├── IDC_super_TransformerST.py ├── Mouse_Lung_histology.py ├── README.md ├── ST-figure1.png ├── TransformerST analysis ├── 151508 │ ├── comparison │ │ ├── comparison.tsv │ │ └── readme │ └── readme ├── DLPFC.ARI_boxplot.R ├── DLPFC_BayesSpace.R ├── DLPFC_SpaGCN.py ├── DLPFC_comp.R ├── Figure 2.ipynb ├── output │ └── DLPFC │ │ ├── 151507 │ │ └── readme │ │ ├── 151508 │ │ └── readme │ │ ├── 151509 │ │ └── readme │ │ ├── 151510 │ │ └── readme │ │ ├── 151669 │ │ └── readme │ │ ├── 151670 │ │ └── readme │ │ ├── 151671 │ │ └── readme │ │ ├── 151672 │ │ └── readme │ │ ├── 151673 │ │ └── readme │ │ ├── 151674 │ │ └── readme │ │ ├── 151675 │ │ └── readme │ │ ├── 151676 │ │ └── readme │ │ └── readme └── readme ├── TransformerST-new.png ├── Vision Transformer ├── README ├── contour_util.py ├── dataset.py ├── main.py ├── transformer.py ├── utils.py └── vis_model.py ├── progress ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── __init__.cpython-39.pyc │ ├── bar.cpython-38.pyc │ └── bar.cpython-39.pyc ├── bar.py ├── counter.py └── spinner.py ├── requirements.txt └── src ├── BaseModel ├── BaseCellModel.py ├── BatchClassifier.py └── readme ├── TransformerST_graph_func.py ├── TransformerST_model.py ├── TransformerST_train_adaptive.py ├── TransformerST_utils_func.py ├── Utils ├── SCTransform.py ├── calculate_dis.py ├── clustering_func.py ├── contour_util.py ├── decoder.py ├── gat_v2conv.py ├── helpers.py ├── linear.py ├── network_utils.py ├── quantize_1d.py ├── readme └── scVI.py ├── __pycache__ ├── BaseCellModel.cpython-39.pyc ├── SCTransform.cpython-38.pyc ├── SCTransform.cpython-39.pyc ├── SEDR_model.cpython-38.pyc ├── SEDR_model.cpython-39.pyc ├── SEDR_model1.cpython-39.pyc ├── SEDR_train.cpython-38.pyc ├── SEDR_train.cpython-39.pyc ├── SEDR_train1.cpython-38.pyc ├── SEDR_train1.cpython-39.pyc ├── SEDR_train_adaptive.cpython-39.pyc ├── SEDR_train_adaptive_gai_super.cpython-39.pyc ├── SEDR_train_adaptive_super.cpython-39.pyc ├── SEDR_train_new.cpython-39.pyc ├── SEDR_train_super.cpython-39.pyc ├── SEDR_train_super_gai.cpython-39.pyc ├── TransformerST_graph_func.cpython-39.pyc ├── TransformerST_model.cpython-39.pyc ├── TransformerST_train_adaptive.cpython-39.pyc ├── TransformerST_utils_func.cpython-39.pyc ├── calculate_dis.cpython-39.pyc ├── clustering_func.cpython-38.pyc ├── contour_util.cpython-39.pyc ├── decoder.cpython-39.pyc ├── gat_v2conv.cpython-39.pyc ├── graph_agg.cpython-39.pyc ├── graph_func.cpython-38.pyc ├── graph_func.cpython-39.pyc ├── helpers.cpython-39.pyc ├── linear.cpython-39.pyc ├── model_utils.cpython-39.pyc ├── network_utils.cpython-39.pyc ├── submodules.cpython-39.pyc ├── util.cpython-39.pyc ├── utils_func.cpython-38.pyc └── utils_func.cpython-39.pyc ├── decoder.py ├── gat_v2conv.py ├── graph_agg.py ├── model_utils.py ├── submodules.py └── util.py /IDC_super_TransformerST.py: -------------------------------------------------------------------------------- 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