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README.md
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@@ -93,12 +93,51 @@ A subset of the molecules in B3DB has numerical `logBB` values (1058 compounds),
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while the whole dataset has categorical (`BBB+` or `BBB-`) BBB permeability labels
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(7807 compounds). Some physicochemical properties of the molecules are also provided.
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## Data splits
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The original B3DB dataset does not define splits, so here we have used the `Realistic Split` method described
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in [(Martin et al., 2018)](https://doi.org/10.1021/acs.jcim.7b00166).
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## Citation
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Please use the following citation in any publication using our *B3DB* dataset:
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while the whole dataset has categorical (`BBB+` or `BBB-`) BBB permeability labels
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(7807 compounds). Some physicochemical properties of the molecules are also provided.
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## Usage
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Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library.
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First, from the commandline install the datasets package
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$ pip install datasets
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then, from within python load the datasets library
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>>> import datasets
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and load one of the `B3DB` datasets, e.g.,
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>>> B3DB_classification = datasets.load_dataset("maomlab/B3DB", name = "B3DB_classification")
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Downloading readme: 100%|████████████████████████| 4.40k/4.40k [00:00<00:00, 1.35MB/s]
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Downloading data: 100%|██████████████████████████| 680k/680k [00:00<00:00, 946kB/s]
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Downloading data: 100%|██████████████████████████| 2.11M/2.11M [00:01<00:00, 1.28MB/s]
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Generating test split: 100%|█████████████████████| 1951/1951 [00:00<00:00, 20854.95 examples/s]
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Generating train split: 100%|████████████████████| 5856/5856 [00:00<00:00, 144260.80 examples/s]
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and inspecting the loaded dataset
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>>> B3DB_classification
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B3DB_classification
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DatasetDict({
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test: Dataset({
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features: ['NO.', 'compound_name', 'IUPAC_name', 'SMILES', 'CID', 'logBB', 'BBB+/BBB-', 'Inchi', 'threshold', 'reference', 'group', 'comments', 'ClusterNo', 'MolCount'],
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num_rows: 1951
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})
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train: Dataset({
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features: ['NO.', 'compound_name', 'IUPAC_name', 'SMILES', 'CID', 'logBB', 'BBB+/BBB-', 'Inchi', 'threshold', 'reference', 'group', 'comments', 'ClusterNo', 'MolCount'],
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num_rows: 5856
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})
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})
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## Data splits
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The original B3DB dataset does not define splits, so here we have used the `Realistic Split` method described
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in [(Martin et al., 2018)](https://doi.org/10.1021/acs.jcim.7b00166).
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## Citation
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Please use the following citation in any publication using our *B3DB* dataset:
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