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kipoi_interpret

Model interepretation plugin for Kipoi.

CircleCI Coverage status

Installation

pip install kipoi_interpret

Usage example

# list all available methods
kipoi_interpret.importance_scores.available_methods()

Available methods:

# Gradient-based methods
from kipoi_interpret.importance_scores.gradient import Gradient, GradientXInput
# In-silico mutagenesis-based methods
from kipoi_interpret.importance_scores.ism import Mutation
# DeepLift
from kipoi_interpret.importance_scores.referencebased import DeepLift

Gradient * input example

# seqa = one-hot-encoded DNA sequence
import kipoi
model = kipoi.get_model("<my-model>")
ginp = GradientXInput(model)
val = ginp.score(batch_input)  # val is an array of importance scores

See notebooks/1-DNA-seq-model-example.ipynb for an example.

Release History

  • 0.1.0
    • First release to PyPI