesimilarity, currently it crashes

  M test/edu/ucla/sspace/common/SimilarityTest.java - adding a simple test case for cosinesimilarity, currently it crashes
• Dec 10, 2009

  r695 (M index-fix/src/edu/ucla/sspace/vector/SparseIntVector.ja...) committed by FozzietheBeat   -   M index-fix/src/edu/ucla/sspace/vector/SparseIntVector.java - Fix the javadoc to be more accurate M index-fix/src/edu/ucla/sspace/mains/FlyingHermitMain.java - fix command line arguments to be correct

  M index-fix/src/edu/ucla/sspace/vector/SparseIntVector.java - Fix the javadoc to be more accurate M index-fix/src/edu/ucla/sspace/mains/FlyingHermitMain.java - fix command line arguments to be correct

Last 30 days

• Dec 08, 2009

  r694 (-- Merging the VectorMath changes in the trunk to the branch...) committed by FozzietheBeat   -   -- Merging the VectorMath changes in the trunk to the branch M src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java - Updated to use VectorMath _M src/edu/ucla/sspace/beagle M src/edu/ucla/sspace/beagle/Beagle.java - Updated to use VectorMath M src/edu/ucla/sspace/hermit/FlyingHermit.java - Updated to use VectorMath -- Below this line are changes merged from the trunk. _M src/edu/ucla/sspace/vector _M src/edu/ucla/sspace/vector/AmortizedSparseVector.java _M src/edu/ucla/sspace/vector/Vector.java A + src/edu/ucla/sspace/vector/VectorMath.java _M src/edu/ucla/sspace/vector/SparseVector.java _M src/edu/ucla/sspace/vector/DenseVector.java MM src/edu/ucla/sspace/vector/Vectors.java _M src/edu/ucla/sspace/vector/CompactSparseVector.java _M src/edu/ucla/sspace/vector/VectorIO.java _M src/edu/ucla/sspace/matrix _M src/edu/ucla/sspace/matrix/AtomicMatrix.java M src/edu/ucla/sspace/matrix/Matrix.java _M src/edu/ucla/sspace/matrix/OnDiskMatrix.java M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java M src/edu/ucla/sspace/matrix/SparseMatrix.java

  -- Merging the VectorMath changes in the trunk to the branch M src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java - Updated to use VectorMath _M src/edu/ucla/sspace/beagle M src/edu/ucla/sspace/beagle/Beagle.java - Updated to use VectorMath M src/edu/ucla/sspace/hermit/FlyingHermit.java - Updated to use VectorMath -- Below this line are changes merged from the trunk. _M src/edu/ucla/sspace/vector _M src/edu/ucla/sspace/vector/AmortizedSparseVector.java _M src/edu/ucla/sspace/vector/Vector.java A + src/edu/ucla/sspace/vector/VectorMath.java _M src/edu/ucla/sspace/vector/SparseVector.java _M src/edu/ucla/sspace/vector/DenseVector.java MM src/edu/ucla/sspace/vector/Vectors.java _M src/edu/ucla/sspace/vector/CompactSparseVector.java _M src/edu/ucla/sspace/vector/VectorIO.java _M src/edu/ucla/sspace/matrix _M src/edu/ucla/sspace/matrix/AtomicMatrix.java M src/edu/ucla/sspace/matrix/Matrix.java _M src/edu/ucla/sspace/matrix/OnDiskMatrix.java M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java M src/edu/ucla/sspace/matrix/SparseMatrix.java
• Dec 08, 2009

  r693 (Address some Change list comments and add java doc M sr...) committed by FozzietheBeat   -   Address some Change list comments and add java doc M src/edu/ucla/sspace/beagle/Beagle.java - fix a name in a private beagle function - improve the java doc for the same function M src/edu/ucla/sspace/clustering/ClusterMap.java - Add javadoc. D src/edu/ucla/sspace/clustering/Cluster.java - removed and moved into OnlineKMeansClustering. M src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java - Add javadoc. - Moved Cluster code as private class. M src/edu/ucla/sspace/clustering/OnlineClustering.java - Add javadoc. M src/edu/ucla/sspace/clustering/OnlineClusteringGenerator.java - Add javadoc. M src/edu/ucla/sspace/common/Similarity.java - Fixed a call to toArray M src/edu/ucla/sspace/vector/Vectors.java - Changed FixedTernaryVector to TernaryVector based on david's updates D src/edu/ucla/sspace/vector/FixedTernaryVector.java - Removed M src/edu/ucla/sspace/index/DoubleVectorGeneratorMap.java - Add javadoc. M src/edu/ucla/sspace/index/RandomIndexVectorGenerator.java - Add javadoc. M src/edu/ucla/sspace/index/DefaultPermutationFunction.java - Updated to function over generic Vectors - Has a special case for TernaryVectors - Slightly optimized for SparseVectors - Add javadoc. M src/edu/ucla/sspace/index/GaussianVectorGenerator.java - Add javadoc. M src/edu/ucla/sspace/index/IntegerVectorGeneratorMap.java - Add javadoc. M src/edu/ucla/sspace/index/PermutationFunction.java - Updated to function over generic Vectors - Add javadoc. M src/edu/ucla/sspace/index/WindowedPermutationFunction.java - Updated to function over generic Vectors - Add javadoc.

  Address some Change list comments and add java doc M src/edu/ucla/sspace/beagle/Beagle.java - fix a name in a private beagle function - improve the java doc for the same function M src/edu/ucla/sspace/clustering/ClusterMap.java - Add javadoc. D src/edu/ucla/sspace/clustering/Cluster.java - removed and moved into OnlineKMeansClustering. M src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java - Add javadoc. - Moved Cluster code as private class. M src/edu/ucla/sspace/clustering/OnlineClustering.java - Add javadoc. M src/edu/ucla/sspace/clustering/OnlineClusteringGenerator.java - Add javadoc. M src/edu/ucla/sspace/common/Similarity.java - Fixed a call to toArray M src/edu/ucla/sspace/vector/Vectors.java - Changed FixedTernaryVector to TernaryVector based on david's updates D src/edu/ucla/sspace/vector/FixedTernaryVector.java - Removed M src/edu/ucla/sspace/index/DoubleVectorGeneratorMap.java - Add javadoc. M src/edu/ucla/sspace/index/RandomIndexVectorGenerator.java - Add javadoc. M src/edu/ucla/sspace/index/DefaultPermutationFunction.java - Updated to function over generic Vectors - Has a special case for TernaryVectors - Slightly optimized for SparseVectors - Add javadoc. M src/edu/ucla/sspace/index/GaussianVectorGenerator.java - Add javadoc. M src/edu/ucla/sspace/index/IntegerVectorGeneratorMap.java - Add javadoc. M src/edu/ucla/sspace/index/PermutationFunction.java - Updated to function over generic Vectors - Add javadoc. M src/edu/ucla/sspace/index/WindowedPermutationFunction.java - Updated to function over generic Vectors - Add javadoc.
• Dec 08, 2009

  r692 (fixed compilation bug) committed by David.Jurgens   -   fixed compilation bug

