├── LICENSE ├── MAE-pytorch ├── README.md ├── __pycache__ │ ├── dataset_folder.cpython-37.pyc │ ├── datasets.cpython-37.pyc │ ├── masking_generator.cpython-37.pyc │ ├── modeling_finetune.cpython-37.pyc │ ├── modeling_pretrain.cpython-37.pyc │ └── utils.cpython-37.pyc ├── dataset_folder.py ├── datasets.py ├── engine_for_finetuning.py ├── engine_for_pretraining.py ├── files │ ├── ILSVRC2012_val_00031649.JPEG │ └── LIBDpatch_224.jpg ├── masking_generator.py ├── modeling_finetune.py ├── modeling_pretrain.py ├── my_modeling_pretrain.py ├── optim_factory.py ├── requirements.txt ├── run_class_finetuning.py ├── run_mae_extract_feature.py ├── run_mae_pretraining.py ├── run_mae_vis.py ├── transforms.py └── utils.py ├── README.md ├── conST_151673.pth ├── conST_cluster.ipynb ├── imgs └── conST-workflow.png ├── input ├── adatax.npy └── graphdict.npy ├── output └── spatialLIBD │ └── 151673 │ └── conST │ ├── conST_leiden_plot.jpg │ ├── conST_leiden_plot_refined.jpg │ ├── conST_result.npy │ └── metadata.tsv ├── progress ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── __init__.cpython-38.pyc │ ├── bar.cpython-37.pyc │ └── bar.cpython-38.pyc ├── bar.py ├── counter.py └── spinner.py └── src ├── __pycache__ ├── graph_func.cpython-37.pyc ├── layers.cpython-37.pyc ├── model.cpython-37.pyc ├── training.cpython-37.pyc └── utils_func.cpython-37.pyc ├── graph_func.py ├── layers.py ├── model.py ├── moran_geary_func.py ├── svg_func.py ├── training.py └── utils_func.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/LICENSE -------------------------------------------------------------------------------- /MAE-pytorch/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/README.md -------------------------------------------------------------------------------- /MAE-pytorch/__pycache__/dataset_folder.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/__pycache__/dataset_folder.cpython-37.pyc -------------------------------------------------------------------------------- /MAE-pytorch/__pycache__/datasets.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/__pycache__/datasets.cpython-37.pyc -------------------------------------------------------------------------------- /MAE-pytorch/__pycache__/masking_generator.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/__pycache__/masking_generator.cpython-37.pyc -------------------------------------------------------------------------------- /MAE-pytorch/__pycache__/modeling_finetune.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/__pycache__/modeling_finetune.cpython-37.pyc -------------------------------------------------------------------------------- /MAE-pytorch/__pycache__/modeling_pretrain.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/__pycache__/modeling_pretrain.cpython-37.pyc -------------------------------------------------------------------------------- /MAE-pytorch/__pycache__/utils.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/__pycache__/utils.cpython-37.pyc -------------------------------------------------------------------------------- /MAE-pytorch/dataset_folder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/dataset_folder.py -------------------------------------------------------------------------------- /MAE-pytorch/datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/datasets.py -------------------------------------------------------------------------------- /MAE-pytorch/engine_for_finetuning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/engine_for_finetuning.py -------------------------------------------------------------------------------- /MAE-pytorch/engine_for_pretraining.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /MAE-pytorch/files/ILSVRC2012_val_00031649.JPEG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/files/ILSVRC2012_val_00031649.JPEG -------------------------------------------------------------------------------- /MAE-pytorch/files/LIBDpatch_224.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/files/LIBDpatch_224.jpg -------------------------------------------------------------------------------- /MAE-pytorch/masking_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/masking_generator.py -------------------------------------------------------------------------------- /MAE-pytorch/modeling_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/modeling_finetune.py -------------------------------------------------------------------------------- /MAE-pytorch/modeling_pretrain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/modeling_pretrain.py -------------------------------------------------------------------------------- /MAE-pytorch/my_modeling_pretrain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/my_modeling_pretrain.py -------------------------------------------------------------------------------- /MAE-pytorch/optim_factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/optim_factory.py -------------------------------------------------------------------------------- /MAE-pytorch/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/requirements.txt -------------------------------------------------------------------------------- /MAE-pytorch/run_class_finetuning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/run_class_finetuning.py -------------------------------------------------------------------------------- /MAE-pytorch/run_mae_extract_feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/run_mae_extract_feature.py -------------------------------------------------------------------------------- /MAE-pytorch/run_mae_pretraining.