Multiple Instance Fine-mapping (MIFM)

"Multiple instance fine-mapping: predicting causal regulatory variants with a deep sequence model"

This repository contains:

• a script for training an MIFM model: src/train.py
• weights for an already trained model used for the experiments in the paper: checkpoints/a7a0q7ar.ckpt
• a script for making predictions using a pretrained model: src/load_and_predict.py
• example files for the prediction script: example_data

Predicting using a pretrained model:

To predict based on genomic coordinates (chromosome and bp location):

python src/load_and_predict.py \
  --out_file=out.txt \
  --coordinates_file=example_data/variant_coordinates.tsv

To predict directly from DNA sequences (as strings):

python src/load_and_predict.py \
  --out_file=out.txt \
  --sequences_file=example_data/sequences.csv