  fixed compilation bug
• Dec 08, 2009

  r691 (Major updates to the vector package to clean up the javadoc ...) committed by David.Jurgens   -   Major updates to the vector package to clean up the javadoc and view classes M src/edu/ucla/sspace/vector/AtomicVector.java - Clarified javadoc - Updated to use new DoubleVector API M src/edu/ucla/sspace/vector/ViewVectorAsDoubleVector.java - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/TernaryVector.java - Changed from class to interface - Fixed bug where input indices may not have been in sorted order D src/edu/ucla/sspace/vector/ViewDoubleAsDoubleVector.java A + src/edu/ucla/sspace/vector/DoubleVectorView.java - Renamed for easier comprehension - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/ScaledVector.java - Updated to use new DoubleVector API - Clarified javadoc. This class still need more description of how the values are affected by scaling M src/edu/ucla/sspace/vector/SparseHashVector.java - Made into a generic Number vector, rather than a DoubleVector A src/edu/ucla/sspace/vector/SparseHashIntegerVector.java A src/edu/ucla/sspace/vector/SparseHashDoubleVector.java - Added type-specific subclasses of SparseHashVector M src/edu/ucla/sspace/vector/ViewDoubleAsDoubleSparseVector.java - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/Vectors.java - Removed support for TernaryVector operation on DoubleVectors - Added support for wrapping arrays with Vector instances - Made the atomic and synchronized vector methods return DoubleVector types rather than the actual class doing the work - Added support for getting an empty Vector instance of the same type as the vector argument D src/edu/ucla/sspace/vector/ViewIntAsDoubleVector.java A + src/edu/ucla/sspace/vector/IntAsDoubleVector.java - Renamed for added clarity - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/CompactSparseVector.java - Updated to use new DoubleVector API - Removed knownLength behavior; vector now always has a fixed length M src/edu/ucla/sspace/vector/DenseIntVector.java - Added additional javadoc - Updated to use new IntegerVector API M src/edu/ucla/sspace/vector/SparseScaledVector.java - Updated to use new DoubleVector API - Updated constructor to use more precise generics M src/edu/ucla/sspace/vector/AmortizedSparseVector.java - Updated to use new DoubleVector API A src/edu/ucla/sspace/vector/IntArrayAsVector.java A src/edu/ucla/sspace/vector/DoubleArrayAsVector.java - Added wrapper classes that Vectors are backed by arrays M src/edu/ucla/sspace/vector/SynchronizedVector.java - Updated to use new DoubleVector API D src/edu/ucla/sspace/vector/ViewIntAsDoubleSparseVector.java A + src/edu/ucla/sspace/vector/IntAsSparseDoubleVector.java - Updated to use new DoubleVector API - Renamed to for clarity - Improve subclassing re-use D src/edu/ucla/sspace/vector/ViewAbstractDoubleVector.java A + src/edu/ucla/sspace/vector/VectorView.java - Renamed and made into a generic Vector<Number> baseclass - Added support for type-specific subclasses to extend the functionality M src/edu/ucla/sspace/vector/IntegerVector.java - Clarified the javadoc - Removed the set(int[]) method - Removed the size parameter from the toArray() method - Added a type-specific overload of the getValue() method M src/edu/ucla/sspace/vector/SparseVector.java - Now extends Vector - Clarified javadoc M src/edu/ucla/sspace/vector/DenseVector.java - Updated to use new DoubleVector API - Constructor now copies the values from any double[] argument, rather than just wrapping them M src/edu/ucla/sspace/vector/FixedTernaryVector.java - Updated to use new IntegerVector API - No longer impements the now-gone TernaryVector interface - This class needs to be removed M src/edu/ucla/sspace/vector/SparseIntVector.java - Updated to use new IntegerVector API - Addded javadoc M src/edu/ucla/sspace/vector/DoubleVector.java - Clarified the javadoc - Removed the set(double[]) method - Removed the size parameter from the toArray() method - Added a type-specific overload of the getValue() method M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java M src/edu/ucla/sspace/matrix/SparseMatrix.java M src/edu/ucla/sspace/matrix/SparseOnDiskMatrix.java M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java M src/edu/ucla/sspace/mains/FixedDurationTemporalRandomIndexingMain.java M src/edu/ucla/sspace/common/Similarity.java - Updated to use new DoubleVector API M src/edu/ucla/sspace/common/SemanticSpace.java - Clarified javadoc on calling conventions M build.xml A test/edu/ucla/sspace/vector A test/edu/ucla/sspace/vector/VectorsTest.java - Added the start of unit tests for the Vectors class M test/edu/ucla/sspace/util/SparseDoubleArrayTests.java - Fixed javadoc typo

  Major updates to the vector package to clean up the javadoc and view classes M src/edu/ucla/sspace/vector/AtomicVector.java - Clarified javadoc - Updated to use new DoubleVector API M src/edu/ucla/sspace/vector/ViewVectorAsDoubleVector.java - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/TernaryVector.java - Changed from class to interface - Fixed bug where input indices may not have been in sorted order D src/edu/ucla/sspace/vector/ViewDoubleAsDoubleVector.java A + src/edu/ucla/sspace/vector/DoubleVectorView.java - Renamed for easier comprehension - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/ScaledVector.java - Updated to use new DoubleVector API - Clarified javadoc. This class still need more description of how the values are affected by scaling M src/edu/ucla/sspace/vector/SparseHashVector.java - Made into a generic Number vector, rather than a DoubleVector A src/edu/ucla/sspace/vector/SparseHashIntegerVector.java A src/edu/ucla/sspace/vector/SparseHashDoubleVector.java - Added type-specific subclasses of SparseHashVector M src/edu/ucla/sspace/vector/ViewDoubleAsDoubleSparseVector.java - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/Vectors.java - Removed support for TernaryVector operation on DoubleVectors - Added support for wrapping arrays with Vector instances - Made the atomic and synchronized vector methods return DoubleVector types rather than the actual class doing the work - Added support for getting an empty Vector instance of the same type as the vector argument D src/edu/ucla/sspace/vector/ViewIntAsDoubleVector.java A + src/edu/ucla/sspace/vector/IntAsDoubleVector.java - Renamed for added clarity - Clarified javadoc - Updated to use new DoubleVector API - Updated with new subclassing to remove redundant code M src/edu/ucla/sspace/vector/CompactSparseVector.java - Updated to use new DoubleVector API - Removed knownLength behavior; vector now always has a fixed length M src/edu/ucla/sspace/vector/DenseIntVector.java - Added additional javadoc - Updated to use new IntegerVector API M src/edu/ucla/sspace/vector/SparseScaledVector.java - Updated to use new DoubleVector API - Updated constructor to use more precise generics M src/edu/ucla/sspace/vector/AmortizedSparseVector.java - Updated to use new DoubleVector API A src/edu/ucla/sspace/vector/IntArrayAsVector.java A src/edu/ucla/sspace/vector/DoubleArrayAsVector.java - Added wrapper classes that Vectors are backed by arrays M src/edu/ucla/sspace/vector/SynchronizedVector.java - Updated to use new DoubleVector API D src/edu/ucla/sspace/vector/ViewIntAsDoubleSparseVector.java A + src/edu/ucla/sspace/vector/IntAsSparseDoubleVector.java - Updated to use new DoubleVector API - Renamed to for clarity - Improve subclassing re-use D src/edu/ucla/sspace/vector/ViewAbstractDoubleVector.java A + src/edu/ucla/sspace/vector/VectorView.java - Renamed and made into a generic Vector<Number> baseclass - Added support for type-specific subclasses to extend the functionality M src/edu/ucla/sspace/vector/IntegerVector.java - Clarified the javadoc - Removed the set(int[]) method - Removed the size parameter from the toArray() method - Added a type-specific overload of the getValue() method M src/edu/ucla/sspace/vector/SparseVector.java - Now extends Vector - Clarified javadoc M src/edu/ucla/sspace/vector/DenseVector.java - Updated to use new DoubleVector API - Constructor now copies the values from any double[] argument, rather than just wrapping them M src/edu/ucla/sspace/vector/FixedTernaryVector.java - Updated to use new IntegerVector API - No longer impements the now-gone TernaryVector interface - This class needs to be removed M src/edu/ucla/sspace/vector/SparseIntVector.java - Updated to use new IntegerVector API - Addded javadoc M src/edu/ucla/sspace/vector/DoubleVector.java - Clarified the javadoc - Removed the set(double[]) method - Removed the size parameter from the toArray() method - Added a type-specific overload of the getValue() method M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java M src/edu/ucla/sspace/matrix/SparseMatrix.java M src/edu/ucla/sspace/matrix/SparseOnDiskMatrix.java M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java M src/edu/ucla/sspace/mains/FixedDurationTemporalRandomIndexingMain.java M src/edu/ucla/sspace/common/Similarity.java - Updated to use new DoubleVector API M src/edu/ucla/sspace/common/SemanticSpace.java - Clarified javadoc on calling conventions M build.xml A test/edu/ucla/sspace/vector A test/edu/ucla/sspace/vector/VectorsTest.java - Added the start of unit tests for the Vectors class M test/edu/ucla/sspace/util/SparseDoubleArrayTests.java - Fixed javadoc typo
• Dec 07, 2009

