filter out compounds from gene-gene relationship benchmark #100
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fedecomitani
approved these changes
May 27, 2025
kian-kd
reviewed
May 27, 2025
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "map_data_gene_only = map_data.query(\"perturbation_type == 'CRISPR'\") # only use CRISPR perturbations for gene-gene benchmarks\n", |
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may need to do .reset_index()after .query
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hmm good point. Should be fine, based on this line, but I'll double check -
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A few users have pointed out that compounds are included in the gene-gene recall metric. This PR filters compounds out of the dataframe before computing the
known_relationship_benchmarkThanks Luke Nightingale (@LukeOZN) for pointing this out!