Figure 1.
MIDER workflow.
Figure 2.
One of the MIDER outputs, shown for Benchmark B2: a 3D plot of the mutual information between a variable (X3) and the rest, for different time lags between variables.
Table 1.
Benchmarks.
Figure 3.
PR curves (recall in horizontal axis, precision in vertical axis) of all the benchmarks (B1–B7) for five network inference methods (ARACNE, CLR, MRNET, TDARACNE, and MIDER) and for the community prediction. Solid lines and small dots correspond to the (P,R) values obtained by changing the threshold for detecting interactions. Large square points correspond to the (P,R) values obtained with the default (out of the box) settings of each method.
Figure 4.
The color maps show precision (left panel) and recall (central panel) achieved by each method and for each benchmark with its default settings, as well as the area under precision-recall curve (AUPR, right panel). Numerical values are in the range [0–1], and are represented in colors according to the scale in the right (green = good, blue = bad).
Figure 5.
First reaction steps of glycolysis.
Figure 6.
Reaction chain with 8 species.
Figure 7.
Reaction chain with 4 species.
Figure 8.
IRMA.
Figure 9.
MAPK cascade.