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README.md
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## Model description
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[cdsBERT](https://doi.org/10.1101/2023.09.15.558027) is pLM with a codon vocabulary that was seeded with [ProtBERT](https://huggingface.co/Rostlab/prot_bert_bfd) and trained with a novel vocabulary extension pipeline called MELD. cdsBERT offers a highly biologically relevant latent space with excellent EC number prediction surpassing ProtBERT.
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## How to use
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import re
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import torch
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import torch.nn.functional as F
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from transformers import
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model = BertModel.from_pretrained('lhallee/cdsBERT') # load model
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tokenizer = BertTokenizer.from_pretrained('lhallee/cdsBERT') # load tokenizer
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## Model description
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[cdsBERT+](https://doi.org/10.1101/2023.09.15.558027) is pLM with a codon vocabulary that was seeded with [ProtBERT](https://huggingface.co/Rostlab/prot_bert_bfd) and trained with a novel vocabulary extension pipeline called MELD. cdsBERT+ offers a highly biologically relevant latent space with excellent EC number prediction surpassing ProtBERT.
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## How to use
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import re
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import torch
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import torch.nn.functional as F
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from transformers import BertModel, BertTokenizer
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model = BertModel.from_pretrained('lhallee/cdsBERT') # load model
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tokenizer = BertTokenizer.from_pretrained('lhallee/cdsBERT') # load tokenizer
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