JAMA-based linear algebra routines replaced with MTJ. Faster operation with the option to use native libraries for even more speed
General efficiency improvements in core, filters and some classifiers
GaussianProcesses now handles instance weights
New Knowledge Flow implementation. Engine completely rewritten from scratch with a simplified API
New Workbench GUI
GUI package manager now has a search facility
FixedDictionaryStringToWordVector filter allows the use of an external dictionary for vectorization. DictionarySaver converter can be used to create a dictionary file
In packages
Packages that were using JAMA are now using MTJ
New netlibNativeOSX, netlibNativeWindows and netlibNativeLinux packages providing native reference implementations (and system-optimized implementation in the case of OSX) of BLAS, LAPACK and ARPACK linear algebra
New elasticNet package, courtesy of Nikhil Kinshore
New niftiLoader package for loading a directory with MIR data in NIfTI format into Weka
New percentageErrorMetrics package - provides plugin evaluation metrics for root mean square percentage error and mean absolute percentage error
New iterativeAbsoluteErrorRegression package - provides a meta learner that fits a regression model to minimize absolute error
New largeScaleKernelLearning package - contains filters for large-scale kernel-based learning
discriminantAnalysis package now contains an implementation for LDA and QDA
New Knowledge Flow component implementations in various packages
newKnowledgeFlowStepExamples package - contains code examples for new Knowledge Flow API discussion in the Weka Manual
RPlugin updated to latest version of MLR
scatterPlot3D and associationRulesVisualizer packages updated with latest Java 3D libraries
Support for pluggable activation functions in the multiLayerPerceptrons package