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/logs | ||
/datasets/graph | ||
.ruff_cache |
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# #!/bin/bash | ||
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mkdir -p ~/miniconda3 | ||
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh | ||
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 | ||
rm -rf ~/miniconda3/miniconda.sh | ||
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~/miniconda3/bin/conda init bash | ||
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#conda create -n topox python=3.11.3 | ||
#conda activate topox |
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_target_: topobenchmarkx.io.load.loaders.GraphLoader | ||
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# USE python train.py dataset.transforms.one_hot_node_degree_features.degrees_fields=x to run this config | ||
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defaults: | ||
- transforms/data_manipulations: node_feat_to_float | ||
- transforms/data_manipulations: node_degrees | ||
- transforms/[email protected]_hot_node_degree_features: one_hot_node_degree_features | ||
- transforms: ${get_default_transform:graph,${model}} | ||
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# Data definition | ||
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data_split_dir: ${paths.data_dir}data_splits/${dataset.parameters.data_name} | ||
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# Dataset parameters | ||
num_features: 1 # here basically I specify the initial num features in mutang at x aka x_0 | ||
num_features: 21 # torch_geometric ZINC dataset has 21 atom types | ||
max_node_degree: 20 # Use it to one_hot encode node degrees. Additional parameter to run dataset.transforms.one_hot_node_degree_features.degrees_fields=x | ||
num_classes: 1 | ||
task: regression | ||
loss_type: mse | ||
monitor_metric: mae | ||
task_level: graph | ||
data_seed: 0 | ||
split_type: 'fixed' # either k-fold or test | ||
split_type: 'fixed' # ZINC accept only <fixed> split | ||
#k: 10 # for k-Fold Cross-Validation | ||
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# Dataloader parameters | ||
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2 changes: 1 addition & 1 deletion
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configs/dataset/transforms/data_manipulations/node_degrees.yaml
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_target_: topobenchmarkx.transforms.data_transform.DataTransform | ||
transform_name: "NodeDegrees" | ||
transform_type: "data manipulation" | ||
selected_fields: ["edge_index", "incidence"] #"incidence" | ||
selected_fields: ["edge_index"] # "incidence" | ||
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3 changes: 1 addition & 2 deletions
3
configs/dataset/transforms/graph2cell_lifting/cell_cycles.yaml
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_target_: topobenchmarkx.transforms.data_transform.DataTransform | ||
transform_type: 'lifting' | ||
transform_name: "CellCyclesLifting" | ||
k_value: 1 | ||
complex_dim: ${oc.select:dataset.parameters.max_dim_if_lifted,3} | ||
max_cell_length: 6 | ||
max_cell_length: 10 | ||
preserve_edge_attr: ${oc.select:dataset.parameters.preserve_edge_attr_if_lifted,False} |
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