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--- |
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library_name: transformers |
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tags: [] |
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--- |
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## THIS PROTEIN VEC ADAPTATION WAS MODIFIED FROM https://github.com/tymor22/protein-vec |
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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 |
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We have added a Huggingface compatible wrapper for the model in protvec.py |
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Please consider liking the model page and starring the github repo if you are going to use it :) |
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``` |
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https://huggingface.co/lhallee/ProteinVec |
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https://github.com/lhallee/ProteinVecHuggingface |
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``` |
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Clone and install |
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``` |
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git clone https://github.com/lhallee/ProteinVecHuggingface.git |
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pip install torch pytorch_lightning transformers |
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``` |
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To use from hugggingface |
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``` |
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from transformers import T5Tokenizer |
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from protvec import ProteinVec, ProteinVecConfig |
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tokenizer = T5Tokenizer.from_pretrained('lhallee/ProteinVec') |
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model = ProteinVec.from_pretrained('lhallee/ProteinVec', config=ProteinVecConfig()) |
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``` |
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Embed a single sequence with ```embed``` |
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``` |
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model.to_eval() |
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model = model.cuda() # remove if cpu inference |
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embedding = model.embed('SEQWENCE').detach().cpu() # torch.tensor(1, 512) |
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``` |
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Use a particular AspectVec by setting the ```inference_mask``` |
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``` |
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model.aspect_to_keys_dict # dictionary showing the aspects |
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### The model is set to ALL by default to use full ProteinVec |
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model.inference_mask = model.get_mask('EC') # for Enzyme Comission AspectVec |
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embedding = model.embed(...) |
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``` |
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To half precision weights |
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``` |
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model.to_half() |
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``` |
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## The license for the protein vec code |
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### BSD 3-Clause License |
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Copyright (c) 2023, Tymor Hamamsy |
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Redistribution and use in source and binary forms, with or without |
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modification, are permitted provided that the following conditions are met: |
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1. Redistributions of source code must retain the above copyright notice, this |
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list of conditions and the following disclaimer. |
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2. Redistributions in binary form must reproduce the above copyright notice, |
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this list of conditions and the following disclaimer in the documentation |
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and/or other materials provided with the distribution. |
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3. Neither the name of the copyright holder nor the names of its |
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contributors may be used to endorse or promote products derived from |
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this software without specific prior written permission. |
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" |
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE |
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE |
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE |
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL |
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR |
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER |
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, |
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE |
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
