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Table 1 GNT and GNA benchmark parameters

From: PyGNA: a unified framework for geneset network analysis

Parameter Description GNT-SBM GNT-HDN GNA-SBM
n Number of nodes 1000 1000 1000
k Number of blocks 7 9
\(p_0\) Baseline connection probability 0.01, 0.02, 0.05 0.006, 0, 02 0.01, 0.02
m Size of the geneset 20, 50, 100 \(9, \dots , 200\) 50, 80
\(\alpha\) Within block connection probability scaling 2, 3, 5, 10 2, 5
\(\beta\) Between block connection probability scaling 0 0, 10
\(p_{hd}\) HDN connection probability 0.5, 0.2, 0.1, 0.08, 0.05, 0.01
  1. For each model, we report the name of the parameter, a short description and its setting. A dash is reported when the parameter is not used