library_name: transformers
tags: []
THIS PROTEIN VEC ADAPTATION WAS MODIFIED FROM https://github.com/tymor22/protein-vec
All credit for the original work goes to Tymor Hamamsy and the following authors of this paper https://www.biorxiv.org/content/10.1101/2023.11.26.568742v1
We have added a Huggingface compatible wrapper for the model in protvec.py
Please consider liking the model page and starring the github repo if you are going to use it :)
https://huggingface.co/lhallee/ProteinVec
https://github.com/lhallee/ProteinVecHuggingface
Clone and install
git clone https://github.com/lhallee/ProteinVecHuggingface.git
pip install torch pytorch_lightning transformers
To use from hugggingface
from transformers import T5Tokenizer
from protvec import ProteinVec, ProteinVecConfig
tokenizer = T5Tokenizer.from_pretrained('lhallee/ProteinVec')
model = ProteinVec.from_pretrained('lhallee/ProteinVec', config=ProteinVecConfig())
Embed a single sequence with embed
model.to_eval()
model = model.cuda() # remove if cpu inference
embedding = model.embed('SEQWENCE').detach().cpu() # torch.tensor(1, 512)
Use a particular AspectVec by setting the inference_mask
model.aspect_to_keys_dict # dictionary showing the aspects
### The model is set to ALL by default to use full ProteinVec
model.inference_mask = model.get_mask('EC') # for Enzyme Comission AspectVec
embedding = model.embed(...)
To half precision weights
model.to_half()
The license for the protein vec code
BSD 3-Clause License
Copyright (c) 2023, Tymor Hamamsy
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
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