https://github.com/lamm-mit/collagentransformer

CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach
https://github.com/lamm-mit/collagentransformer

learning machine nlp protein

Last synced: about 1 year ago
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CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach

• Host: GitHub
• URL: https://github.com/lamm-mit/collagentransformer
• Owner: lamm-mit
• Created: 2022-09-06T17:03:23.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-04-06T08:49:00.000Z (about 3 years ago)
• Last Synced: 2025-03-27T01:01:33.941Z (about 1 year ago)
• Topics: learning, machine, nlp, protein
• Language: Jupyter Notebook
• Homepage:
• Size: 240 KB
• Stars: 9
• Watchers: 1
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

          
# CollagenTransformer

![image](https://user-images.githubusercontent.com/101393859/192001862-cab20dbb-2829-4614-845c-accccae55c44.png)

Original paper: 

CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach

Authors: Eesha Khare, Constancio Gonzalez-Obeso, David L. Kaplan, Markus J. Buehler

mbuehler@mit.edu 

ACS Biomaterials Science & Engineering

https://pubs.acs.org/doi/full/10.1021/acsbiomaterials.2c00737 

## This repository includes two pretrained models

BERT-based transformer model: https://github.com/lamm-mit/CollagenTransformer/blob/main/CollagenTransformer_ProtBERT_Inference.ipynb

Small transformer model: https://github.com/lamm-mit/CollagenTransformer/blob/main/CollagenTransformer_SmallTransformer_Inference.ipynb 

## Training and inference

BERT-based transformer model: https://github.com/lamm-mit/CollagenTransformer/blob/main/CollagenTransformer_ProtBERT_training%20and%20inference.ipynb