Building a competition submission using an existing model

This example shows you how to generate a submission for the community warmup using an existing model

Loading up the data for the competition

from biolearn.data_library import GeoData

#Download the data file for the warmup challenge linked here https://www.synapse.org/#!Synapse:syn52966292/wiki/625231
DOWNLOADED_DATA_FILE_PATH="ADD YOUR PATH HERE"
challenge_data = GeoData.from_methylation_matrix(DOWNLOADED_DATA_FILE_PATH)
challenge_data

Use the Lin model to predict the age

from biolearn.model_gallery import ModelGallery

#Lin scored the best so lets use that
results = ModelGallery().get("Lin").predict(challenge_data)
results

Save a csv in the correct format for submission

Now we save this to a csv in the expected format.

submission = results.rename_axis("sampleId")
submission = submission.rename(columns={"Predicted": "predictedAge"})
submission.to_csv("lin_submission.csv")
#You can submit this file to the community warmup challenge by following the instructions below
submission

Estimated memory usage: 0 MB