From 07e795a0f171d8e059e4977aeae2b384003f7746 Mon Sep 17 00:00:00 2001 From: Julien St-Laurent Date: Wed, 30 Apr 2025 13:58:34 -0400 Subject: [PATCH] chore: Update bucket path --- experimental/graphium/config_small_gcn.yaml | 12 ++++++------ experimental/graphium/config_small_gcn_qm9.yaml | 4 ++-- experimental/graphium/config_small_gcn_zinc.yaml | 4 ++-- experimental/graphium/config_small_gin.yaml | 12 ++++++------ experimental/graphium/config_small_gine.yaml | 12 ++++++------ experimental/graphium/running-multitask-ipu.ipynb | 12 ++++++------ 6 files changed, 28 insertions(+), 28 deletions(-) diff --git a/experimental/graphium/config_small_gcn.yaml b/experimental/graphium/config_small_gcn.yaml index c0b9f3f..cba7156 100644 --- a/experimental/graphium/config_small_gcn.yaml +++ b/experimental/graphium/config_small_gcn.yaml @@ -56,12 +56,12 @@ datamodule: qm9: df: null df_path: data/neurips2023/small-dataset/qm9.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["A", "B", "C", "mu", "alpha", "homo", "lumo", "gap", "r2", "zpve", "u0", "u298", "h298", "g298", "cv", "u0_atom", "u298_atom", "h298_atom", "g298_atom"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` + splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` seed: *seed task_level: graph label_normalization: @@ -71,24 +71,24 @@ datamodule: tox21: df: null df_path: data/neurips2023/small-dataset/Tox21-7k-12-labels.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["NR-AR", "NR-AR-LBD", "NR-AhR", "NR-Aromatase", "NR-ER", "NR-ER-LBD", "NR-PPAR-gamma", "SR-ARE", "SR-ATAD5", "SR-HSE", "SR-MMP", "SR-p53"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/Tox21_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt` + splits_path: data/neurips2023/small-dataset/Tox21_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt` seed: *seed task_level: graph zinc: df: null df_path: data/neurips2023/small-dataset/ZINC12k.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["SA", "logp", "score"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` + splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` seed: *seed task_level: graph label_normalization: diff --git a/experimental/graphium/config_small_gcn_qm9.yaml b/experimental/graphium/config_small_gcn_qm9.yaml index 211eed0..5181d38 100644 --- a/experimental/graphium/config_small_gcn_qm9.yaml +++ b/experimental/graphium/config_small_gcn_qm9.yaml @@ -45,12 +45,12 @@ datamodule: qm9: df: null df_path: data/neurips2023/small-dataset/qm9.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["A", "B", "C", "mu", "alpha", "homo", "lumo", "gap", "r2", "zpve", "u0", "u298", "h298", "g298", "cv", "u0_atom", "u298_atom", "h298_atom", "g298_atom"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` + splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` seed: *seed task_level: graph label_normalization: diff --git a/experimental/graphium/config_small_gcn_zinc.yaml b/experimental/graphium/config_small_gcn_zinc.yaml index 55f4e11..2613b69 100644 --- a/experimental/graphium/config_small_gcn_zinc.yaml +++ b/experimental/graphium/config_small_gcn_zinc.yaml @@ -45,12 +45,12 @@ datamodule: zinc: df: null df_path: data/neurips2023/small-dataset/ZINC12k.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["SA", "logp", "score"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` + splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` seed: *seed task_level: graph label_normalization: diff --git a/experimental/graphium/config_small_gin.yaml b/experimental/graphium/config_small_gin.yaml index 429f92f..763b41f 100644 --- a/experimental/graphium/config_small_gin.yaml +++ b/experimental/graphium/config_small_gin.yaml @@ -56,12 +56,12 @@ datamodule: qm9: df: null df_path: data/neurips2023/small-dataset/qm9.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["A", "B", "C", "mu", "alpha", "homo", "lumo", "gap", "r2", "zpve", "u0", "u298", "h298", "g298", "cv", "u0_atom", "u298_atom", "h298_atom", "g298_atom"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` + splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` seed: *seed task_level: graph label_normalization: @@ -71,24 +71,24 @@ datamodule: tox21: df: null df_path: data/neurips2023/small-dataset/Tox21-7k-12-labels.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["NR-AR", "NR-AR-LBD", "NR-AhR", "NR-Aromatase", "NR-ER", "NR-ER-LBD", "NR-PPAR-gamma", "SR-ARE", "SR-ATAD5", "SR-HSE", "SR-MMP", "SR-p53"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/Tox21_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt` + splits_path: data/neurips2023/small-dataset/Tox21_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt` seed: *seed task_level: graph zinc: df: null df_path: data/neurips2023/small-dataset/ZINC12k.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["SA", "logp", "score"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` + splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` seed: *seed task_level: graph label_normalization: diff --git a/experimental/graphium/config_small_gine.yaml b/experimental/graphium/config_small_gine.yaml index 2690710..dbbb22a 100644 --- a/experimental/graphium/config_small_gine.yaml +++ b/experimental/graphium/config_small_gine.yaml @@ -56,12 +56,12 @@ datamodule: qm9: df: null df_path: data/neurips2023/small-dataset/qm9.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["A", "B", "C", "mu", "alpha", "homo", "lumo", "gap", "r2", "zpve", "u0", "u298", "h298", "g298", "cv", "u0_atom", "u298_atom", "h298_atom", "g298_atom"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` + splits_path: data/neurips2023/small-dataset/qm9_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt` seed: *seed task_level: graph label_normalization: @@ -71,24 +71,24 @@ datamodule: tox21: df: null df_path: data/neurips2023/small-dataset/Tox21-7k-12-labels.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["NR-AR", "NR-AR-LBD", "NR-AhR", "NR-Aromatase", "NR-ER", "NR-ER-LBD", "NR-PPAR-gamma", "SR-ARE", "SR-ATAD5", "SR-HSE", "SR-MMP", "SR-p53"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/Tox21_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt` + splits_path: data/neurips2023/small-dataset/Tox21_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt` seed: *seed task_level: graph zinc: df: null df_path: data/neurips2023/small-dataset/ZINC12k.csv.gz - # wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz + # wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz # or set path as the URL directly smiles_col: "smiles" label_cols: ["SA", "logp", "score"] # sample_size: 2000 # use sample_size for test - splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` + splits_path: data/neurips2023/small-dataset/ZINC12k_random_splits.pt # Download with `wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt` seed: *seed task_level: graph label_normalization: diff --git a/experimental/graphium/running-multitask-ipu.ipynb b/experimental/graphium/running-multitask-ipu.ipynb index b83d85d..2197afb 100644 --- a/experimental/graphium/running-multitask-ipu.ipynb +++ b/experimental/graphium/running-multitask-ipu.ipynb @@ -217,13 +217,13 @@ "dataset_directory = os.getenv(\"DATASETS_DIR\")\n", "\n", "if not os.path.exists(dataset_directory + \"/data/neurips2023/small-dataset\"):\n", - " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9.csv.gz\n", - " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz\n", - " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz\n", + " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9.csv.gz\n", + " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz\n", + " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k.csv.gz\n", "\n", - " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt\n", - " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt\n", - " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt\n", + " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9_random_splits.pt\n", + " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21_random_splits.pt\n", + " !wget -P $DATASETS_DIR/data/neurips2023/small-dataset/ https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/ZINC12k_random_splits.pt\n", " print(\"Datasets have been successfully downloaded.\")\n", "else:\n", " print(\"Datasets are already downloaded.\")"