├── README.md ├── asset └── main_method_sccello.png ├── data ├── .DS_Store ├── README.md ├── cancer_drug_response │ └── DeepCDR_data │ │ ├── 223drugs_pubchem_smiles.txt │ │ ├── CCLE │ │ ├── Cell_lines_annotations_20181226.txt │ │ ├── GDSC_IC50.csv │ │ ├── IC50_thred.txt │ │ ├── genomic_copynumber_561celllines_710genes_demap_features.csv │ │ ├── genomic_expression_561celllines_697genes_demap_features.csv │ │ ├── genomic_methylation_561celllines_808genes_demap_features.csv │ │ └── genomic_mutation_34673_demap_features.csv │ │ ├── GDSC │ │ ├── 1.Drug_listMon Jun 24 09_00_55 2019.csv │ │ └── drug_graph_feat │ │ │ ├── 10027278.hkl │ │ │ ├── 10074640.hkl │ │ │ ├── 10077147.hkl │ │ │ ├── 10096043.hkl │ │ │ ├── 10109823.hkl │ │ │ ├── 10113978.hkl │ │ │ ├── 10127622.hkl │ │ │ ├── 10172943.hkl │ │ │ ├── 10184653.hkl │ │ │ ├── 10196499.hkl │ │ │ ├── 10200390.hkl │ │ │ ├── 10302451.hkl │ │ │ ├── 10341154.hkl │ │ │ ├── 10384072.hkl │ │ │ ├── 10390396.hkl │ │ │ ├── 10451420.hkl │ │ │ ├── 10459196.hkl │ │ │ ├── 10461815.hkl │ │ │ ├── 104842.hkl │ │ │ ├── 11152667.hkl │ │ │ ├── 11178236.hkl │ │ │ ├── 11282283.hkl │ │ │ ├── 11316960.hkl │ │ │ ├── 11327430.hkl │ │ │ ├── 11338033.hkl │ │ │ ├── 11364421.hkl │ │ │ ├── 11373846.hkl │ │ │ ├── 11404337.hkl │ │ │ ├── 11433190.hkl │ │ │ ├── 11455910.hkl │ │ │ ├── 11485656.hkl │ │ │ ├── 11493598.hkl │ │ │ ├── 11609586.hkl │ │ │ ├── 11617559.hkl │ │ │ ├── 11624601.hkl │ │ │ ├── 11625818.hkl │ │ │ ├── 11626560.hkl │ │ │ ├── 11626927.hkl │ │ │ ├── 11634725.hkl │ │ │ ├── 11640390.hkl │ │ │ ├── 11647372.hkl │ │ │ ├── 11667893.hkl │ │ │ ├── 11676786.hkl │ │ │ ├── 11707110.hkl │ │ │ ├── 11713159.hkl │ │ │ ├── 11754511.hkl │ │ │ ├── 11844351.hkl │ │ │ ├── 11960529.hkl │ │ │ ├── 11977753.hkl │ │ │ ├── 123631.hkl │ │ │ ├── 126565.hkl │ │ │ ├── 126941.hkl │ │ │ ├── 1401.hkl │ │ │ ├── 148124.hkl │ │ │ ├── 156422.hkl │ │ │ ├── 159324.hkl │ │ │ ├── 160355.hkl │ │ │ ├── 16038120.hkl │ │ │ ├── 16095342.hkl │ │ │ ├── 16663089.hkl │ │ │ ├── 16720766.hkl │ │ │ ├── 16722836.hkl │ │ │ ├── 16725726.hkl │ │ │ ├── 16747388.hkl │ │ │ ├── 16760646.hkl │ │ │ ├── 176158.hkl │ │ │ ├── 176167.hkl │ │ │ ├── 176870.hkl │ │ │ ├── 17755052.hkl │ │ │ ├── 20635522.hkl │ │ │ ├── 208908.hkl │ │ │ ├── 216239.hkl │ │ │ ├── 216326.hkl │ │ │ ├── 2314623.hkl │ │ │ ├── 23725625.hkl │ │ │ ├── 2375.hkl │ │ │ ├── 24180719.hkl │ │ │ ├── 24756910.hkl │ │ │ ├── 24772860.hkl │ │ │ ├── 24776445.hkl │ │ │ ├── 24785538.hkl │ │ │ ├── 24825971.hkl │ │ │ ├── 24826799.hkl │ │ │ ├── 24889392.hkl │ │ │ ├── 24894414.hkl │ │ │ ├── 