  r690 (Fixed more spelling error) committed by David.Jurgens   -   Fixed more spelling error

  Fixed more spelling error
• Dec 07, 2009

  r689 (Fixed spelling error) committed by David.Jurgens   -   Fixed spelling error

  Fixed spelling error
• Dec 07, 2009

  PurandareAndPedersen (Overview of the Purandare and Pedersen context-clustering se...) Wiki page added by David.Jurgens   -   Revision r688 Created wiki page through web user interface.

  Revision r688 Created wiki page through web user interface.
• Dec 07, 2009

  PurandareAndPetersen Wiki page deleted by David.Jurgens   -   Revision r687 Deleting wiki page PurandareAndPetersen.

  Revision r687 Deleting wiki page PurandareAndPetersen.
• Dec 07, 2009

  issue 37 (Addition of Purandare & Petersen S-Space, Vector refactoring...) Status changed by David.Jurgens   -   Set review issue status to: Done

  Status: Done

  Set review issue status to: Done

  Status: Done
• Dec 06, 2009

  issue 38 (Vector and index reformulation) reported by FozzietheBeat   -   Purpose of code changes on this branch: - Allow for optimizations for vectors holding double and integer values. Vector is now a generic interface of Number, whereas most current Vector implementations are just a DoubleVector. New vectors are IntegerVectors for use in RI based sspaces. - A new interface for vector generation and permutations. There is also a map interface which allows for the automation of index vector generation based on use of a vector generator. When reviewing my code changes, please focus on: Possible implications of current design Lack of clear JavaDoc Please focus on the vector and index packages. Others either have minor changes based on these updates, or, like the clustering package, are not quite finished being documented. After the review, I'll merge this branch into: /trunk But first i'll reformulate the RI based code to use the updates checked here.

  Purpose of code changes on this branch: - Allow for optimizations for vectors holding double and integer values. Vector is now a generic interface of Number, whereas most current Vector implementations are just a DoubleVector. New vectors are IntegerVectors for use in RI based sspaces. - A new interface for vector generation and permutations. There is also a map interface which allows for the automation of index vector generation based on use of a vector generator. When reviewing my code changes, please focus on: Possible implications of current design Lack of clear JavaDoc Please focus on the vector and index packages. Others either have minor changes based on these updates, or, like the clustering package, are not quite finished being documented. After the review, I'll merge this branch into: /trunk But first i'll reformulate the RI based code to use the updates checked here.
• Dec 06, 2009

  r686 (A src/edu/ucla/sspace/clustering/ClusterMap.java - A cl...) committed by FozzietheBeat   -   A src/edu/ucla/sspace/clustering/ClusterMap.java - A cluster map that maps strings to online clustering instances. A src/edu/ucla/sspace/clustering/OnlineClustering.java - An interface for online clustering implementations A src/edu/ucla/sspace/clustering/OnlineClusteringGenerator.java - A generator for on line clustering. D src/edu/ucla/sspace/hermit/HermitRedux.java - removed D src/edu/ucla/sspace/hermit/HierarchicalAgglomerativeClustering.java - removed A src/edu/ucla/sspace/vector/ViewVectorAsDoubleVector.java A src/edu/ucla/sspace/vector/ViewIntAsDoubleSparseVector.java A src/edu/ucla/sspace/vector/ViewAbstractDoubleVector.java A src/edu/ucla/sspace/vector/ViewDoubleAsDoubleSparseVector.java A src/edu/ucla/sspace/vector/ViewIntAsDoubleVector.java - new views for vectors, casting them up to double vectors A src/edu/ucla/sspace/vector/Vector.java - new interface for all vectors A src/edu/ucla/sspace/vector/IntegerVector.java - Basic interface for all integer based vectors A src/edu/ucla/sspace/vector/FixedTernaryVector.java - a fixed ternary vector

  A src/edu/ucla/sspace/clustering/ClusterMap.java - A cluster map that maps strings to online clustering instances. A src/edu/ucla/sspace/clustering/OnlineClustering.java - An interface for online clustering implementations A src/edu/ucla/sspace/clustering/OnlineClusteringGenerator.java - A generator for on line clustering. D src/edu/ucla/sspace/hermit/HermitRedux.java - removed D src/edu/ucla/sspace/hermit/HierarchicalAgglomerativeClustering.java - removed A src/edu/ucla/sspace/vector/ViewVectorAsDoubleVector.java A src/edu/ucla/sspace/vector/ViewIntAsDoubleSparseVector.java A src/edu/ucla/sspace/vector/ViewAbstractDoubleVector.java A src/edu/ucla/sspace/vector/ViewDoubleAsDoubleSparseVector.java A src/edu/ucla/sspace/vector/ViewIntAsDoubleVector.java - new views for vectors, casting them up to double vectors A src/edu/ucla/sspace/vector/Vector.java - new interface for all vectors A src/edu/ucla/sspace/vector/IntegerVector.java - Basic interface for all integer based vectors A src/edu/ucla/sspace/vector/FixedTernaryVector.java - a fixed ternary vector
• Dec 06, 2009

