BioDiscML-1.9

BioDiscML 1.9

Bug-fix release. Results differ from 1.8.14: metrics, the FB/BF searches and the random sampling were fixed. See "Changes in 1.9" in the readme for details.

Main changes

• Metrics. For a binary class, SEN, SPE, FPR, FNR, PPV, FDR, F-score and AUPRC are those of the positive class (new option positiveClass), not class-weighted averages: in 1.8.14, SEN was always equal to ACC. The .632+ bootstrap estimate is fixed, and averages ignore undefined (NaN) values.
• Search. FB and BF run their backward step again (they were identical to F and B since 1.8.12). maxNumberOfFeaturesInModel is enforced.
• Reproducibility. New option seed (default 1) for every random number generator. The short test no longer shuffles the shared training data. Repeated holdout and bootstrap samples are stratified.
• Parallel runs. Fixed race conditions that could make -bestmodel loop forever while writing details.txt, or garble the values written to the result files.
• -bestmodel. Models are sorted numerically, the thresholds are inclusive, the metric name is not case-sensitive, and one failing model no longer stops the others.
• -predict works for regression models.
• Input and config files. Validation columns are matched by name, instances without a class label are ignored, IDs of several input files are matched ignoring case, booleans accept yes/no, 1/0 and on/off, and unknown options are reported.
• Exit code. BioDiscML exits with code 1 when it fails, so that schedulers and pipelines see the failure.
• New -version option.

Download

BioDiscML-1.9.zip contains biodiscml.jar, config.conf, readme.md and LICENSE.txt. It requires Java 8.

BioDiscML-1.8.14

Added the support of a model that is not able to perform a prediction due to lack of information

BioDiscML-1.8.13

Improved dataset creation

BioDiscML-1.8.12

Fixed a few bugs

BioDiscML-1.8.11

fixed some bugs

BioDiscML-1.8.10

v1.8.10

increase random number

BioDiscML-1.8.9

Improved log
fix bugs and prediction on new data

BioDiscML-1.8.8

bug fixes
added some functions

BioDiscML-1.8.7

• Added second level of debug
• Fixed parsing options
• Option to print failed models

BioDiscML-1.8.6

fixed some bugs