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danaomics's Introduction

danaomics: understanding mRNA degradation using Transformers

Team members: Dana Udwin, Naomi Lee, Danny Adkins

0. Background

Requires CometML to log experiments. Create a .comet.config file and populate it with your credentials, or contact me and I can share mine you privately.

1. Data

First, ensure you have the Kaggle CLI by following the steps listed at https://www.kaggle.com/docs/api.

Next, download the Stanford COVID vaccine dataset from within your project's base directory:

kaggle competitions download -c stanford-covid-vaccine

2. Training the model

The command line arguments are as follows:

-T: train

-t: test

-s: save model after run

-l: load presaved model

python3 main.py -T to train without saving

python3 main.py -Ts to train and save the model file

3. Evaluating the model

python3 main.py -Tt to train and test in the same run

python3 main.py -lt to test from a preloaded model file

4. Visualization

danaomics's People

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