Table 3.
Means (SDs) of prediction mean squared error (PMSE), number of removed informative variables (q1) and number of removed non-informative variables (q0) with an additional L1 penalty for only target genes (L1-T) or all the genes (L1-A), or with different weights in network-based regression from 100 simulated datasets. The minimal mean PMSEs for each set-up are boldfaced.
| Set-up | Methods |
p1 = 44, p0 = 66
|
||
|---|---|---|---|---|
| PMSE | q1 | q0 | ||
| 1 | γ = 2, L1-T | 127.2 (23.7) | 7.1 (2.8) | 56.0 (6.8) |
| γ = 8, L1-T | 122.9 (26.5) | 3.2 (2.8) | 60.4 (4.7) | |
| γ = ∞, L1-T | 128.3 (27.3) | 4.7 (2.9) | 59.3 (4.6) | |
| γ = 2, L1-A | 148.2 (32.5) | 7.6 (3.6) | 59.2 (5.6) | |
| γ = 8, L1-A | 144.8 (36.6) | 5.8 (4.2) | 59.1 (5.6) | |
| γ = ∞, L1-A | 161.8 (48.5) | 9.0 (4.8) | 57.5 (6.1) | |
| γ = 2, wi = di | 190.3 (56.9) | 11.6 (5.4) | 59.4 (6.4) | |
| γ = 8, wi = di | 188.2 (38.6) | 13.5 (4.4) | 57.8 (6.4) | |
| γ = ∞, | 114.1 (22.5) | 0.1 (0.8) | 55.3 (10.7) | |
| 2 | γ = 2, L1-T | 136.3 (28.4) | 15.7 (4.7) | 60.9 (4.3) |
| γ = 8, L1-T | 151.7 (36.4) | 16.0 (7.2) | 60.9 (5.0) | |
| γ = ∞, L1-T | 154.9 (45.4) | 16.9 (7.0) | 60.5 (5.2) | |
| γ = 2, L1-A | 163.2 (47.2) | 20.6 (7.0) | 60.9 (5.4) | |
| γ = 8, L1-A | 176.0 (56.2) | 22.0 (8.8) | 61.3 (6.0) | |
| γ = ∞, L1-A | 186.3 (60.6) | 25.1 (8.7) | 61.7 (6.3) | |
| γ = 2, wi = di | 199.5 (69.5) | 27.7 (9.0) | 62.4 (5.7) | |
| γ = 8, wi = di | 242.1 (96.4) | 31.6 (11.4) | 61.0 (6.5) | |
| γ = ∞, | 127.2 (24.3) | 3.0 (4.9) | 56.4 (8.5) | |
| 3 | γ = 2, L1-T | 92.6 (18.1) | 10.0 (2.7) | 58.7 (5.1) |
| γ = 8, L1-T | 98.2 (25.0) | 7.2 (4.8) | 61.4 (4.1) | |
| γ = ∞, L1-T | 99.7 (23.0) | 8.2 (4.2) | 60.3 (4.9) | |
| γ = 2, L1-A | 113.5 (31.6) | 11.9 (4.6) | 60.3 (4.9) | |
| γ = 8, L1-A | 115.5 (36.5) | 11.2 (5.8) | 60.9 (5.2) | |
| γ = ∞, L1-A | 129.2 (44.3) | 14.2 (6.3) | 59.9 (6.5) | |
| γ = 2, wi = di | 153.5 (43.8) | 18.3 (6.5) | 61.9 (6.4) | |
| γ = 8, wi = di | 137.7 (58.9) | 16.9 (5.3) | 58.7 (6.3) | |
| γ = ∞, | 86.2 (18.9) | 0.7 (2.2) | 56.7 (9.3) | |
| 4 | γ = 2, L1-T | 100.0 (20.0) | 17.5 (4.8) | 61.2 (4.0) |
| γ = 8, L1-T | 115.7 (31.7) | 17.7 (8.2) | 61.3 (6.1) | |
| γ = ∞, L1-T | 116.4 (31.6) | 18.7 (7.6) | 60.7 (6.3) | |
| γ = 2, L1-A | 125.3 (33.4) | 22.3 (7.3) | 61.7 (5.6) | |
| γ = 8, L1-A | 140.8 (45.5) | 25.3 (8.8) | 62.6 (5.4) | |
| γ = ∞, L1-A | 144.3 (45.7) | 26.9 (8.3) | 62.9 (5.0) | |
| γ = 2, wi = di | 163.2 (54.8) | 31.4 (8.6) | 63.8 (3.5) | |
| γ = 8, wi = di | 202.6 (65.7) | 36.2 (10.7) | 62.4 (6.3) | |
| γ = ∞, | 92.6 (18.5) | 4.8 (6.2) | 57.9 (7.2) | |
| Set-up | Methods |
p1 = 24, p0 = 86
|
||
| PMSE | q1 | q0 | ||
| 5 | γ = 2, L1-T | 90.3 (17.4) | 3.8 (1.9) | 68.9 (4.7) |
| γ = 8, L1-T | 100.6 (22.7) | 3.2 (2.7) | 66.3 (5.1) | |
| γ = ∞, L1-T | 102.1 (27.0) | 4.0 (2.7) | 65.7 (7.1) | |
| γ = 2, L1-A | 114.6 (34.1) | 5.8 (3.3) | 69.8 (5.6) | |
| γ = 8, L1-A | 120.1 (34.8) | 6.6 (3.8) | 68.7 (7.3) | |
| γ = ∞, L1-A | 133.4 (43.8) | 8.3 (4.1) | 69.7 (8.7) | |
| γ = 2, wi = di | 151.8 (50.2) | 10.4 (4.1) | 72.9 (8.8) | |
| γ = 8, wi = di | 173.8 (103.2) | 11.9 (6.6) | 71.1 (10.8) | |
| γ = ∞, | 83.2 (15.1) | 0.3 (1.1) | 59.7 (8.1) | |