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Table 1 Benchmarks for path and cycle enumeration

From: Computing paths and cycles in biological interaction graphs

Network Nodes Edges Enumeration of cycles Enumeration of input-output paths
    Number of cycles EMC Johnson Number of I/O paths EMC Breadth-first
     [s] [s]   [s] [s]
T-cell 94 138 100 0.1 0.04 8058 0.98 0.27
EGFR 106 230 237 0.15 0.07 384766 131 21
T-cell+EGFR 200 410 337 6.0 ± 0.9 0.14 ± 0.01 n/a n/a n/a
Regulon DB 1493 3565 132 194 0.77 44194 4716 38
CA1 neuron 512 1047 n/a n/a n/a n/a n/a n/a
Cancer signaling 1240 3144 n/a n/a n/a n/a n/a n/a
  1. The running times when using elementary modes computation (columns "EMC") are compared with those of the graph-algorithms (Johnson's algorithm and breadth-first search, respectively). The number of edges refers to unique edges (parallel edges with the same sign and half-edges are removed before calculation). The values for the combined network "T-cell+EGFR" are mean and standard error over ten runs with different random connections between the two networks. An entry n/a indicates that the procedure quickly ran out of memory (3 GB) because of a combinatorial explosion of paths or cycles. The platform used was MATLAB 2006 b under 32 bit Linux with an Intel E6600 processor.