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download all LargeMix datasets in a single command #1

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download all LargeMix datasets in a single command #1

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884f98e
download LargeMix datasets in a single command
blazejba Dec 11, 2023
c5378b8
remove Gradient link from README
kerstink-GC Mar 12, 2024
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5 changes: 0 additions & 5 deletions README.md
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---

[![Run on Gradient](https://assets.paperspace.io/img/gradient-badge.svg)](https://ipu.dev/sdGggS)
[![PyPI](https://img.shields.io/pypi/v/graphium)](https://pypi.org/project/graphium/)
[![Conda](https://img.shields.io/conda/v/conda-forge/graphium?label=conda&color=success)](https://anaconda.org/conda-forge/graphium)
[![PyPI - Downloads](https://img.shields.io/pypi/dm/graphium)](https://pypi.org/project/graphium/)
Expand Down Expand Up @@ -34,10 +33,6 @@ A deep learning library focused on graph representation learning for real-world

Visit https://graphium-docs.datamol.io/.

[![Run on Gradient](https://assets.paperspace.io/img/gradient-badge.svg)](https://ipu.dev/sdGggS)

You can try running Graphium on Graphcore IPUs for free on Gradient by clicking on the button above.

## Installation for developers

### For CPU and GPU developers
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33 changes: 33 additions & 0 deletions download_datasets.sh
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#!/bin/bash

# Function to download dataset
download_dataset() {
local dataset_url=$1
local dataset_path=$2

# Create directory if it does not exist
mkdir -p $(dirname "${dataset_path}")

# Download the dataset
wget -O "${dataset_path}" "${dataset_url}"
}

# L1000_VCAP
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/LINCS_L1000_VCAP_0-4.csv.gz" "graphium/data/neurips2023/large-dataset/LINCS_L1000_VCAP_0-2_th2.csv.gz"
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/l1000_vcap_random_splits.pt" "graphium/data/neurips2023/large-dataset/l1000_vcap_random_splits.pt"

# l1000_MCF7
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/LINCS_L1000_MCF7_0-4.csv.gz" "graphium/data/neurips2023/large-dataset/LINCS_L1000_MCF7_0-2_th2.csv.gz"
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/l1000_mcf7_random_splits.pt" "graphium/data/neurips2023/large-dataset/l1000_mcf7_random_splits.pt"

# PCBA_1328
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/PCBA_1328_1564k.parquet" "graphium/data/neurips2023/large-dataset/PCBA_1328_1564k.parquet"
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/pcba_1328_random_splits.pt" "graphium/data/neurips2023/large-dataset/pcba_1328_random_splits.pt"

# PCQM4M_G25
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/PCQM4M_G25_N4.parquet" "graphium/data/neurips2023/large-dataset/PCQM4M_G25_N4.parquet"
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/pcqm4m_g25_n4_random_splits.pt" "graphium/data/neurips2023/large-dataset/pcqm4m_g25_n4_random_splits.pt"

# PCQM4M_N4
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/PCQM4M_G25_N4.parquet" "graphium/data/neurips2023/large-dataset/PCQM4M_G25_N4.parquet"
download_dataset "https://storage.googleapis.com/graphium-public/datasets/neurips_2023/Large-dataset/pcqm4m_g25_n4_random_splits.pt" "graphium/data/neurips2023/large-dataset/pcqm4m_g25_n4_random_splits.pt"