Allow subsetting TOL classifier #59
Open
Conversation
This file contains 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
Adds functions to TreeOfLifeClassifier to allow subsetting the embeddings. The get_label_data() method returns a dataframe of the labels for the TOL txt embeddings. The create_taxa_filter() method creates a filter (boolean array) for the txt embeddings based on a taxa and values. The apply_filter() method filters the classifier for a filter. The filter is a boolean array with the same length as the txt embeddings. Part of #56
egrace479
reviewed
Nov 12, 2024
Co-authored-by: Elizabeth Campolongo <[email protected]>
Co-authored-by: Elizabeth Campolongo <[email protected]>
|
Should there maybe be a disclaimer somewhere that incorrect training spellings for taxa may adversely affect the filter bevahior? This would impact the example in the notebook: |
|
I don't think we need a special disclaimer for that. Otherwise we'll also need disclaimers for all the synonyms etc that aren't properly consolidated to canonical name, etc. Those who want to understand the prediction in detail will invariably have to familiarize themselves with the paper and the data and processing code repositories. |
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Outdated suggestions cannot be applied.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.
Adds functions to TreeOfLifeClassifier to allow subsetting the embeddings. The get_label_data() method returns a dataframe of the labels for the TOL txt embeddings. The create_taxa_filter() method creates a filter (boolean array) for the txt embeddings based on a taxa and values. The apply_filter() method filters the classifier for a filter. The filter is a boolean array with the same length as the txt embeddings.
Part of #56