Table 2.
Results from 100,000 Monte Carlo simulations of four hypothetical four-gene networks (A, B, C, D)a describing the ability of the TAO-Gen algorithm to specify the correct network.
| Frequency (%) of resulting optimal network structure
|
Rank (%) of the posterior likelihood for the true network over all possible 543 acyclic networks
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample size | True model |  |
 |
 |
 |
 |
 |
 |
1 | 2 | 3 | 4–10 |
| 100 arrays | A | 922 (92) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 68 (7) | 0 (0) | 922 (92) | 52 (5) | 10 (1) | 16 (2) |
| 1,000 sims | B | 977 (98) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 6 (1) | 0 (0) | 977 (98) | 17 (2) | 4 (0.4) | 2 (0.2) |
| C | 929 (93) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 71 (7) | 0 (0) | 929 (93) | 50 (5) | 8 (1) | 13 (1) | |
| D | 980 (98) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 6 (1) | 0 (0) | 980 (98) | 13 (1) | 5 (0.5) | 2 (0.2) | |
| 50 arrays | A | 1,716 (86) | 4 (0.2) | 3 (0.2) | 6 (0.3) | 4 (0.2) | 165 (8) | 0 (0) | 1,716 (87) | 157 (8) | 34 (2) | 70 (4) |
| 2,000 sims | B | 1,841 (92) | 8 (0.4) | 0 (0) | 4 (0.2) | 8 (0.4) | 41 (2) | 0 (0) | 1,841 (92) | 82 (4) | 20 (1) | 55 (3) |
| C | 1,745 (87) | 6 (0.3) | 4 (0.2) | 3 (0.2) | 6 (0.3) | 175 (9) | 0 (0) | 1,745 (88) | 128 (6) | 41 (2) | 62 (3) | |
| D | 1,860 (93) | 4 (0.2) | 0 (0) | 2 (0.1) | 0 (0) | 46 (2) | 0 (0) | 1,860 (93) | 68 (3) | 30 (2) | 42 (2) | |
| 25 arrays | A | 2,920 (73) | 76 (2) | 72 (2) | 56 (1) | 77 (2) | 328 (8) | 3 (0.1) | 2,920 (73) | 423 (10) | 112 (3) | 387 (10) |
| 4,000 sims | B | 3,179 (80) | 92 (2) | 55 (1) | 48 (1) | 47 (1) | 192 (5) | 8 (0.2) | 3,179 (79) | 348 (9) | 133 (3) | 249 (6) |
| C | 2,891 (72) | 60 (1) | 100 (2) | 56 (1) | 76 (2) | 296 (7) | 4 (0.1) | 2,891 (72) | 404 (10) | 114 (3) | 444 (11) | |
| D | 3,086 (77) | 76 (2) | 96 (2) | 48 (1) | 48 (1) | 164 (4) | 8 (0.2) | 3,086 (77) | 328 (8) | 149 (4) | 365 (9) | |
| 10 arrays | A | 3,198 (32) | 909 (9) | 741 (7) | 230 (2) | 149 (2) | 328 (3) | 497 (5) | 3,198 (32) | 1,027 (10) | 781 (8) | 2,389 (24) |
| 10,000 sims | B | 3,768 (38) | 1,002 (10) | 1,051 (10) | 220 (2) | 309 (3) | 378 (4) | 567 (6) | 3,768 (38) | 966 (10) | 821 (8) | 2,519 (25) |
| C | 3,177 (32) | 892 (9) | 691 (7) | 230 (2) | 151 (2) | 398 (4) | 457 (5) | 3,177 (32) | 1,232 (12) | 769 (8) | 2,347 (23) | |
| D | 3,768 (38) | 1,052 (10) | 1,031 (10) | 280 (3) | 259 (3) | 538 (5) | 477 (5) | 3,768 (38) | 1,146 (11) | 871 (9) | 2,371 (24) | |
a
(A) β14 = 2.0, β13 = 0.8, β23 = 0.8, β34 = −1.3, σ1 = σ2 = σ3 = σ4 = 1.0
(B) β14 = 2.0, β13 = 0.8, β23 = 0.8, β34 = −5.0, σ1 = σ2 = σ3 = σ4 = 1.0
(C) β14 = 2.0, β13 = 0.8, β23 = 0.8, β34 = −1.3, σ1 = σ2 = σ3 = σ4 = 1/3
(D) β14 = 2.0, β13 = 0.8, β23 = 0.8, β34 = −5.0, σ1 = σ2 = σ3 = σ4 = 1/3