  r685 (Major fixes: - Reformulate the Vector package. - Add ...) committed by FozzietheBeat   -   Major fixes: - Reformulate the Vector package. - Add a IntegerVector and DoubleVector - Vector is now a basic generic interface. - SemanticSpace returns a Vector - Clean up the Clustering package - Clean up the index package. D term_results.py - Remove the eval script. AM + src/edu/ucla/sspace/clustering/Cluster.java - Move cluster package to clustering. A + src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java - Move cluster package to clustering. - Added a single online clustering implementation. D src/edu/ucla/sspace/clustering/HierarchicalAgglomerativeClustering.java - Move cluster package to clustering. - Removed from davids update. D src/edu/ucla/sspace/clustering/ClutoClustering.java - Move cluster package to clustering. - Removed from davids update. M src/edu/ucla/sspace/fft/FastFourierTransform.java - Update to take in the vector updates M src/edu/ucla/sspace/beagle/Beagle.java - Include all the beagle convolution code D src/edu/ucla/sspace/purandare - removed from davids update D src/edu/ucla/sspace/cluster - moved to clustering M src/edu/ucla/sspace/temporal/FileBasedTemporalSemanticSpace.java - update based on vector changes. M src/edu/ucla/sspace/temporal/TemporalSemanticSpaceUtils.java - update based on vector changes. M src/edu/ucla/sspace/common/SemanticSpaceIO.java - update based on vector changes. M src/edu/ucla/sspace/common/Similarity.java - update based on vector changes. D src/edu/ucla/sspace/common/DocumentSpace.java - Removed M src/edu/ucla/sspace/hermit/FlyingHermit.java - update based on vector changes. - update based on clusteirng changes - update based on index changes. D src/edu/ucla/sspace/hermit/BottomUpHermit.java - removed D src/edu/ucla/sspace/hermit/SecondOrderFlyingHermit.java - removed D src/edu/ucla/sspace/hermit/NonFlyingHermit.java - removed M src/edu/ucla/sspace/vector/AtomicVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/AmortizedSparseVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SynchronizedVector.java - update based on vector changes. D src/edu/ucla/sspace/vector/Vector.java - update based on vector changes. - Now is a generic interface of numbers AM + src/edu/ucla/sspace/vector/ViewDoubleAsDoubleVector.java - Created a new view decorator for doubles. AM + src/edu/ucla/sspace/vector/TernaryVector.java - now a raw interface. M src/edu/ucla/sspace/vector/ScaledVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SparseVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/DenseVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SparseHashVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/Vectors.java - math operations are now efficiently implemented for both Double and Integer vectors. - update based on vector changes. M src/edu/ucla/sspace/vector/CompactSparseVector.java - update based on vector changes. D src/edu/ucla/sspace/vector/IndexVector.java - Changed to TernaryVector M src/edu/ucla/sspace/vector/VectorIO.java - update based on vector changes. AM + src/edu/ucla/sspace/vector/SparseIntVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SparseScaledVector.java - update based on vector changes. AM + src/edu/ucla/sspace/vector/DenseIntVector.java - update based on vector changes. D src/edu/ucla/sspace/vector/ViewVector.java - Moved to a variety of View instances. A + src/edu/ucla/sspace/vector/DoubleVector.java - update based on vector changes. M src/edu/ucla/sspace/matrix/ArrayMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/DiagonalMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/Matrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SynchronizedMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SvdlibcSparseBinaryMatrixBuilder.java - update based on vector changes. M src/edu/ucla/sspace/matrix/NoTransform.java - update based on vector changes. M src/edu/ucla/sspace/matrix/MatlabSparseMatrixBuilder.java - update based on vector changes. M src/edu/ucla/sspace/matrix/Transform.java - update based on vector changes. M src/edu/ucla/sspace/matrix/MatrixBuilder.java - update based on vector changes. M src/edu/ucla/sspace/matrix/OnDiskMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/RowMaskedMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SparseMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/TfIdfTransform.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SparseOnDiskMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/MatrixIO.java - update based on vector changes. M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/LogEntropyTransform.java - update based on vector changes. M src/edu/ucla/sspace/mains/FixedDurationTemporalRandomIndexingMain.java - update based on vector changes. D src/edu/ucla/sspace/mains/HermitReduxMain.java - removed from davids branch AM + src/edu/ucla/sspace/mains/FlyingHermitMain.java - update based on vector changes. M src/edu/ucla/sspace/mains/BeagleMain.java - update based on vector changes. D src/edu/ucla/sspace/mains/PurandareMain.java - removed from davids branch D src/edu/ucla/sspace/mains/HermitMain.java - removed AM + src/edu/ucla/sspace/index/RandomIndexVectorGenerator.java - updated based on index generator changes. A src/edu/ucla/sspace/index/DoubleVectorGeneratorMap.java - A new generator map for double vector generators. A src/edu/ucla/sspace/index/DoubleVectorGenerator.java - A new generator interface double vector. AM + src/edu/ucla/sspace/index/GaussianVectorGenerator.java - Replaces BeagleIndexGenerator D src/edu/ucla/sspace/index/IndexUser.java - removed D src/edu/ucla/sspace/index/BeagleIndexUser.java - Removed, code moved into Beagle.java D src/edu/ucla/sspace/index/RandomIndexUser.java - Removed, code is now just use of permutation functions and vector operations. D src/edu/ucla/sspace/index/SparseRandomIndexVector.java - moved to SparseIntVector D src/edu/ucla/sspace/index/DenseRandomIndexVector.java - moved to DenseIntVector M src/edu/ucla/sspace/index/PermutationFunction.java - updated based on vector updates. D src/edu/ucla/sspace/index/IndexGenerator.java - Removed D src/edu/ucla/sspace/index/BeagleIndexGenerator.java - Removed - now GaussianVectorGenerator M src/edu/ucla/sspace/index/WindowedPermutationFunction.java D src/edu/ucla/sspace/index/RandomIndexGenerator.java - Moved to RandomIndexVectorGenerator M src/edu/ucla/sspace/index/DefaultPermutationFunction.java - updated based on vector updates. A src/edu/ucla/sspace/index/IntegerVectorGeneratorMap.java - new map for storing and generating integer vectors AM + src/edu/ucla/sspace/index/IntegerVectorGenerator.java - new interface for generating integer vectors M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java - updated based on vector updates. D display.py - removed D hermit_result.py - removed M build.xml - should be reverted

