├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── biollm ├── __init__.py ├── algorithm │ ├── __init__.py │ ├── annotation.py │ ├── drug.py │ ├── grn.py │ └── perturbation.py ├── config │ ├── anno │ │ ├── cellplm_ms.toml │ │ ├── geneformer.toml │ │ ├── scbert.toml │ │ ├── scbert_covid.toml │ │ ├── scfoundation.toml │ │ ├── scgpt.toml │ │ ├── scgpt_covid.toml │ │ └── scgpt_lung.toml │ ├── drug │ │ ├── drug.toml │ │ ├── geneformer_drug.toml │ │ ├── scbert_drug.toml │ │ ├── scfoundation_drug.toml │ │ └── scgpt_drug.toml │ ├── embeddings │ │ ├── cell_emb │ │ │ ├── cellplm │ │ │ │ └── gse155468.toml │ │ │ ├── gf │ │ │ │ ├── blood.toml │ │ │ │ ├── hpancreas.toml │ │ │ │ ├── hpbmc.toml │ │ │ │ ├── kidney.toml │ │ │ │ ├── liver.toml │ │ │ │ └── zheng68k.toml │ │ │ ├── scbert │ │ │ │ ├── blood.toml │ │ │ │ ├── hpancreas.toml │ │ │ │ ├── hpbmc.toml │ │ │ │ ├── kidney.toml │ │ │ │ ├── liver.toml │ │ │ │ └── zheng68k.toml │ │ │ ├── scf │ │ │ │ ├── blood.toml │ │ │ │ ├── hpancreas.toml │ │ │ │ ├── hpbmc.toml │ │ │ │ ├── kidney.toml │ │ │ │ ├── liver.toml │ │ │ │ └── zheng68k.toml │ │ │ └── scgpt │ │ │ │ ├── blood.toml │ │ │ │ ├── hpancreas.toml │ │ │ │ ├── hpbmc.toml │ │ │ │ ├── kidney.toml │ │ │ │ └── liver.toml │ │ └── gene_exp_emb │ │ │ ├── gf.toml │ │ │ ├── scbert.toml │ │ │ ├── scf.toml │ │ │ └── scgpt.toml │ └── grn │ │ ├── geneformer_GB.toml │ │ ├── geneformer_GC.toml │ │ ├── geneformer_GM.toml │ │ ├── scbert_GB.toml │ │ ├── scbert_GC.toml │ │ ├── scbert_GM.toml │ │ ├── scfoundation_GB.toml │ │ ├── scfoundation_GC.toml │ │ ├── scfoundation_GM.toml │ │ ├── scgpt_GB.toml │ │ ├── scgpt_GC.toml │ │ └── scgpt_GM.toml ├── data_preprocess │ ├── __init__.py │ ├── cellplm_handler.py │ ├── data_handler.py │ ├── drug_data_process.py │ ├── geneformer_handler.py │ ├── scbert_handler.py │ ├── scfoundation_handler.py │ └── scgpt_handler.py ├── dataset │ ├── __init__.py │ ├── sc_dataset.py │ ├── scbert_dataset.py │ └── scgpt_dataset.py ├── evaluate │ ├── __init__.py │ ├── bm_cell_embedding.py │ ├── bm_metrices_anno.py │ ├── bm_metrices_gears.py │ ├── bm_metrices_grn.py │ ├── bm_metrices_pert.py │ ├── c5.all.v2023.2.Hs.symbols.gmt │ ├── drug_plot.py │ ├── integration.py │ ├── perturbation.py │ └── pw_gene_graph.py ├── loader │ ├── __init__.py │ ├── cellplm.py │ ├── geneformer.py │ ├── loader_base.py │ ├── mamba.py │ ├── scbert.py │ ├── scfoundation.py │ └── scgpt.py ├── model │ ├── __init__.py │ ├── annotation.py │ ├── drug.py │ ├── grad_reverse.py │ ├── grn.py │ ├── loss.py │ └── perturbation.py ├── repo │ ├── CellPLM │ │ ├── __init__.py │ │ ├── decoder │ │ │ ├── __init__.py │ │ │ ├── mlp.py │ │ │ └── zinb.py │ │ ├── embedder │ │ │ ├── __init__.py │ │ │ └── omics.py │ │ ├── encoder │ │ │ ├── __init__.py │ │ │ ├── mlp.py │ │ │ └── transformer.py │ │ ├── head │ │ │ ├── __init__.py │ │ │ └── downstream.py │ │ ├── latent │ │ │ ├── __init__.py │ │ │ ├── adversarial.py │ │ │ ├── autoencoders.py │ │ │ └── contrastive.py │ │ ├── layer │ │ │ ├── __init__.py │ │ │ ├── cosformer.py │ │ │ ├── flowformer.py │ │ │ ├── performer.py │ │ │ └── transformer.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ └── cellformer.py │ │ ├── objective │ │ │ ├── __init__.py │ │ │ ├── autoencoder.py │ │ │ └── zinb.py │ │ ├── pipeline │ │ │ ├── __init__.py │ │ │ ├── cell_embedding.py │ │ │ ├── cell_type_annotation.py │ │ │ ├── experimental.py │ │ │ └── imputation.