├── .gitignore ├── LICENSE ├── README.Rmd ├── README.md ├── bin ├── .gitignore ├── README.md └── init ├── resources ├── github_mark.svg └── orcid_id.svg ├── sample_data └── predict_modality │ ├── openproblems_bmmc_cite_starter │ ├── openproblems_bmmc_cite_starter.test_mod1.h5ad │ ├── openproblems_bmmc_cite_starter.test_mod2.h5ad │ ├── openproblems_bmmc_cite_starter.train_mod1.h5ad │ └── openproblems_bmmc_cite_starter.train_mod2.h5ad │ └── openproblems_bmmc_multiome_starter │ ├── openproblems_bmmc_multiome_starter.test_mod1.h5ad │ ├── openproblems_bmmc_multiome_starter.test_mod2.h5ad │ ├── openproblems_bmmc_multiome_starter.train_mod1.h5ad │ └── openproblems_bmmc_multiome_starter.train_mod2.h5ad └── src ├── joint_embedding └── methods │ ├── Guanlab-dengkw │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ └── test.sh │ ├── jae │ ├── README.md │ ├── model_architecture.png │ ├── resources │ │ └── utils.py │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── test.sh │ └── train │ │ ├── config.vsh.yaml │ │ └── script.py │ └── lsl_ae │ ├── run │ ├── config.vsh.yaml │ └── script.py │ └── test.sh ├── match_modality └── methods │ ├── clue │ ├── README.md │ ├── clue_architecture.jpg │ ├── resources │ │ ├── scglue-0.1.1-py3-none-any.whl │ │ └── utils.py │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── test.sh │ └── train │ │ ├── config.vsh.yaml │ │ └── script.py │ └── novel │ ├── README.md │ ├── novel_architecture1.png │ ├── novel_architecture2.png │ ├── resources │ ├── catalyst_tools.py │ ├── config_ADT2GEX.py │ ├── config_ATAC2GEX.py │ ├── data.py │ ├── models.py │ ├── postprocessing.py │ └── preprocessing.py │ ├── run │ ├── config.vsh.yaml │ └── script.py │ ├── test.sh │ └── train │ ├── config.vsh.yaml │ └── script.py ├── predict_modality └── methods │ ├── AXX │ ├── .gitignore │ ├── README.md │ ├── resources │ │ ├── const.py │ │ ├── models.py │ │ ├── predict.py │ │ ├── test.py │ │ ├── train.py │ │ ├── utils.py │ │ └── yaml │ │ │ ├── mlp_ADT2GEX.yaml │ │ │ ├── mlp_ATAC2GEX.yaml │ │ │ └── mlp_GEX2ADT.yaml │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── test.sh │ └── train │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── DANCE │ ├── resources │ │ ├── baseline.py │ │ └── graph_util.py │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── test.sh │ └── train │ │ ├── config.vsh.yaml │ │ ├── generate_extra_files.py │ │ ├── h.all.v7.4.entrez.gmt │ │ ├── h.all.v7.4.symbols.gmt │ │ ├── hetero_arg_version_v5.py │ │ └── script.sh │ ├── Guanlab-dengkw │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ └── test.sh │ ├── LS_lab │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ └── test.sh │ ├── cajal │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── test.sh │ └── train │ │ ├── ADT_list_df_updated.csv │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── novel │ ├── README.md │ ├── novel_architecture.jpg │ ├── resources │ │ └── helper_functions.py │ ├── run │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── test.sh │ └── train │ │ ├── config.vsh.yaml │ │ └── script.py │ └── scJoint │ ├── .gitignore │ ├── README.md │ ├── resources │ ├── modules │ │ └── model_ae.py │ ├── opts.py │ ├── preprocess │ │ ├── save_filter_genes.py │ │ ├── save_highlyvar_genes.py │ │ └── save_idf_matrix.py │ ├── train.py │ ├── trainer │ │ ├── __init__.py │ │ ├── trainer_batchgan.py │ │ ├── trainer_cycle.py │ │ └── trainer_nn.py │ └── utils │ │ ├── __init__.py │ │ ├── dataloader.py │ │ ├── loss.py │ │ └── metric.py │ ├── run │ ├── config.vsh.yaml │ └── script.py │ ├── test.sh │ └── train │ ├── config.vsh.yaml │ └── train.sh ├── resources ├── nextflow.config └── nextflow_moremem.config └── sync_datasets.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openproblems-bio/neurips2021_multimodal_topmethods/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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