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 | – |