Undeprecate one constructor that's actually useful
Add command line to ParameterOptimizer
Update to Commons Compress 1.5
Fix handling of degenerate 1-dimension case
Better logging
Change default alpha to 1. Change handling of negative values -- now, negative values are reconstructed as "0" in the model, not "1", and with weight equal to the absolute value of the (negative) weight. Both changes will result in different behavior, though, the second only has effect in the unusual case of negative weights in the input. Both are observed to improve results on several data sets. This is still subject to change.
Update plugin versions