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bystrogenomics / bystro

Natural Language Search and Analysis of High Dimensional Genomic Data
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Batch Domain Adaptation #569

Closed austinTalbot7241993 closed 2 months ago

austinTalbot7241993 commented 2 months ago

This PR implements a novel method for domain adaptation when a single control sample is included in each batch. This is the univariate version only.

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago

Walkthrough

The changes introduce a new file batch_adaptation.py that implements domain adaptation techniques to correct for batch effects in data analysis. It features the BatchAdaptationUnivariate class, which includes methods for fitting a model to data and transforming new datasets. Additionally, a testing module is added in test_batch_adaptation.py to validate the functionality of the BatchAdaptationUnivariate class through simulated datasets and unit tests.

Changes

Files Change Summary
python/python/bystro/domain_adaptation/batch_adaptation.py Added batch_adaptation.py with sample_from_data_list function and BatchAdaptationUnivariate class, including methods for fitting and transforming data.
python/python/bystro/domain_adaptation/tests/test_batch_adaptation.py Introduced testing module with simulate_data function and test_univariate_adaptation for validating BatchAdaptationUnivariate.

Poem

In the land of data where rabbits play,
New tools for batches have come our way!
With means and variances, we hop and adjust,
Ensuring our results are fair and robust.
So let’s celebrate with a joyful cheer,
For clean data paths are finally here! 🐇✨

[!TIP]

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Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 946de28108272c9495f4a1fd86f81107a702f9b6 and 48ba6934c990ae8ee7300f85381705152e47b898.
Files selected for processing (1) * python/python/bystro/domain_adaptation/batch_adaptation.py (1 hunks)
Files skipped from review due to trivial changes (1) * python/python/bystro/domain_adaptation/batch_adaptation.py
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