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--- |
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license: cc-by-4.0 |
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--- |
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# DeepLoc-2.0 Training Data |
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Dataset from https://services.healthtech.dtu.dk/services/DeepLoc-2.0/ used to train the DeepLoc-2.0 model. |
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## Data preparation |
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Data downloaded and processed using the following Python script: |
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```python |
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import pandas as pd |
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df = pd.read_csv('https://services.healthtech.dtu.dk/services/DeepLoc-2.0/data/Swissprot_Train_Validation_dataset.csv').drop(['Unnamed: 0', 'Partition'], axis=1) |
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df = df.melt(['Kingdom', 'ACC', 'Sequence','Membrane'], var_name='Location').query('value == 1.0').drop(labels='value', axis=1).astype({'Membrane': 'int8'}) |
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train = df.sample(frac=0.8) |
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df = df.drop(train.index) |
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val = df.sample(frac=0.5) |
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test = df.drop(val.index) |
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train = train.reset_index(drop=True) |
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val = val.reset_index(drop=True) |
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test = test.reset_index(drop=True) |
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train.to_parquet('deeploc-train.parquet', index=False) |
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val.to_parquet('deploc-val.parquet', index=False) |
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test.to_parquet('deeploc-test.parquet', index=False) |
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``` |
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## Citation |
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**DeepLoc-2.0:** |
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``` |
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Vineet Thumuluri and others, DeepLoc 2.0: multi-label subcellular localization prediction using protein language models, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W228–W234, https://doi.org/10.1093/nar/gkac278 |
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``` |
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The DeepLoc data is a derivative of the UniProt dataset: |
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**UniProt** |
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``` |
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The UniProt Consortium |
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UniProt: the Universal Protein Knowledgebase in 2023 |
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Nucleic Acids Res. 51:D523–D531 (2023) |
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``` |
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