  Major fixes: - Reformulate the Vector package. - Add a IntegerVector and DoubleVector - Vector is now a basic generic interface. - SemanticSpace returns a Vector - Clean up the Clustering package - Clean up the index package. D term_results.py - Remove the eval script. AM + src/edu/ucla/sspace/clustering/Cluster.java - Move cluster package to clustering. A + src/edu/ucla/sspace/clustering/OnlineKMeansClustering.java - Move cluster package to clustering. - Added a single online clustering implementation. D src/edu/ucla/sspace/clustering/HierarchicalAgglomerativeClustering.java - Move cluster package to clustering. - Removed from davids update. D src/edu/ucla/sspace/clustering/ClutoClustering.java - Move cluster package to clustering. - Removed from davids update. M src/edu/ucla/sspace/fft/FastFourierTransform.java - Update to take in the vector updates M src/edu/ucla/sspace/beagle/Beagle.java - Include all the beagle convolution code D src/edu/ucla/sspace/purandare - removed from davids update D src/edu/ucla/sspace/cluster - moved to clustering M src/edu/ucla/sspace/temporal/FileBasedTemporalSemanticSpace.java - update based on vector changes. M src/edu/ucla/sspace/temporal/TemporalSemanticSpaceUtils.java - update based on vector changes. M src/edu/ucla/sspace/common/SemanticSpaceIO.java - update based on vector changes. M src/edu/ucla/sspace/common/Similarity.java - update based on vector changes. D src/edu/ucla/sspace/common/DocumentSpace.java - Removed M src/edu/ucla/sspace/hermit/FlyingHermit.java - update based on vector changes. - update based on clusteirng changes - update based on index changes. D src/edu/ucla/sspace/hermit/BottomUpHermit.java - removed D src/edu/ucla/sspace/hermit/SecondOrderFlyingHermit.java - removed D src/edu/ucla/sspace/hermit/NonFlyingHermit.java - removed M src/edu/ucla/sspace/vector/AtomicVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/AmortizedSparseVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SynchronizedVector.java - update based on vector changes. D src/edu/ucla/sspace/vector/Vector.java - update based on vector changes. - Now is a generic interface of numbers AM + src/edu/ucla/sspace/vector/ViewDoubleAsDoubleVector.java - Created a new view decorator for doubles. AM + src/edu/ucla/sspace/vector/TernaryVector.java - now a raw interface. M src/edu/ucla/sspace/vector/ScaledVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SparseVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/DenseVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SparseHashVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/Vectors.java - math operations are now efficiently implemented for both Double and Integer vectors. - update based on vector changes. M src/edu/ucla/sspace/vector/CompactSparseVector.java - update based on vector changes. D src/edu/ucla/sspace/vector/IndexVector.java - Changed to TernaryVector M src/edu/ucla/sspace/vector/VectorIO.java - update based on vector changes. AM + src/edu/ucla/sspace/vector/SparseIntVector.java - update based on vector changes. M src/edu/ucla/sspace/vector/SparseScaledVector.java - update based on vector changes. AM + src/edu/ucla/sspace/vector/DenseIntVector.java - update based on vector changes. D src/edu/ucla/sspace/vector/ViewVector.java - Moved to a variety of View instances. A + src/edu/ucla/sspace/vector/DoubleVector.java - update based on vector changes. M src/edu/ucla/sspace/matrix/ArrayMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/DiagonalMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/Matrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SynchronizedMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SvdlibcSparseBinaryMatrixBuilder.java - update based on vector changes. M src/edu/ucla/sspace/matrix/NoTransform.java - update based on vector changes. M src/edu/ucla/sspace/matrix/MatlabSparseMatrixBuilder.java - update based on vector changes. M src/edu/ucla/sspace/matrix/Transform.java - update based on vector changes. M src/edu/ucla/sspace/matrix/MatrixBuilder.java - update based on vector changes. M src/edu/ucla/sspace/matrix/OnDiskMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/RowMaskedMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SparseMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/TfIdfTransform.java - update based on vector changes. M src/edu/ucla/sspace/matrix/SparseOnDiskMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/MatrixIO.java - update based on vector changes. M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java - update based on vector changes. M src/edu/ucla/sspace/matrix/LogEntropyTransform.java - update based on vector changes. M src/edu/ucla/sspace/mains/FixedDurationTemporalRandomIndexingMain.java - update based on vector changes. D src/edu/ucla/sspace/mains/HermitReduxMain.java - removed from davids branch AM + src/edu/ucla/sspace/mains/FlyingHermitMain.java - update based on vector changes. M src/edu/ucla/sspace/mains/BeagleMain.java - update based on vector changes. D src/edu/ucla/sspace/mains/PurandareMain.java - removed from davids branch D src/edu/ucla/sspace/mains/HermitMain.java - removed AM + src/edu/ucla/sspace/index/RandomIndexVectorGenerator.java - updated based on index generator changes. A src/edu/ucla/sspace/index/DoubleVectorGeneratorMap.java - A new generator map for double vector generators. A src/edu/ucla/sspace/index/DoubleVectorGenerator.java - A new generator interface double vector. AM + src/edu/ucla/sspace/index/GaussianVectorGenerator.java - Replaces BeagleIndexGenerator D src/edu/ucla/sspace/index/IndexUser.java - removed D src/edu/ucla/sspace/index/BeagleIndexUser.java - Removed, code moved into Beagle.java D src/edu/ucla/sspace/index/RandomIndexUser.java - Removed, code is now just use of permutation functions and vector operations. D src/edu/ucla/sspace/index/SparseRandomIndexVector.java - moved to SparseIntVector D src/edu/ucla/sspace/index/DenseRandomIndexVector.java - moved to DenseIntVector M src/edu/ucla/sspace/index/PermutationFunction.java - updated based on vector updates. D src/edu/ucla/sspace/index/IndexGenerator.java - Removed D src/edu/ucla/sspace/index/BeagleIndexGenerator.java - Removed - now GaussianVectorGenerator M src/edu/ucla/sspace/index/WindowedPermutationFunction.java D src/edu/ucla/sspace/index/RandomIndexGenerator.java - Moved to RandomIndexVectorGenerator M src/edu/ucla/sspace/index/DefaultPermutationFunction.java - updated based on vector updates. A src/edu/ucla/sspace/index/IntegerVectorGeneratorMap.java - new map for storing and generating integer vectors AM + src/edu/ucla/sspace/index/IntegerVectorGenerator.java - new interface for generating integer vectors M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java - updated based on vector updates. D display.py - removed D hermit_result.py - removed M build.xml - should be reverted
• Dec 05, 2009

  r684 (Major features: 1) Addition of the Purandare & Petersen s-s...) committed by David.Jurgens   -   Major features: 1) Addition of the Purandare & Petersen s-space 2) Addition of two clustering algorithms (with support for Cluto) 3) Refatoring of Vectors into Vectors and VectorMath 4) New Matrix formats and minor improvements 5) OnDiskMatrix now uses memory mapped file backing; added support for a SparseOnDiskMatrix Details: A + src/edu/ucla/sspace/clustering - Added package for clustering algorithms A + src/edu/ucla/sspace/clustering/HierarchicalAgglomerativeClustering.java - Added native Java implementation of HA Clustering A + src/edu/ucla/sspace/clustering/ClutoClustering.java - Added support for HA clustering using the Cluto library A + src/edu/ucla/sspace/purandare A + src/edu/ucla/sspace/purandare/PurandareFirstOrder.java - Added new semantic space based on Purandare and Petersen's context clustering algorithm MM src/edu/ucla/sspace/common/Similarity.java - Added optimized case for computing the cosine similarity on sparse vectors M src/edu/ucla/sspace/vector/SparseHashVector.java M src/edu/ucla/sspace/util/SparseHashArray.java - Now implements Serializable MM src/edu/ucla/sspace/vector/Vectors.java A + src/edu/ucla/sspace/vector/VectorMath.java - Split arithmetic operations out of Vectors into new VectorMath class - Cleaned up decorator methods in Vectors to be more succinct and have more stringent error conditions - Added more argument checking for VectorMath operations M src/edu/ucla/sspace/matrix/Matrix.java - Added javadoc comment regarding the nature of Vector types returned by methods M src/edu/ucla/sspace/matrix/SvdlibcSparseBinaryMatrixBuilder.java M src/edu/ucla/sspace/matrix/MatlabSparseMatrixBuilder.java - Added support for transposing the matrices as they are built, which lets users build one row at a time, versus one column at a time M src/edu/ucla/sspace/matrix/Matrices.java - Added support for getting a matrix builder that transposes the data MM src/edu/ucla/sspace/matrix/OnDiskMatrix.java - Major overhaul to use memory-mapped files internally rather than one giant RandomAccessFile. This should be a large performance increase. A + src/edu/ucla/sspace/matrix/SparseOnDiskMatrix.java - Added a sparse wrapper around OnDiskMatrix that returns SparseVector instances for its methods M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - Updated with new constructor that sets an initial size for the matrix - Updated to use a sparse internal row mapping, which saves space and increases efficiency. A + src/edu/ucla/sspace/matrix/RowMaskedMatrix.java - Added a new Matrix that allows selected rows of an input matrix to be combined together as a contiguous Matrix. This allows users to take a subset of a potentially large matrix and operate on it without having to copy the data into a new smaller matrix. M src/edu/ucla/sspace/matrix/SparseMatrix.java - Now uses Vectors API M src/edu/ucla/sspace/matrix/MatrixIO.java - Added partial support for the CLUTO matrix formats M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java - Fixed bug where getRowVector() would return null if the row did not exist A + src/edu/ucla/sspace/mains/PurandareMain.java - Added an initial Main class for running the Purandare and Petersen code M src/edu/ucla/sspace/ri/DefaultPermutationFunction.java - Fixed race condition A + src/edu/ucla/sspace/util/WorkerThread.java - Added new support class for continuously running work Runnables from a shared queue MM build.xml - Removed missing unit tests - Added support for Hermit and Purandare & Petersen executable jar - Moved destination for -lib and -src jars to the lib/ directory, instead of bin/ M src/edu/ucla/sspace/beagle/Beagle.java M src/edu/ucla/sspace/beagle/BeagleIndexBuilder.java M src/edu/ucla/sspace/common/CachingOnDiskSemanticSpace.java M src/edu/ucla/sspace/common/DocumentVectorBuilder.java M src/edu/ucla/sspace/hermit/FlyingHermit.java M src/edu/ucla/sspace/coals/Coals.java M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java MM src/edu/ucla/sspace/ri/RandomIndexing.java - Updated to use new Vectors and VectorMath API M src/edu/ucla/sspace/lsa/LatentSemanticAnalysis.java - Fixed indentation MM src/edu/ucla/sspace/common/OnDiskSemanticSpace.java - Adjusted formatting

