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Recognizing and generating knotted molecular structures by machine learning

Try our model

Dataset

Download our dataset from here

Classification

TransKnot is a Transformer-based model that classifies knots of different types.

This repository contains the training code in Jupyter Notebook to play with:

train.ipynb

Our model architecture schematics:

TransKnot model architecture

Generation

KnotFormer is a Transformer-based diffusion model that generates accurate knots of different types

  • To train the diffusion model: python diffusion_train.py

  • To train the classifier: python classifier_train.py

  • To generate: use generate.ipynb

Our model architecture schematics: TransKnot model architecture

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Classify and generate polymer knots

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