TABLE 1.
Comparison of four methods under different settings
| Zero (%) | ZIPFA | Log-SVD | PSVDOS | GOMMS | |||||
|---|---|---|---|---|---|---|---|---|---|
| L2 loss | |||||||||
| 0% | 2.35 | (1.75) | 2.85 | (0.22) | 2.15 | (0.15) | 4.47 | (0.39) | |
| Setting (1) | 20% | 4.53 | (0.38) | 32.84 | (1.56) | 7.07 | (0.67) | 6.20 | (0.67) |
| 40% | 12.44 | (2.18) | 171.16 | (4.57) | 33.93 | (2.57) | 47.21 | (8.82) | |
| Setting (2) | 20% | 3.94 | (0.34) | 37.65 | (1.79) | 7.65 | (0.78) | 5.60 | (0.58) |
| 40% | 28.37 | (6.14) | 210.88 | (4.42) | 41.32 | (4.59) | 26.74 | (6.87) | |
| Setting (3) | 20% | 5.10 | (0.41) | 29.89 | (1.43) | 6.74 | (0.46) | 7.25 | (0.77) |
| 40% | 8.99 | (1.29) | 144.85 | (3.93) | 30.35 | (2.46) | 8.14 | (0.92) | |
| Setting (4) | 20% | 7.62 | (1.43) | 26.56 | (1.26) | 7.84 | (0.54) | 10.79 | (1.17) |
| 40% | 18.96 | (2.63) | 95.66 | (2.99) | 32.34 | (1.49) | 21.10 | (2.64) | |
| Setting (5) | 20% | 5.16 | (0.73) | 46.67 | (3.25) | 11.26 | (1.91) | 5.29 | (0.46) |
| 40% | 18.35 | (3.04) | 178.06 | (7.09) | 36.65 | (7.33) | 6.23 | (0.61) | |
| Setting (6.1) | 20% | 54.30 | (3.86) | 158.55 | (4.09) | 55.91 | (4.16) | 49.64 | (16.73) |
| 40% | 108.38 | (5.61) | 425.31 | (4.88) | 210.84 | (12.82) | 475.17 | (46.67) | |
| Setting (6.2) | 20% | 52.50 | (3.46) | 87.89 | (4.29) | 32.89 | (1.76) | 30.50 | (2.08) |
| 40% | 111.62 | (5.32) | 375.38 | (6.31) | 144.68 | (6.80) | 256.66 | (39.89) | |
| Clustering accuracy by taxa/samples | |||||||||
| 0% | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | |
| Setting (1) | 20% | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.92 | 1.00 |
| 40% | 1.00 | 1.00 | 0.91 | 0.97 | 0.98 | 0.86 | 0.87 | 1.00 | |
| Setting (2) | 20% | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.95 | 1.00 |
| 40% | 1.00 | 1.00 | 0.66 | 0.72 | 0.92 | 0.77 | 0.92 | 1.00 | |
| Setting (3) | 20% | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.91 | 1.00 |
| 40% | 0.99 | 1.00 | 0.99 | 1.00 | 0.99 | 0.94 | 0.82 | 1.00 | |
| Setting (4) | 20% | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.84 | 1.00 |
| 40% | 0.96 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.73 | 1.00 | |
| Setting (5) | 20% | 1.00 | 1.00 | 0.99 | 0.99 | 1.00 | 0.91 | 0.99 | 1.00 |
| 40% | 1.00 | 1.00 | 0.77 | 0.83 | 0.94 | 0.82 | 0.93 | 1.00 | |
| Setting (6.1) | 20% | 0.86 | 0.79 | 0.94 | 1.00 | 0.77 | 0.63 | 0.48 | 0.44 |
| 40% | 0.65 | 0.93 | 0.71 | 0.75 | 0.39 | 0.37 | 0.41 | 0.34 | |
| Setting (6.2) | 20% | 0.86 | 0.62 | 1.00 | 0.99 | 0.92 | 0.64 | 0.84 | 0.69 |
| 40% | 0.77 | 0.73 | 0.69 | 0.94 | 0.48 | 0.42 | 0.35 | 0.34 | |
Note. The best results in each setting are in boldface.