  Major features: 1) Addition of the Purandare & Petersen s-space 2) Addition of two clustering algorithms (with support for Cluto) 3) Refatoring of Vectors into Vectors and VectorMath 4) New Matrix formats and minor improvements 5) OnDiskMatrix now uses memory mapped file backing; added support for a SparseOnDiskMatrix Details: A + src/edu/ucla/sspace/clustering - Added package for clustering algorithms A + src/edu/ucla/sspace/clustering/HierarchicalAgglomerativeClustering.java - Added native Java implementation of HA Clustering A + src/edu/ucla/sspace/clustering/ClutoClustering.java - Added support for HA clustering using the Cluto library A + src/edu/ucla/sspace/purandare A + src/edu/ucla/sspace/purandare/PurandareFirstOrder.java - Added new semantic space based on Purandare and Petersen's context clustering algorithm MM src/edu/ucla/sspace/common/Similarity.java - Added optimized case for computing the cosine similarity on sparse vectors M src/edu/ucla/sspace/vector/SparseHashVector.java M src/edu/ucla/sspace/util/SparseHashArray.java - Now implements Serializable MM src/edu/ucla/sspace/vector/Vectors.java A + src/edu/ucla/sspace/vector/VectorMath.java - Split arithmetic operations out of Vectors into new VectorMath class - Cleaned up decorator methods in Vectors to be more succinct and have more stringent error conditions - Added more argument checking for VectorMath operations M src/edu/ucla/sspace/matrix/Matrix.java - Added javadoc comment regarding the nature of Vector types returned by methods M src/edu/ucla/sspace/matrix/SvdlibcSparseBinaryMatrixBuilder.java M src/edu/ucla/sspace/matrix/MatlabSparseMatrixBuilder.java - Added support for transposing the matrices as they are built, which lets users build one row at a time, versus one column at a time M src/edu/ucla/sspace/matrix/Matrices.java - Added support for getting a matrix builder that transposes the data MM src/edu/ucla/sspace/matrix/OnDiskMatrix.java - Major overhaul to use memory-mapped files internally rather than one giant RandomAccessFile. This should be a large performance increase. A + src/edu/ucla/sspace/matrix/SparseOnDiskMatrix.java - Added a sparse wrapper around OnDiskMatrix that returns SparseVector instances for its methods M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - Updated with new constructor that sets an initial size for the matrix - Updated to use a sparse internal row mapping, which saves space and increases efficiency. A + src/edu/ucla/sspace/matrix/RowMaskedMatrix.java - Added a new Matrix that allows selected rows of an input matrix to be combined together as a contiguous Matrix. This allows users to take a subset of a potentially large matrix and operate on it without having to copy the data into a new smaller matrix. M src/edu/ucla/sspace/matrix/SparseMatrix.java - Now uses Vectors API M src/edu/ucla/sspace/matrix/MatrixIO.java - Added partial support for the CLUTO matrix formats M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java - Fixed bug where getRowVector() would return null if the row did not exist A + src/edu/ucla/sspace/mains/PurandareMain.java - Added an initial Main class for running the Purandare and Petersen code M src/edu/ucla/sspace/ri/DefaultPermutationFunction.java - Fixed race condition A + src/edu/ucla/sspace/util/WorkerThread.java - Added new support class for continuously running work Runnables from a shared queue MM build.xml - Removed missing unit tests - Added support for Hermit and Purandare & Petersen executable jar - Moved destination for -lib and -src jars to the lib/ directory, instead of bin/ M src/edu/ucla/sspace/beagle/Beagle.java M src/edu/ucla/sspace/beagle/BeagleIndexBuilder.java M src/edu/ucla/sspace/common/CachingOnDiskSemanticSpace.java M src/edu/ucla/sspace/common/DocumentVectorBuilder.java M src/edu/ucla/sspace/hermit/FlyingHermit.java M src/edu/ucla/sspace/coals/Coals.java M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java MM src/edu/ucla/sspace/ri/RandomIndexing.java - Updated to use new Vectors and VectorMath API M src/edu/ucla/sspace/lsa/LatentSemanticAnalysis.java - Fixed indentation MM src/edu/ucla/sspace/common/OnDiskSemanticSpace.java - Adjusted formatting
• Dec 04, 2009

  r683 (Updates based on code review M src/edu/ucla/sspace/clust...) committed by David.Jurgens   -   Updates based on code review M src/edu/ucla/sspace/clustering/HierarchicalAgglomerativeClustering.java - Cleaned up errors in javadoc M src/edu/ucla/sspace/clustering/ClutoClustering.java - Clustering no longer throws an IOException but instead now throws an IOError - Modified clustering name to be more specific - Wrapped internal calls with a generic interface so future extensions can easily support Cluto's additional functionality - Updated logging to be verbose rather than info, which it should have been originally M src/edu/ucla/sspace/purandare/PurandareFirstOrder.java - Updated to use SparseMatrix instead of GrowingSparseMatrix - Updated to use new ClutoClustering API M src/edu/ucla/sspace/vector/Vectors.java - Updated copy with a SparseVector optimization A src/edu/ucla/sspace/vector/VectorMath.java - Added missing VectorMath class M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - Moved copying code into Vectors.java M src/edu/ucla/sspace/matrix/SparseMatrix.java - Replaced copying code with call to Vectors.copy M src/edu/ucla/sspace/mains/PurandareMain.java - Fixed typo - Removed class-level javadoc in favor of referring to the wiki page on the clss M src/edu/ucla/sspace/ri/DefaultPermutationFunction.java - Fixed possible race condition

  Updates based on code review M src/edu/ucla/sspace/clustering/HierarchicalAgglomerativeClustering.java - Cleaned up errors in javadoc M src/edu/ucla/sspace/clustering/ClutoClustering.java - Clustering no longer throws an IOException but instead now throws an IOError - Modified clustering name to be more specific - Wrapped internal calls with a generic interface so future extensions can easily support Cluto's additional functionality - Updated logging to be verbose rather than info, which it should have been originally M src/edu/ucla/sspace/purandare/PurandareFirstOrder.java - Updated to use SparseMatrix instead of GrowingSparseMatrix - Updated to use new ClutoClustering API M src/edu/ucla/sspace/vector/Vectors.java - Updated copy with a SparseVector optimization A src/edu/ucla/sspace/vector/VectorMath.java - Added missing VectorMath class M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - Moved copying code into Vectors.java M src/edu/ucla/sspace/matrix/SparseMatrix.java - Replaced copying code with call to Vectors.copy M src/edu/ucla/sspace/mains/PurandareMain.java - Fixed typo - Removed class-level javadoc in favor of referring to the wiki page on the clss M src/edu/ucla/sspace/ri/DefaultPermutationFunction.java - Fixed possible race condition
• Dec 04, 2009

  PurandareAndPetersen (An overview of the Purandare and Petersen context clustering...) Wiki page added by David.Jurgens   -   Revision r682 Created wiki page through web user interface.

