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A combination of GPT-2 trained from scratch on masking histone modification patterns rather than the English language and XGBoost, predicting differential gene expression from histone modifications.

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ZovcIfzm/GeneGPT2

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STEPS TO REPRODUCE

Simple steps:

Go to google colab and follow steps there. Involves running the cells, and uploading data from this repo (GeneGPT2/data) to Colab. https://colab.research.google.com/drive/1VrCl76AX0mfQiflgbUMz042qG3htV7Vg#scrollTo=ESBxuVVkyJ_L

Specific steps (if you want to get a glimpse of it without going to colab):

Run the first two cells on colab (import packages, mount to google drive). Then follow the instructions shown in the next cell to upload data.

Then run the rest of the cells.

The model's results will be printed.

If you wish to change hyperparameters, you can edit the model configuration cell shown below. This step is also on the colab file:

That's it!

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A combination of GPT-2 trained from scratch on masking histone modification patterns rather than the English language and XGBoost, predicting differential gene expression from histone modifications.

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