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data.py │ │ │ ├── eval.py │ │ │ ├── mask.py │ │ │ ├── pe.py │ │ │ └── sparse.py │ ├── __init__.py │ ├── gears │ │ ├── __init__.py │ │ ├── data_utils.py │ │ ├── gears.py │ │ ├── inference.py │ │ ├── model.py │ │ ├── pertdata.py │ │ ├── utils.py │ │ └── version.py │ ├── geneformer │ │ ├── __init__.py │ │ ├── collator_for_classification.py │ │ ├── emb_extractor.py │ │ ├── geneformer_token_dictionary.pkl │ │ ├── in_silico_perturber.py │ │ ├── in_silico_perturber_stats.py │ │ ├── pretrainer.py │ │ └── tokenizer.py │ ├── scbert │ │ ├── README.md │ │ ├── __init__.py │ │ ├── attn_sum_save.py │ │ ├── data │ │ │ └── __init__.py │ │ ├── finetune.py │ │ ├── lr_baseline_crossorgan.py │ │ ├── performer_pytorch │ │ │ ├── __init__.py │ │ │ ├── performer_pytorch.py │ │ │ └── reversible.py │ │ ├── predict.py │ │ ├── preprocess.py │ │ ├── pretrain.py │ │ ├── requirements.txt │ │ └── utils.py │ ├── scfoundation │ │ ├── DeepCDR │ │ │ ├── README.md │ │ │ ├── plot.ipynb │ │ │ └── prog │ │ │ │ ├── layers │ │ │ │ ├── __init__.py │ │ │ │ └── graph.py │ │ │ │ ├── model.py │ │ │ │ ├── process_drug.py │ │ │ │ ├── run.sh │ │ │ │ ├── run_DeepCDR.py │ │ │ │ ├── run_DeepCDR_leave_drug.py │ │ │ │ └── run_pytorch_embedding.py │ │ ├── GEARS │ │ │ ├── Plot.ipynb │ │ │ ├── README.md │ │ │ ├── gears │ │ │ │ ├── __init__.py │ │ │ │ ├── data_utils.py │ │ │ │ ├── gears.py │ │ │ │ ├── genes_with_hi_mean.npy │ │ │ │ ├── inference.py │ │ │ │ ├── model.py │ │ │ │ ├── pertdata.py │ │ │ │ ├── utils.py │ │ │ │ └── version.py │ │ │ ├── modules │ │ │ │ ├── __init__.py │ │ │ │ ├── attention.py │ │ │ │ ├── encoders.py │ │ │ │ ├── mae_autobin.py │ │ │ │ ├── performer_module.py │ │ │ │ ├── reversible.py │ │ │ │ └── transformer.py │ │ │ ├── run_sh │ │ │ │ ├── run_singlecell-adamson.sh │ │ │ │ ├── run_singlecell-dixit.sh │ │ │ │ ├── run_singlecell_maeautobin-0.1B-res0-adamson.sh │ │ │ │ ├── run_singlecell_maeautobin-0.1B-res0-dixit.sh │ │ │ │ ├── run_singlecell_maeautobin-0.1B-res0-norman.sh │ │ │ │ ├── run_singlecell_maeautobin-demo-baseline.sh │ │ │ │ ├── run_singlecell_maeautobin-demo-emb-train.sh │ │ │ │ ├── run_singlecell_maeautobin-demo-emb.sh │ │ │ │ └── run_singlecell_norman.sh │ │ │ └── train.py │ │ ├── LICENSE │ │ ├── OS_scRNA_gene_index.19264.tsv │ │ ├── README.md │ │ ├── SCAD │ │ │ ├── README.md │ │ │ ├── model │ │ │ │ ├── SCAD_train_binarized_5folds-pub.py │ │ │ │ └── SCADmodules.py │ │ │ ├── plot-publish.ipynb │ │ │ ├── run.sh │ │ │ ├── run_embedding_bulk.py │ │ │ └── run_embedding_sc.py │ │ ├── __init__.py │ │ ├── ablation │ │ │ ├── README.md │ │ │ ├── ablation-00.ipynb │ │ │ ├── ablation-01.ipynb │ │ │ └── ablation-02.ipynb │ │ ├── annotation │ │ │ ├── README.md │ │ │ └── celltype-plot.ipynb │ │ ├── apiexample │ │ │ ├── README.md │ │ │ ├── client.py │ │ │ └── example.sh │ │ ├── enhancement │ │ │ ├── Baron_evaluation.ipynb │ │ │ ├── PBMC68k_evaluation.ipynb │ │ │ ├── README.md │ │ │ ├── run.sh │ │ │ └── run_embedding_sc.py │ │ ├── finetune_model.py │ │ ├── genemodule │ │ │ ├── README.md │ │ │ └── plot_geneemb.ipynb │ │ ├── get_embedding.py │ │ ├── load.py │ │ ├── mapping │ │ │ ├── README.md │ │ │ └── mapping-publish.ipynb │ │ ├── model │ │ │ ├── OS_scRNA_gene_index.19264.tsv │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── check_consistency.ipynb │ │ │ ├── demo.sh │ │ │ ├── finetune_model.py │ │ │ ├── get_embedding.py │ │ │ ├── load.py │ │ │ ├── models │ │ │ │ └── download.txt │ │ │ ├── pretrainmodels │ │ │ │ ├── __init__.py │ │ │ │ ├── mae_autobin.py │ │ │ │ ├── performer.py │ │ │ │ ├── pytorchTransformer.py │ │ │ │ ├── reversible.py │ │ │ │ ├── select_model.py │ │ │ │ └── transformer.py │ │ │ └── training_hyperparameter.txt │ │ ├── preprocessing │ │ │ ├── OS_scRNA_gene_index.19264.tsv │ │ │ ├── README.md │ │ │ ├── demo.ipynb │ │ │ ├── demo.sh │ │ │ ├── down.sh │ │ │ └── scRNA_workflow.py │ │ └── pretrainmodels │ │ │ ├── __init__.py │ │ │ ├── mae_autobin.py │ │ │ ├── performer.py │ │ │ ├── pytorchTransformer.py │ │ │ ├── reversible.py │ │ │ ├── select_model.py │ │ │ └── transformer.py │ ├── scgpt │ │ ├── __init__.py │ │ ├── data_collator.py │ │ ├── data_sampler.py │ │ ├── loss.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── dsbn.py │ │ │ ├── generation_model.py │ │ │ ├── grad_reverse.py │ │ │ ├── model.py │ │ │ └── multiomic_model.py │ │ ├── preprocess.py │ │ ├── scbank │ │ │ ├── __init__.py │ │ │ ├── data.py │ │ │ ├── databank.py │ │ │ ├── monitor.py │ │ │ └── setting.py │ │ ├── tasks │ │ │ ├── __init__.py │ │ │ ├── cell_emb.py │ │ │ └── grn.py │ │ ├── tokenizer │ │ │ ├── __init__.py │ │ │ ├── default_census_vocab.json │ │ │ ├── default_gene_vocab.json │ │ │ └── gene_tokenizer.py │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ └── util.py │ ├── scmamba │ │ ├── README.md │ │ ├── __init__.py │ │ ├── graph │ │ │ ├── KGbased_finetune.py │ │ │ ├── __init__.py │ │ │ ├── graph_Prep.py │ │ │ ├── graph_construction.py │ │ │ └── remove_cycle.py │ │ ├── scLLM_utils │ │ │ ├── __init__.py │ │ │ ├── dataloader.py │ │ │ ├── dataset.py │ │ │ ├── h5ad2lmdb.py │ │ │ ├── lmdb_preprocess.py │ │ │ ├── pretrain_testdataset.py │ │ │ └── utils.py │ │ ├── scgpt │ │ │ ├── __init__.py │ │ │ ├── data_collator.py │ │ │ ├── data_sampler.py │ │ │ ├── downstream │ │ │ │ ├── Pretraining.py │ │ │ │ ├── __init__.py │ │ │ │ ├── cell_annotation.py │ │ │ │ ├── finetune_integration.py │ │ │ │ ├── finetune_utils.py │ │ │ │ └── gene_regulatory_network.py │ │ │ ├── loss.py │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── dsbn.py │ │ │ │ ├── generation_model.py │ │ │ │ ├── grad_reverse.py │ │ │ │ └── model.py │ │ │ ├── preprocess.py │ │ │ ├── scbank │ │ │ │ ├── __init__.py │ │ │ │ ├── data.py │ │ │ │ ├── databank.py │ │ │ │ ├── monitor.py │ │ │ │ └── setting.py │ │ │ ├── tokenizer │ │ │ │ ├── __init__.py │ │ │ │ ├── default_cellxgene_vocab.json │ │ │ │ ├── default_gene_vocab.json │ │ │ │ └── gene_tokenizer.py │ │ │ ├── trainer.py │ │ │ └── utils │ │ │ │ ├── __init__.py │ │ │ │ └── util.py │ │ ├── scmamba │ │ │ ├── BiMamba.py │ │ │ ├── __init__.py │ │ │ ├── mambaLM.py │ │ │ ├── mamba_CA.py │ │ │ ├── mamba_CA_new.py │ │ │ ├── mamba_intergration.py │ │ │ └── mamba_pretrain.