24951314.hkl │ │ │ ├── 24978538.hkl │ │ │ ├── 25022668.hkl │ │ │ ├── 25102847.hkl │ │ │ ├── 25124816.hkl │ │ │ ├── 25126798.hkl │ │ │ ├── 25167777.hkl │ │ │ ├── 25195352.hkl │ │ │ ├── 25222038.hkl │ │ │ ├── 25257557.hkl │ │ │ ├── 25262965.hkl │ │ │ ├── 2726824.hkl │ │ │ ├── 2733526.hkl │ │ │ ├── 300471.hkl │ │ │ ├── 3005532.hkl │ │ │ ├── 3062316.hkl │ │ │ ├── 31703.hkl │ │ │ ├── 3218.hkl │ │ │ ├── 3385.hkl │ │ │ ├── 3463933.hkl │ │ │ ├── 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│ ├── 82146.hkl │ │ │ ├── 8249.hkl │ │ │ ├── 84691.hkl │ │ │ ├── 85668777.hkl │ │ │ ├── 9549184.hkl │ │ │ ├── 9810884.hkl │ │ │ ├── 9813758.hkl │ │ │ ├── 9826308.hkl │ │ │ ├── 9826528.hkl │ │ │ ├── 9858940.hkl │ │ │ ├── 9863776.hkl │ │ │ ├── 9868037.hkl │ │ │ ├── 9874913.hkl │ │ │ ├── 9884685.hkl │ │ │ ├── 9903786.hkl │ │ │ ├── 9907093.hkl │ │ │ ├── 9910224.hkl │ │ │ ├── 9911830.hkl │ │ │ ├── 9914412.hkl │ │ │ ├── 9931953.hkl │ │ │ ├── 9938202.hkl │ │ │ ├── 9943465.hkl │ │ │ ├── 9952773.hkl │ │ │ ├── 9956119.hkl │ │ │ ├── 9956222.hkl │ │ │ └── 9967941.hkl │ │ ├── Missing_data_pre │ │ └── records_pre_all.txt │ │ ├── anti_drug.info │ │ └── cancer_cell_line.info ├── cell_taxonomy │ ├── celltype_relationship.json │ └── cl.owl ├── example_h5ad │ └── example.h5ad ├── marker_gene │ ├── celllabel2typesquality.csv │ └── cellmarkers.tsv ├── new_pretrain │ ├── general_CLid2cellname.pkl │ ├── pretrain_frac100_cell_type_idmap.pkl │ └── pretrain_frac100_clid2name.pkl └── token_vocabulary │ ├── gene_median_dictionary.pkl │ ├── token_dictionary.pkl │ ├── vocab_id2name.csv │ └── vocab_ids_notFoundName.csv └── sccello ├── configs ├── .DS_Store ├── cell_level │ ├── cancer_drug_response_bert_nonparametric.json │ ├── cell_type_classification_bert_clustering.json │ ├── cell_type_classification_bert_training.json │ └── cell_type_classification_bert_training_probing.json └── pretrain │ ├── ds_config_zero.json │ ├── sccello_bert_model.json │ └── sccello_bert_training.json ├── script ├── run_cancer_drug_response.py ├── run_cell_type_classification.py ├── run_cell_type_clustering.py ├── run_data_transformation.py ├── run_marker_gene_prediction.py ├── run_novel_cell_type_classification.py └── run_pretrain_prototype_contrastive.py └── src ├── cell_ontology.py ├── collator ├── collator_for_classification.py └── collator_for_pretraining.py ├── data ├── data_proc.py ├── dataset.py └── tokenizer.py ├── model_prototype_contrastive.py ├── pretrainer.py └── utils ├── config.py ├── data_loading.py 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