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--- |
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license: mit |
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tags: |
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- protein |
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- thermostability |
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--- |
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__Purpose__: classifies protein sequence into Thermophilic (> 60C) or Mesophilic (<40C) by host organism growth temperature. |
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__Training__: |
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ProteinBERT (Rostlab/prot_bert) was fine tuned on a class balanced version of learn2therm (see [here]()), about 250k protein amino acid sequences. |
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Training parameters below: |
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TODO |
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See the [training repository](https://github.com/BeckResearchLab/learn2thermML) for code. |
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__Usage__: |
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Prepare sequences identically to using the original pretrained model: |
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``` |
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from transformers import BertModelForSequenceClassification, BertTokenizer |
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import torch |
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import re |
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tokenizer = BertTokenizer.from_pretrained("evankomp/learn2therm", do_lower_case=False ) |
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model = BertModelForSequenceClassification.from_pretrained("evankomp/learn2therm") |
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sequence_Example = "A E T C Z A O" |
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sequence_Example = re.sub(r"[UZOB]", "X", sequence_Example) |
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encoded_input = tokenizer(sequence_Example, return_tensors='pt') |
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output = torch.argmax(model(**encoded_input), dim=1) |
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``` |
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1 indicates thermophilic, 0 mesophilic. |
