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[Masked Diffusion Language Models (MDLMs)](arxiv.org/pdf/2406.07524), introduced by Sahoo et al, provide strong generative capabilities to BERT-style models. In this work, we pre-train and fine-tune ESM-2-150M protein language model (pLM) on the MDLM objective to scaffold functional motifs and unconditionally generate realistic, high-quality membrane protein sequences.
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## Model Usage
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MeMDLM leverages an internal backbone for generation, which is a fine-tuned version of the ESM-2-150M pLM. This backbone model can be accessed through this repo:
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```python
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from transformers import AutoTokenizer, AutoModelForMaskedLM
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tokenizer = AutoTokenizer.from_pretrained("ChatterjeeLab/MeMDLM")
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model = AutoModelForMaskedLM.from_pretrained("ChatterjeeLab/MeMDLM")
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input_sequence = "QMMALTFITYIGCGLSSIFLSVTLVILIQLCAALLLLNLIFLLDSWIALYnTRGFCIAVAVFLHYFLLVSFTWMGLEAFHMYLKFCIVGWGIPAVVVSIVLTISPDNYGidFCWINSNVVFYITVVGYFCVIFLLNVSMFIVVLVQLCRIKKKKQLGDL"
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inputs = tokenizer(input_sequence, return_tensors="pt")
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output = model(**inputs)
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filled_protein_seq = tokenizer.decode(output.squeeze()) # contains the output protein sequence with filled mask tokens
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```
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## Repository Authors
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[Shrey Goel](mailto:[email protected]), Undergraduate Student at Duke University <br>
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[Masked Diffusion Language Models (MDLMs)](arxiv.org/pdf/2406.07524), introduced by Sahoo et al, provide strong generative capabilities to BERT-style models. In this work, we pre-train and fine-tune ESM-2-150M protein language model (pLM) on the MDLM objective to scaffold functional motifs and unconditionally generate realistic, high-quality membrane protein sequences.
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## Repository Authors
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[Shrey Goel](mailto:[email protected]), Undergraduate Student at Duke University <br>
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