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vahuynh / dynGENIE3

Semi-parametric approach for the inference of gene regulatory networks from time series of expression data

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Python - random permutation edges with score 0

carissableker opened this issue · comments

commented

What is the reasoning behind randomly permuting the edges with score 0 in get_link_list?

dynGENIE3/dynGENIE3_python/dynGENIE3.py

Line 111 in ce8a35a

# Random permutation of edges with score equal to 0

Does it make sense to simply throw these edges away?

commented

Hi,

This permutation is there only because of the way I evaluate the predicted ranking of edges. When I know the true network, I typically evaluate the predicted ranking by computing the area under the precision-recall curve (AUPR). Given the way I compute this AUPR in practice, I would get an AUPR that is over-estimated if I throw away the edges with score 0.