  Revision r682 Created wiki page through web user interface.
• Dec 03, 2009

  issue 37 (Addition of Purandare & Petersen S-Space, Vector refactoring...) Status changed by FozzietheBeat   -   Set review issue status to: Started

  Status: Started

  Set review issue status to: Started

  Status: Started
• Dec 03, 2009

  issue 37 (Addition of Purandare & Petersen S-Space, Vector refactoring...) reported by David.Jurgens   -   Purpose of code changes on this branch: Three major updates: 1. Addition of Purandare & Petersen S-Space code 2. Initial refactoring of the Vectors class (VectorMath) 3. Addition of HAC and Cluto Clustering classes When reviewing my code changes, please focus on: 1. The P&P class is big, but should be reasonable clear to follow. Please let me know if some parts seem unusual or could be improved. 2. If I am missing any updates/improvements to other Matrix classes based on the changes to the Vectors class. 3. Whether we could standardize the API for the clustering classes. This might be solved with a package-level javadoc, or just by convention. At this time, I'm still against creating an interface, given the variety of APIs we expect. 4. P&P uses some bigram statistics. Eventually, I'd like to fold these in to a separate utility. We have that Bigram-extractor code, which isn't included. Ideally, there should be something for dealing with n-way contingency tables, but at the moment, I only have code for 2-way (i.e. bigram) tables. If you think we might want to fold this in now, or at least start the refactoring let me know. Otherwise, we can do it in a separate merge. 5. Ignore any hermit-related classes. These won't be included in the merge. After the review, I'll merge this branch into: /trunk

  Purpose of code changes on this branch: Three major updates: 1. Addition of Purandare & Petersen S-Space code 2. Initial refactoring of the Vectors class (VectorMath) 3. Addition of HAC and Cluto Clustering classes When reviewing my code changes, please focus on: 1. The P&P class is big, but should be reasonable clear to follow. Please let me know if some parts seem unusual or could be improved. 2. If I am missing any updates/improvements to other Matrix classes based on the changes to the Vectors class. 3. Whether we could standardize the API for the clustering classes. This might be solved with a package-level javadoc, or just by convention. At this time, I'm still against creating an interface, given the variety of APIs we expect. 4. P&P uses some bigram statistics. Eventually, I'd like to fold these in to a separate utility. We have that Bigram-extractor code, which isn't included. Ideally, there should be something for dealing with n-way contingency tables, but at the moment, I only have code for 2-way (i.e. bigram) tables. If you think we might want to fold this in now, or at least start the refactoring let me know. Otherwise, we can do it in a separate merge. 5. Ignore any hermit-related classes. These won't be included in the merge. After the review, I'll merge this branch into: /trunk
• Dec 03, 2009

  r681 (Fixes to P&P and slight refactoring of Vector-related code ...) committed by David.Jurgens   -   Fixes to P&P and slight refactoring of Vector-related code M src/edu/ucla/sspace/purandare/PurandareFirstOrder.java - Prespecified the size context matrix which ensure that the vector addition will work when building the sense vectors. M src/edu/ucla/sspace/vector/Vectors.java - Factored out vector addition into separate class. This provides a cleaner separation of functionality when future vector arithmetic operations are added - Cleaned up javadoc - Improved API through more informative error conditions. NullPointer and IllegalArgument exceptions are now thrown in expected cases M src/edu/ucla/sspace/vector/ViewVector.java - Cleaned up the javadoc to reflect the current package-private purpose of the class M src/edu/ucla/sspace/matrix/Matrix.java - Added comments to the get*Vector() methods to reflect that instances should specify whether the vector represents a snapshot or a view of the matrix's data. M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - Added new constructor that allows the user to specify the initial size of the empty matrix. This allows the get*Vector() operations to return a uniform size as the matrix is being build. - Updated the rows to be managed through a sparse mapping, rather than to hold a giant list of possibly empty rows. This also improves access time when setting a large row value M src/edu/ucla/sspace/matrix/SparseMatrix.java M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java M src/edu/ucla/sspace/beagle/Beagle.java M src/edu/ucla/sspace/beagle/BeagleIndexBuilder.java M src/edu/ucla/sspace/common/CachingOnDiskSemanticSpace.java M src/edu/ucla/sspace/hermit/FlyingHermit.java M src/edu/ucla/sspace/coals/Coals.java M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java M src/edu/ucla/sspace/ri/RandomIndexing.java - Updates to use new Vector and VectorMath API M build.xml - Removed call to non-existent unit test

  Fixes to P&P and slight refactoring of Vector-related code M src/edu/ucla/sspace/purandare/PurandareFirstOrder.java - Prespecified the size context matrix which ensure that the vector addition will work when building the sense vectors. M src/edu/ucla/sspace/vector/Vectors.java - Factored out vector addition into separate class. This provides a cleaner separation of functionality when future vector arithmetic operations are added - Cleaned up javadoc - Improved API through more informative error conditions. NullPointer and IllegalArgument exceptions are now thrown in expected cases M src/edu/ucla/sspace/vector/ViewVector.java - Cleaned up the javadoc to reflect the current package-private purpose of the class M src/edu/ucla/sspace/matrix/Matrix.java - Added comments to the get*Vector() methods to reflect that instances should specify whether the vector represents a snapshot or a view of the matrix's data. M src/edu/ucla/sspace/matrix/GrowingSparseMatrix.java - Added new constructor that allows the user to specify the initial size of the empty matrix. This allows the get*Vector() operations to return a uniform size as the matrix is being build. - Updated the rows to be managed through a sparse mapping, rather than to hold a giant list of possibly empty rows. This also improves access time when setting a large row value M src/edu/ucla/sspace/matrix/SparseMatrix.java M src/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java M src/edu/ucla/sspace/beagle/Beagle.java M src/edu/ucla/sspace/beagle/BeagleIndexBuilder.java M src/edu/ucla/sspace/common/CachingOnDiskSemanticSpace.java M src/edu/ucla/sspace/hermit/FlyingHermit.java M src/edu/ucla/sspace/coals/Coals.java M src/edu/ucla/sspace/esa/ExplicitSemanticAnalysis.java M src/edu/ucla/sspace/ri/RandomIndexing.java - Updates to use new Vector and VectorMath API M build.xml - Removed call to non-existent unit test
• Dec 02, 2009

  r680 (M index/DefaultPermutationFunction.java - Clean up the ...) committed by FozzietheBeat   -   M index/DefaultPermutationFunction.java - Clean up the default perm setup. - Use an array of Functons instead of a map. - Clean up some comments. M index/PermutationFunction.java - Update the javadoc to be more descriptive. D index/BeagleIndexBuilder.java - Removed! M index/WindowedPermutationFunction.java - Update the javadoc.

