Native MI estimators + minor fixes#48
Merged
Merged
Conversation
…e been replaced by validated python drop-ins
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
information.yamlconfiguration file.np.naninstead.jpype1and JIDT dependencies (see validation tests below) due to inefficiencies with the Python-Java interface. JIDT functions located inpyhctsa/toolboxes/infodynamics-disthave been replaced with native python ports.infotheorytoolbox inpyhctsa/toolboxescontaining the ported mutual information functions for the Gaussian, Kraskov1 and Kraskov2 estimators. Dropped kernel estimator as it was not used in the original hctsa feature set.requirements.txtandpyproject.tomlto reflect dropping ofjpype1dep.Validation of Gaussian, Kraskov1, and Kraskov2 MI estimators
To verify the consistency between the original JIDT-implemented estimators and the proposed native Python implementations, outputs for the three estimators (Gaussian, Kraskov1, Kraskov2) were compared on the empirical1000 dataset. For each of the 1000 time series instances, 264 features were computed across several master operations (which themselves rely on the mutual information estimators e.g., automutual_info_stats_*). Across the 264 features (spanning all three estimators), all were found to have pearson r ~ 1, and MAE at or below machine precision, confirming consistency between implementations.
Comparison between JIDT and native Python port results:
java_versus_javaless_results.csv
Raw results:
java_results.txt
javaless_results.txt