Notebooks for comparing chemical representations with morphological representations
make_parquets notebook is just for reference. The output are the following files:
#minimol: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/minimol_embeddings/minimol_embeddings__Kim_et_al_subset_final.parquet #minimol with BROAD MOA labels: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/minimol_embeddings/minimol_embeddings__Kim_et_al_subset_final_with_JUMPMOA.parquet #minimol cluster: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/minimol_embeddings/minimol_clusters.csv
#chemical checker sign2: gs://calico-reference-embeddings/embeddings/Chemical_Checker_Embeddings/parquets/JUMPCP_CC_Sign2_Global_Signatures.parquet #chemical checker sign3: gs://calico-reference-embeddings/embeddings/Chemical_Checker_Embeddings/parquets/JUMPCP_Sign3_CC_final.parquet #chemical checker sign3 clustered: gs://calico-reference-embeddings/Chemical_Checker_Embeddings/parquets/sign3_clusters.csv #chemical checker sign3 with MOA labels: gs://calico-reference-embeddings/embeddings/Chemical_Checker_Embeddings/parquets/JUMPCP_Sign3_CC_final_JUMP_MOA.parquet'
#bayer DINO: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/Bayer_DINO_embeddings/BAYER_DINO_embeddings_nonorm_final.parquet #bayer DINO+post processing: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/Bayer_DINO_embeddings/BAYER_DINO_embeddings_normed_final.parquet #bayer DINO+post processing ACTIVES: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/Bayer_DINO_embeddings/Bayer_DINO_embeddings_normed_final-actives_only.parquet #bayer DINO actives with moa: gs://calico-reference-embeddings/Annotations_from_Roman/Bayer_data_harmonized/Bayer_DINO_embeddings/Bayer_DINO_embeddings_normed_final-actives_only_with_MOA.parquet
#openphenom-384: gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_384.parquet #openphenom-384 sphered+madrobustize: gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_384_sphered_mad_robustized.parquet #openphenom-1920: gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_1920.parquet #openphenom-1920 sphered+madrobustize: gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_1920_sphered_mad_robustized.parquet #openphenom-384 sphered+madrobustize ACTIVES: 'gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_384_sphered_mad_robustized-ACTIVE.parquet' #openphenom-1920 sphered+madrobustize ACTIVES:'gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_1920_sphered_mad_robustized-ACTIVE.parquet' #openphenom-384 actives + MOA gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_384_sphered_mad_robustized-ACTIVE_with_MOA.parquet #openphenom-1920 actives + MOA gs://calico-reference-embeddings/embeddings/JUMP_Bayer_compounds/OpenPhenom/parquets/openphenom_1920_sphered_mad_robustized-ACTIVE_with_MOA.parquet
The KNN sweep notebook contains the code to run the analyses for kNN comparisons between all of the data sets above
6/12/202 Update: I joined in MOA labels from Jump consortium/Shantanu's group.
The MOA labels are located here: gs://calico-reference-embeddings/embeddings/JUMP MOA annotations/annotations_compound_gene_curated.parquet