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license: cc0-1.0
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---
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license: cc0-1.0
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task_categories:
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- tabular-regression
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language:
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- en
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pretty_name: MolData
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size_categories:
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- 1M<n<10M
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tags:
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- drug discovery
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- bioassay
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dataset_summary: >-
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A comprehensive disease and target-based dataset with 1.4 million molecules, collected from PubChem
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to accelerate molecular machine learning for better drug discovery.
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citation: >-
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@article{KeshavarziArshadi2022,
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title = {MolData, a molecular benchmark for disease and target based machine learning},
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volume = {14},
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ISSN = {1758-2946},
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url = {http://dx.doi.org/10.1186/s13321-022-00590-y},
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DOI = {10.1186/s13321-022-00590-y},
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number = {1},
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journal = {Journal of Cheminformatics},
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publisher = {Springer Science and Business Media LLC},
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author = {Keshavarzi Arshadi, Arash and Salem, Milad and Firouzbakht, Arash and Yuan, Jiann Shiun},
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year = {2022},
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month = mar
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}
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---
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# MolData
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[MolData](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-022-00590-y) is a comprehensive disease and target-based dataset collected from PubChem.
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The dataset contains 1.4 million unique molecules, and it is one the largest efforts to date for democratizing the molecular machine learning.
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## Preprocessing
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We utilized the raw data uploaded on [Github](https://github.com/LumosBio/MolData) and performed several preprocessing:
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1. Sanitize the molecules using RDKit and MolVS (standardize SMILES format)
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2. Rename the columns
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3. Split the dataset (train, test, validation)
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If you would like to try these processes with the original dataset,
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please follow the instructions in the [Preprocessing Script.py](address) file located in our MolData repository.
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