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Add new embeddings folder

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  1. .gitattributes +36 -0
  2. new_embeddings/cell_line_embeddings/cell_line_embedding_qwen3_5120.csv +0 -0
  3. new_embeddings/drug_embeddings/chemberta2MLM_embeddings_cls.csv +3 -0
  4. new_embeddings/drug_embeddings/chemberta2MLM_embeddings_max.csv +3 -0
  5. new_embeddings/drug_embeddings/chemberta2MLM_embeddings_mean.csv +3 -0
  6. new_embeddings/drug_embeddings/chemberta2MLM_invalid_smiles.csv +86 -0
  7. new_embeddings/drug_embeddings/chemberta2MTR_embeddings_cls.csv +3 -0
  8. new_embeddings/drug_embeddings/chemberta2MTR_embeddings_max.csv +3 -0
  9. new_embeddings/drug_embeddings/chemberta2MTR_embeddings_mean.csv +3 -0
  10. new_embeddings/drug_embeddings/chemberta2MTR_invalid_smiles.csv +85 -0
  11. new_embeddings/drug_embeddings/chemberta_invalid_smiles.csv +85 -0
  12. new_embeddings/drug_embeddings/molformer_base_embeddings_cls.sh000.csv +3 -0
  13. new_embeddings/drug_embeddings/molformer_base_embeddings_max.sh000.csv +3 -0
  14. new_embeddings/drug_embeddings/molformer_base_embeddings_mean.sh000.csv +3 -0
  15. new_embeddings/drug_embeddings/molformer_base_invalid_smiles.csv +0 -0
  16. new_embeddings/drug_embeddings/morgan_fingerprint_1024.csv +3 -0
  17. new_embeddings/drug_embeddings/rdkit_200.csv +3 -0
  18. new_embeddings/drug_embeddings/scaled_embeddings/morgan_fingerprint_1024.csv +3 -0
  19. new_embeddings/drug_embeddings/scaled_embeddings/rdkit_200.csv +3 -0
  20. new_embeddings/gene_embeddings/CCLE_1270.csv +3 -0
  21. new_embeddings/gene_embeddings/CCLE_1270_symbol.csv +3 -0
  22. new_embeddings/gene_embeddings/CCLE_300_ENSEMBLID.csv +3 -0
  23. new_embeddings/gene_embeddings/CRISPRGeneEffect.csv +3 -0
  24. new_embeddings/gene_embeddings/embeddings_borzoi_max.csv +3 -0
  25. new_embeddings/gene_embeddings/embeddings_borzoi_mean.csv +3 -0
  26. new_embeddings/gene_embeddings/embeddings_borzoi_median.csv +3 -0
  27. new_embeddings/gene_embeddings/enformer_embeddings_max.csv +3 -0
  28. new_embeddings/gene_embeddings/enformer_embeddings_mean.csv +3 -0
  29. new_embeddings/gene_embeddings/enformer_embeddings_mean_symbol.csv +3 -0
  30. new_embeddings/gene_embeddings/enformer_embeddings_median.csv +3 -0
  31. new_embeddings/gene_embeddings/esm2_embeddings_mean.csv +3 -0
  32. new_embeddings/gene_embeddings/esm2_embeddings_mean_symbol.csv +3 -0
  33. new_embeddings/gene_embeddings/gene2vec_d200.csv +3 -0
  34. new_embeddings/gene_embeddings/genept_3072.csv +3 -0
  35. new_embeddings/gene_embeddings/omics_d256.tsv +3 -0
  36. new_embeddings/gene_embeddings/pops_mat_d256.tsv +3 -0
  37. new_embeddings/gene_embeddings/scaled_embeddings/borzoi_1536.csv +3 -0
  38. new_embeddings/gene_embeddings/scaled_embeddings/esm2_1280.csv +3 -0
  39. new_embeddings/gene_embeddings/scaled_embeddings/gene_effect_1178.csv +3 -0
  40. new_embeddings/gene_embeddings/scaled_embeddings/gene_effect_205.csv +3 -0
  41. new_embeddings/gene_embeddings/scaled_embeddings/genept_3072.csv +3 -0
  42. new_embeddings/gene_embeddings/scaled_embeddings/wikicrow_4096.csv +3 -0
.gitattributes CHANGED
@@ -70,3 +70,39 @@ custom_splits_info/iv_info.csv filter=lfs diff=lfs merge=lfs -text
70
  embeddings/intervention_embeddings/CTRP_with_smiles_simscaled.csv filter=lfs diff=lfs merge=lfs -text
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  embeddings/intervention_embeddings/ccle_T_pca_300_enformer_full_gene_mean_PCA_500_scaled.csv filter=lfs diff=lfs merge=lfs -text
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  embeddings/intervention_embeddings/global_iv_scaledv3.csv filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  embeddings/intervention_embeddings/CTRP_with_smiles_simscaled.csv filter=lfs diff=lfs merge=lfs -text
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  embeddings/intervention_embeddings/ccle_T_pca_300_enformer_full_gene_mean_PCA_500_scaled.csv filter=lfs diff=lfs merge=lfs -text
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  embeddings/intervention_embeddings/global_iv_scaledv3.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/chemberta2MLM_embeddings_cls.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/chemberta2MLM_embeddings_max.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/chemberta2MLM_embeddings_mean.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/chemberta2MTR_embeddings_cls.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/chemberta2MTR_embeddings_max.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/chemberta2MTR_embeddings_mean.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/molformer_base_embeddings_cls.sh000.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/molformer_base_embeddings_max.sh000.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/molformer_base_embeddings_mean.sh000.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/morgan_fingerprint_1024.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/rdkit_200.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/drug_embeddings/scaled_embeddings/morgan_fingerprint_1024.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/CCLE_300_ENSEMBLID.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/embeddings_borzoi_max.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/embeddings_borzoi_median.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/enformer_embeddings_max.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/enformer_embeddings_mean.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/enformer_embeddings_mean_symbol.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/enformer_embeddings_median.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/esm2_embeddings_mean.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/esm2_embeddings_mean_symbol.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/gene2vec_d200.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/genept_3072.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/omics_d256.tsv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/pops_mat_d256.tsv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/scaled_embeddings/borzoi_1536.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/scaled_embeddings/esm2_1280.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/scaled_embeddings/gene_effect_1178.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/scaled_embeddings/gene_effect_205.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/scaled_embeddings/genept_3072.csv filter=lfs diff=lfs merge=lfs -text
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+ new_embeddings/gene_embeddings/scaled_embeddings/wikicrow_4096.csv filter=lfs diff=lfs merge=lfs -text
new_embeddings/cell_line_embeddings/cell_line_embedding_qwen3_5120.csv ADDED
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new_embeddings/drug_embeddings/chemberta2MLM_embeddings_cls.csv ADDED
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