Plugins

To enable additional functionality beyond just running model predictions, a plugin is available:

  • kipoi-interpret: model interpretation.github, docs

Kipoi-interpret

Kipoi-interpret is a general (genomics agnostic) plugin and allows to compute the feature importance scores like saliency maps or DeepLift for Kipoi models.

import kipoi
from kipoi_interpret.importance_scores.gradient import GradientXInput

model = kipoi.get_model("DeepBind/Homo_sapiens/TF/D00765.001_ChIP-seq_GATA1")

val = GradientXInput(model).score(seq_array)[0]
seqlogo_heatmap(val, val.T)

interpret