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_sampler.py │ │ │ ├── test_scbank.py │ │ │ ├── test_scformer.py │ │ │ ├── test_tokenizer.py │ │ │ └── vocab.json │ └── st_performer │ │ ├── README.md │ │ ├── __init__.py │ │ ├── cfgs │ │ ├── ft_config.toml │ │ ├── pretrain_config.toml │ │ └── pretrain_config_g2v.toml │ │ ├── data_parse │ │ ├── __init__.py │ │ ├── data_utils.py │ │ ├── dataset_qc.py │ │ ├── fit_bugs_lmdb.py │ │ ├── lmdb_handler.py │ │ ├── make_dataset.py │ │ ├── preprocess.py │ │ └── stereo_miner_parse.py │ │ ├── dsub_lmdb_write.sh │ │ ├── dsub_run.sh │ │ ├── log_manager.py │ │ ├── main.py │ │ ├── model │ │ ├── __init__.py │ │ ├── embedding.py │ │ ├── learn_rate.py │ │ ├── mamba_example.py │ │ ├── mamba_torch.py │ │ ├── performer_pytorch.py │ │ ├── reversible.py │ │ └── st_performer.py │ │ ├── requirements.txt │ │ ├── run.sh │ │ ├── run_sc_finetune.sh │ │ ├── run_sc_pretrain.sh │ │ ├── sct_dataset.py │ │ ├── test │ │ ├── __init__.py │ │ ├── test_debug.py │ │ └── test_lmdb.py │ │ ├── tokenizer.py │ │ ├── trainer.py │ │ └── utils.py ├── tasks │ ├── __init__.py │ ├── bio_task.py │ ├── cell_annotation.py │ ├── cell_embedding.py │ ├── drug_sensitivity.py │ ├── grn_task.py │ ├── integration │ │ ├── __init__.py │ │ └── intergration_task_scgpt.py │ └── perturbation │ │ ├── __init__.py │ │ ├── gears_task.py │ │ └── pert_task.py ├── test │ └── cfm_emb.py ├── trainer │ ├── __init__.py │ ├── anno_cellplm_train.py │ ├── anno_geneformer_train.py │ ├── anno_scbert_train.py │ ├── anno_scfoundation_train.py │ ├── anno_scgpt_train.py │ ├── integration_scgpt_trainer.py │ ├── pert_scgpt_trainer.py │ ├── pert_scmamba_trainer.py │ └── trainer.py ├── tutorials │ ├── cell_emb.ipynb │ └── cellplm.ipynb └── utils │ ├── __init__.py │ ├── data_sampler.py │ ├── log_manager.py │ ├── plots.py │ ├── preprocess.py │ └── utils.py ├── docs ├── Annotation.md ├── Cell_embedding.md ├── Development.md ├── GRN.md ├── Makefile ├── _static │ └── biollm │ │ └── base │ │ ├── bio_task.html │ │ ├── load_geneformer.html │ │ ├── load_llm.html │ │ ├── load_scbert.html │ │ ├── load_scfoundation.html │ │ └── load_scgpt.html ├── api - auto.rst ├── api.rst ├── biollm.png ├── conf.py ├── configs │ ├── annotation │ │ ├── gf_ft.toml │ │ ├── gf_train.toml │ │ ├── scbert_ft.toml │ │ ├── scbert_train.toml │ │ ├── scf_ft.toml │ │ ├── scf_train.toml │ │ ├── scgpt_ft.toml │ │ └── scgpt_train.toml │ ├── drug │ │ ├── geneformer_drug.toml │ │ ├── scbert_drug.toml │ │ ├── scfoundation_drug.toml │ │ └── scgpt_drug.toml │ └── zero_shots │ │ ├── geneformer_cell_emb.toml │ │ ├── geneformer_gene-expression_emb.toml │ │ ├── geneformer_gene_emb.toml │ │ ├── scbert_cell_emb.toml │ │ ├── scbert_gene-expression_emb.toml │ │ ├── scbert_gene_emb.toml │ │ ├── scfoundation_cell_emb.toml │ │ ├── scfoundation_gene-expression_emb.toml │ │ ├── scfoundation_gene_emb.toml │ │ ├── scgpt_cell_emb.toml │ │ ├── scgpt_gene-expression_emb.toml │ │ ├── scgpt_gene_emb.toml │ │ └── scmamba_cell_emb.toml ├── download.rst ├── drug_task.md ├── img.png ├── img_1.png ├── img_2.png ├── img_3.png ├── img_4.png ├── img_5.png ├── img_6.png ├── img_7.png ├── img_8.png ├── img_9.png ├── index.rst ├── installation.rst ├── introduction.rst └── release.rst ├── requirements-docs.txt ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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