Python - random permutation edges with score 0

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 #10

Open carissableker opened 2 months ago

carissableker commented 2 months ago

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

https://github.com/vahuynh/dynGENIE3/blob/ce8a35af949afc3ae69e38541a966379ae4a9361/dynGENIE3_python/dynGENIE3.py#L111

Does it make sense to simply throw these edges away?

vahuynh commented 2 months ago

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.