  M index/DefaultPermutationFunction.java - Clean up the default perm setup. - Use an array of Functons instead of a map. - Clean up some comments. M index/PermutationFunction.java - Update the javadoc to be more descriptive. D index/BeagleIndexBuilder.java - Removed! M index/WindowedPermutationFunction.java - Update the javadoc.
• Dec 01, 2009

  r679 (Remove the index builder and fix any classes which make refe...) committed by FozzietheBeat   -   Remove the index builder and fix any classes which make reference to it. M sspace/beagle/Beagle.java - Replace the old beagle with the new version using generators and users. D sspace/beagle/BeagleAlt.java - Removed. Content replaces Beagle.java D sspace/hermit/Hermit.java - Removed. M sspace/mains/BeagleMain.java - Modified to use the new version of Beagle. D sspace/index/RandomIndexBuilder.java - Removed M sspace/index/BeagleIndexUser.java - remove an extra newline D sspace/index/IndexBuilder.java - Remove the index builder

  Remove the index builder and fix any classes which make reference to it. M sspace/beagle/Beagle.java - Replace the old beagle with the new version using generators and users. D sspace/beagle/BeagleAlt.java - Removed. Content replaces Beagle.java D sspace/hermit/Hermit.java - Removed. M sspace/mains/BeagleMain.java - Modified to use the new version of Beagle. D sspace/index/RandomIndexBuilder.java - Removed M sspace/index/BeagleIndexUser.java - remove an extra newline D sspace/index/IndexBuilder.java - Remove the index builder
• Dec 01, 2009

  r678 (M src/edu/ucla/sspace/hermit/FlyingHermit.java M hermi...) committed by FozzietheBeat   -   M src/edu/ucla/sspace/hermit/FlyingHermit.java M hermit_result.py - fix the use of mfs

  M src/edu/ucla/sspace/hermit/FlyingHermit.java M hermit_result.py - fix the use of mfs
• Dec 01, 2009

  r677 (M hermit_result.py - add correct mfs computation ) committed by FozzietheBeat   -   M hermit_result.py - add correct mfs computation

  M hermit_result.py - add correct mfs computation
• Nov 30, 2009

  r676 (M hermit_result.py - fix a second bug ) committed by FozzietheBeat   -   M hermit_result.py - fix a second bug

  M hermit_result.py - fix a second bug
• Nov 30, 2009

  r675 (M hermit_result.py - fix a parsing bug ) committed by FozzietheBeat   -   M hermit_result.py - fix a parsing bug

  M hermit_result.py - fix a parsing bug
• Nov 30, 2009

  r674 (M term_results.py - name files based on input given on ...) committed by FozzietheBeat   -   M term_results.py - name files based on input given on the command line M src/edu/ucla/sspace/hermit/FlyingHermit.java - compute accuracy counts and apply labels to clusters M hermit_result.py - take into account cluster titles when computing gained accuracy

  M term_results.py - name files based on input given on the command line M src/edu/ucla/sspace/hermit/FlyingHermit.java - compute accuracy counts and apply labels to clusters M hermit_result.py - take into account cluster titles when computing gained accuracy
• Nov 29, 2009

  r673 (D index-fix/run_hermit.sh - remove the test script ) committed by FozzietheBeat   -   D index-fix/run_hermit.sh - remove the test script

  D index-fix/run_hermit.sh - remove the test script
• Nov 29, 2009

  r672 (M src/edu/ucla/sspace/hermit/FlyingHermit.java - remove...) committed by FozzietheBeat   -   M src/edu/ucla/sspace/hermit/FlyingHermit.java - remove test output

  M src/edu/ucla/sspace/hermit/FlyingHermit.java - remove test output
• Nov 29, 2009

  r671 (M index-fix/run_hermit.sh M index-fix/src/edu/ucla/ssp...) committed by FozzietheBeat   -   M index-fix/run_hermit.sh M index-fix/src/edu/ucla/sspace/hermit/FlyingHermit.java - clean a few uneeded things out M index-fix/src/edu/ucla/sspace/mains/HermitMain.java - auto specify the format used.

  M index-fix/run_hermit.sh M index-fix/src/edu/ucla/sspace/hermit/FlyingHermit.java - clean a few uneeded things out M index-fix/src/edu/ucla/sspace/mains/HermitMain.java - auto specify the format used.
• Nov 29, 2009

  r670 (M term_results.py M run_hermit.sh M display.py - ...) committed by FozzietheBeat   -   M term_results.py M run_hermit.sh M display.py - update the run scripts a bit to be cleaner

  M term_results.py M run_hermit.sh M display.py - update the run scripts a bit to be cleaner
• Nov 29, 2009

  r669 (M src/edu/ucla/sspace/cluster/ExemplarVectorClusterMap.ja...) committed by FozzietheBeat   -   M src/edu/ucla/sspace/cluster/ExemplarVectorClusterMap.java M src/edu/ucla/sspace/cluster/BottomUpVectorClusterMap.java M src/edu/ucla/sspace/cluster/SimpleVectorClusterMap.java - add a method to see where a context would be assigned. M src/edu/ucla/sspace/hermit/FlyingHermit.java - Add suport for a train test split M src/edu/ucla/sspace/mains/HermitMain.java - Add suport for a train test split

  M src/edu/ucla/sspace/cluster/ExemplarVectorClusterMap.java M src/edu/ucla/sspace/cluster/BottomUpVectorClusterMap.java M src/edu/ucla/sspace/cluster/SimpleVectorClusterMap.java - add a method to see where a context would be assigned. M src/edu/ucla/sspace/hermit/FlyingHermit.java - Add suport for a train test split M src/edu/ucla/sspace/mains/HermitMain.java - Add suport for a train test split
• Nov 26, 2009

  r668 (updated to fix the vector access methods. Currently include...) committed by David.Jurgens   -   updated to fix the vector access methods. Currently includes a hack to dump the co-occurrence matrix

  updated to fix the vector access methods. Currently includes a hack to dump the co-occurrence matrix
• Nov 25, 2009

  r667 (A index/WindowedPermutationFunction.java - add a window...) committed by FozzietheBeat   -   A index/WindowedPermutationFunction.java - add a windowed permutation function

  A index/WindowedPermutationFunction.java - add a windowed permutation function
• Nov 25, 2009

  r666 (M run_hermit.sh - Add cleaner runs - Add argument sup...) committed by FozzietheBeat   -   M run_hermit.sh - Add cleaner runs - Add argument support for different permutation functions M src/edu/ucla/sspace/mains/HermitMain.java - Add argument support for different permutation functions M src/edu/ucla/sspace/index/RandomIndexUser.java - Add dynamic loading of permutation functions M display.py - make display cooler M hermit_result.py - fix up the result maker to trim spaces.

  M run_hermit.sh - Add cleaner runs - Add argument support for different permutation functions M src/edu/ucla/sspace/mains/HermitMain.java - Add argument support for different permutation functions M src/edu/ucla/sspace/index/RandomIndexUser.java - Add dynamic loading of permutation functions M display.py - make display cooler M hermit_result.py - fix up the result maker to trim spaces.
• Nov 24, 2009

  r665 (Merging code from the hermit-redux branch ) committed by FozzietheBeat   -   Merging code from the hermit-redux branch

  Merging code from the hermit-redux branch
• Nov 24, 2009

  r664 (M term_results.py - fix a bug in generating a term grap...) committed by FozzietheBeat   -   M term_results.py - fix a bug in generating a term graph. - sort the terms based on their baseline score. M src/edu/ucla/sspace/cluster/SimpleVectorClusterMap.java - rewrite the drop method, but leave it commented out. M src/edu/ucla/sspace/hermit/FlyingHermit.java - Add support for dropping clusters.

  M term_results.py - fix a bug in generating a term graph. - sort the terms based on their baseline score. M src/edu/ucla/sspace/cluster/SimpleVectorClusterMap.java - rewrite the drop method, but leave it commented out. M src/edu/ucla/sspace/hermit/FlyingHermit.java - Add support for dropping clusters.
• Nov 23, 2009

  r663 (fixed bug where the cluto logging from stdout wasn't being p...) committed by David.Jurgens   -   fixed bug where the cluto logging from stdout wasn't being properly recorded

  fixed bug where the cluto logging from stdout wasn't being properly recorded
• Nov 23, 2009

  r662 (fixed bug where CLUTO no-cluster -1 indices around cause an ...) committed by David.Jurgens   -   fixed bug where CLUTO no-cluster -1 indices around cause an index out of bounds exception

  fixed bug where CLUTO no-cluster -1 indices around cause an index out of bounds exception