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/run_mae_pretraining.py -------------------------------------------------------------------------------- /MAE-pytorch/run_mae_vis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/run_mae_vis.py -------------------------------------------------------------------------------- /MAE-pytorch/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/transforms.py -------------------------------------------------------------------------------- /MAE-pytorch/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/MAE-pytorch/utils.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/README.md -------------------------------------------------------------------------------- /conST_151673.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/conST_151673.pth -------------------------------------------------------------------------------- /conST_cluster.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/conST_cluster.ipynb -------------------------------------------------------------------------------- /imgs/conST-workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/imgs/conST-workflow.png -------------------------------------------------------------------------------- /input/adatax.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/input/adatax.npy -------------------------------------------------------------------------------- /input/graphdict.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/input/graphdict.npy -------------------------------------------------------------------------------- /output/spatialLIBD/151673/conST/conST_leiden_plot.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/output/spatialLIBD/151673/conST/conST_leiden_plot.jpg -------------------------------------------------------------------------------- /output/spatialLIBD/151673/conST/conST_leiden_plot_refined.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/output/spatialLIBD/151673/conST/conST_leiden_plot_refined.jpg -------------------------------------------------------------------------------- /output/spatialLIBD/151673/conST/conST_result.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/output/spatialLIBD/151673/conST/conST_result.npy -------------------------------------------------------------------------------- /output/spatialLIBD/151673/conST/metadata.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/output/spatialLIBD/151673/conST/metadata.tsv -------------------------------------------------------------------------------- /progress/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/__init__.py -------------------------------------------------------------------------------- /progress/__pycache__/__init__.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/__pycache__/__init__.cpython-37.pyc -------------------------------------------------------------------------------- /progress/__pycache__/__init__.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/__pycache__/__init__.cpython-38.pyc -------------------------------------------------------------------------------- /progress/__pycache__/bar.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/__pycache__/bar.cpython-37.pyc -------------------------------------------------------------------------------- /progress/__pycache__/bar.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/__pycache__/bar.cpython-38.pyc -------------------------------------------------------------------------------- /progress/bar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/bar.py -------------------------------------------------------------------------------- /progress/counter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/counter.py -------------------------------------------------------------------------------- /progress/spinner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/progress/spinner.py -------------------------------------------------------------------------------- /src/__pycache__/graph_func.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/__pycache__/graph_func.cpython-37.pyc -------------------------------------------------------------------------------- /src/__pycache__/layers.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/__pycache__/layers.cpython-37.pyc -------------------------------------------------------------------------------- /src/__pycache__/model.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/__pycache__/model.cpython-37.pyc -------------------------------------------------------------------------------- /src/__pycache__/training.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/__pycache__/training.cpython-37.pyc -------------------------------------------------------------------------------- /src/__pycache__/utils_func.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/__pycache__/utils_func.cpython-37.pyc -------------------------------------------------------------------------------- /src/graph_func.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/graph_func.py -------------------------------------------------------------------------------- /src/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/layers.py -------------------------------------------------------------------------------- /src/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/model.py -------------------------------------------------------------------------------- /src/moran_geary_func.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/moran_geary_func.py -------------------------------------------------------------------------------- /src/svg_func.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/svg_func.py -------------------------------------------------------------------------------- /src/training.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/training.py -------------------------------------------------------------------------------- /src/utils_func.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ys-zong/conST/HEAD/src/utils_func.py --------------------------------------------------------------------------------