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--- |
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license: apache-2.0 |
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base_model: |
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- nferruz/ProtGPT2 |
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tags: |
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- axolotl |
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- lora |
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- transformers |
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- gpt2 |
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- protein_design |
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--- |
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# Model |
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This is a fine-tuned version of [ProtGPT2](https://huggingface.co/nferruz/ProtGPT2) : a language model that speaks the protein language and can be used for de novo protein design and engineering. |
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<br/> |
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# Dataset |
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Protein data set retrieved from Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB). \ |
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Only the OXIDOREDUCTASE enzymes were used. \ |
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You can find the JSON formatted data @ [oxidos.json](https://github.com/zypchn/pLM/blob/main/data/oxidos.json) |
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<br/> |
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# How to Use? |
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``` |
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>>> from transformers import pipeline |
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>>> pipe = pipeline("text-generation", model="zypchn/ProtGPT2-Oxido") |
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>>> sequences = pipe("", max_length=100, do_sample=True, top_k=950, repetition_penalty=1.2, num_return_sequences=5, eos_token_id=0) |
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# input field has left blank for diversity |
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``` |
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```json |
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[ |
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{"generated_text": "SNANQAPQPQTPTRATDAKKGSYGHPADRVGMEDNKYQVGVFYYDGPNPSYAEWNRDTQFWVETAKTAEKGKFDSIFFADTLGIYDSFKGSFEANLRHGAQFPVNDPLVAISAIAGATTKLGLVATASTTYSEPFHIARRFASLDHLSNGRAGWNIVTSYLDSAARNFGRTEQMEHDERYAIAEEYIDVVYKLWEGSWEDNAVIKDKETGLFTDPAKVHQINHEGEHFRVAGPLNIPRSPQGHPVIFQAGTSERGRDFAARHAEAVFTAQLDLEAGREFYEDIKSRAAKLGRDPDDVKILPGISVFVGKTREEAERKFRELQSLIDEEGALTRFSSYTGTDLSTYDPDGPLPELAGIDPTTPIAKLEGLLGKSKMTVREIALKQGGVSLREYQPFVGATAGSALVGGTPEQIADFMQDWFIEGTVDGFNIMPPYLPDGLEDFVDHVVPELQRRGLFRTEYEGTTLREHLGLAKPLEHHHHHH"}, |
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{"generated_text": "MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMGPCLICRSTSLKCVFCVRDPNGYKKCSKCDAFFCSRECQTEHWQRHHKFECPAAVAQPQIPPLPKPQQKQLTAAELGMFMEVRNQFALLKTNLERLDYEIFILERNVKLANTVTPPTNRTYFQSTMRYAPNPLRPNMTDAMRQQYLDKNKSSAALEHDLKELIKFKCYLLNDEYVEKEREENPFIWEYFLNKEWRKRNVWGNK\n"}, |
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{"generated_text": "MGHHHHHHSSGLVPRGSHMTVEQAKKLRAEAEAQAQIQDKAKAIAQTHGKVEVMVDGKHRVVDLDATTRRQLTDGELQAIVVAAQEAAAKQLKAQRQALLEQHQDAELRKLALEGEIV\nAVITGAAQGIGRAIALRLAKDGFRVAVADIDLAAAEAVAAEIEAKGGKALVIEGDVSREEDVKRLVRKAIDQFGRLDYAVNNAGIQGPLAPTEELPLALWNKVIDVNLTGVFLCMKYEIAQMVKQGRGGAIVNTASVAGLSGQPGMVAYCASKHGVVGLTKTVAIEYAKHGIRINAVAPGFIDTPMVQKLPEEKRARIAAAIPMRRLGQPDEIAAVVAFLLSDDASFITGQCIAVDGGFTAGLLA"}, |
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{"generated_text": "MAASKAADSLAEGAAKLEHHHHHH"}, |
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{"generated_text": "GSKPQPGVQVEGAKCQVLQAVYDFTVQSASELSFKAGDVICVTGQYDPTLGWWLAEERRTGKSGLVPENYVELLSTGPAQHHHHHH"} |
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] |
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``` |
