deanelzingaibm commited on
Commit
d325f39
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1 Parent(s): 56a790f

Add missing protein_seq value so code block works end-to-end

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Based protein_seq here on https://github.com/BiomedSciAI/biomed-multi-alignment/blob/main/mammal/examples/protein_solubility/main_infer.py

Dean Elzinga [email protected]

Files changed (1) hide show
  1. README.md +3 -0
README.md CHANGED
@@ -54,6 +54,9 @@ model.eval()
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  # Load Tokenizer
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  tokenizer_op = ModularTokenizerOp.from_pretrained("ibm/biomed.omics.bl.sm.ma-ted-458m.protein_solubility")
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  # convert to MAMMAL style
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  sample_dict = {"protein_seq": protein_seq}
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  sample_dict = ProteinSolubilityTask.data_preprocessing(
 
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  # Load Tokenizer
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  tokenizer_op = ModularTokenizerOp.from_pretrained("ibm/biomed.omics.bl.sm.ma-ted-458m.protein_solubility")
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+ # protein_seq: FASTA sequence of a protein, input for the model to predict its solubility
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+ protein_seq = "NLMKRCTRGFRKLGKCTTLEEEKCKTLYPRGQCTCSDSKMNTHSCDCKSC"
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+
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  # convert to MAMMAL style
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  sample_dict = {"protein_seq": protein_seq}
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  sample_dict = ProteinSolubilityTask.data_preprocessing(