Table 2 Performance comparison of the different clustering methods on the dataset\(S_1 \sim S_6\). Here, Identity is the parameter of clustering tools, AMI is the abbreviation of adjusted mutual information, FMI is the abbreviation of Fowlkes-Mallows Index, ACC is the abbreviation of accuracy, HOMO is the abbreviation of homogeneity, and COMP is the abbreviation of completeness
Dataset | Tool | Identity (%) | AMI (%) | FMI (%) | ACC (%) | HOMO (%) | COMP (%) | Time (min:sec) |
|---|---|---|---|---|---|---|---|---|
S1 | MeShClust | 80.0 | 58.17 | 34.51 | 42.16 | 64.46 | 54.57 | 1:07.81 |
85.0 | 58.31 | 36.65 | 44.31 | 67.53 | 53.91 | 1:28.03 | ||
90.0 | 62.69 | 40.18 | 36.35 | 86.60 | 51.69 | 0:58.17 | ||
95.0 | 56.66 | 33.69 | 24.86 | 94.59 | 45.62 | 1:00.59 | ||
CD-HIT | 80.0 | 77.63 | 66.28 | 57.32 | 100.00 | 64.61 | 0:01.03 | |
85.0 | 70.51 | 59.47 | 49.78 | 100.00 | 57.06 | 0:01.60 | ||
90.0 | 58.73 | 45.50 | 36.92 | 100.00 | 47.41 | 0:02.67 | ||
95.0 | 41.30 | 26.92 | 18.71 | 100.00 | 37.89 | 0:04.00 | ||
UCLUST | 80.0 | 61.74 | 47.37 | 37.97 | 100.00 | 49.06 | 0:00.59 | |
85.0 | 54.53 | 38.50 | 28.34 | 100.00 | 44.09 | 0:00.80 | ||
90.0 | 44.19 | 27.02 | 17.64 | 100.00 | 38.64 | 0:01.09 | ||
95.0 | 32.67 | 18.10 | 11.48 | 100.00 | 34.33 | 0:01.44 | ||
HycDemux | - | 97.73 | 97.40 | 96.75 | 99.99 | 95.59 | 0:10.95 | |
S2 | MeShClust | 80.0 | 67.10 | 50.96 | 57.66 | 70.45 | 64.98 | 0:55.28 |
85.0 | 67.63 | 52.12 | 52.67 | 83.91 | 58.61 | 1:12.78 | ||
90.0 | 61.96 | 50.08 | 41.15 | 92.98 | 50.83 | 1:00.49 | ||
95.0 | 59.67 | 49.57 | 44.31 | 96.26 | 49.03 | 1:56.98 | ||
CD-HIT | 80.0 | 81.89 | 71.30 | 65.57 | 100.00 | 70.02 | 0:01.40 | |
85.0 | 73.60 | 60.10 | 52.22 | 100.00 | 60.09 | 0:02.36 | ||
90.0 | 60.24 | 42.76 | 33.59 | 100.00 | 48.08 | 0:04.63 | ||
95.0 | 40.52 | 24.03 | 16.17 | 100.00 | 37.37 | 0:07.25 | ||
UCLUST | 80.0 | 63.74 | 45.82 | 35.77 | 100.00 | 50.27 | 0:00.96 | |
85.0 | 53.73 | 32.44 | 22.27 | 100.00 | 43.06 | 0:01.35 | ||
90.0 | 40.88 | 20.52 | 13.63 | 100.00 | 36.89 | 0:01.91 | ||
95.0 | 26.29 | 12.46 | 7.34 | 100.00 | 32.38 | 0:02.44 | ||
HycDemux | - | 99.89 | 99.91 | 99.91 | 100.00 | 95.59 | 0:13.12 | |
S3 | MeShClust | 80.0 | 85.06 | 83.40 | 86.24 | 93.44 | 79.06 | 1:33.12 |
85.0 | 79.99 | 81.27 | 79.19 | 96.50 | 70.48 | 1:58.35 | ||
90.0 | 66.37 | 65.43 | 61.96 | 94.12 | 56.85 | 2:01.84 | ||
95.0 | 57.65 | 58.07 | 45.25 | 99.47 | 48.83 | 1:07.26 | ||
CD-HIT | 80.0 | 88.70 | 83.32 | 78.95 | 100.00 | 79.99 | 0:01.65 | |
85.0 | 81.22 | 74.83 | 67.45 | 100.00 | 69.48 | 0:03.20 | ||
90.0 | 67.86 | 60.14 | 52.22 | 100.00 | 55.24 | 0:06.92 | ||
95.0 | 44.53 | 30.26 | 21.45 | 100.00 | 39.50 | 0:04.00 | ||
UCLUST | 80.0 | 68.75 | 54.50 | 44.48 | 100.00 | 55.08 | 0:01.29 | |
85.0 | 58.44 | 44.18 | 32.51 | 100.00 | 46.91 | 0:01.79 | ||
90.0 | 44.36 | 26.50 | 18.00 | 100.00 | 38.76 | 0:02.46 | ||
95.0 | 26.93 | 14.09 | 8.60 | 100.00 | 32.67 | 0:01.44 | ||
HycDemux | - | 97.78 | 96.90 | 95.39 | 100.00 | 95.67 | 0:19.34 | |
S4 | MeShClust | 80.0 | 54.00 | 24.31 | 32.06 | 65.57 | 50.39 | 0:47.93 |
85.0 | 49.58 | 17.13 | 27.23 | 59.03 | 47.54 | 0:57.78 | ||
90.0 | 55.31 | 28.55 | 23.48 | 87.42 | 49.55 | 1:01.96 | ||
95.0 | 50.60 | 26.03 | 19.31 | 92.11 | 47.40 | 1:04.56 | ||
CD-HIT | 80.0 | 78.29 | 59.75 | 50.20 | 99.99 | 67.34 | 0:01.28 | |
85.0 | 69.95 | 50.26 | 40.07 | 100.00 | 59.80 | 0:01.89 | ||
90.0 | 56.29 | 36.47 | 26.12 | 100.00 | 51.10 | 0:03.31 | ||
95.0 | 35.86 | 20.55 | 12.87 | 100.00 | 43.17 | 0:04.77 | ||
UCLUST | 80.0 | 61.21 | 39.56 | 29.19 | 100.00 | 53.59 | 0:00.79 | |
85.0 | 53.42 | 32.61 | 22.30 | 100.00 | 49.51 | 0:01.03 | ||
90.0 | 40.48 | 21.84 | 13.65 | 100.00 | 44.40 | 0:01.46 | ||
95.0 | 27.05 | 14.30 | 8.36 | 100.00 | 40.78 | 0:01.85 | ||
HycDemux | - | 98.42 | 97.03 | 96.28 | 99.73 | 97.18 | 0:19.96 | |
S5 | MeShClust | 80.0 | 68.39 | 47.68 | 52.91 | 82.86 | 62.65 | 1:03.37 |
85.0 | 62.40 | 36.39 | 46.49 | 82.04 | 57.61 | 1:43.73 | ||
90.0 | 54.90 | 24.28 | 33.06 | 73.30 | 52.13 | 1:55.66 | ||
95.0 | 53.89 | 24.53 | 31.02 | 82.26 | 51.23 | 1:06.23 | ||
CD-HIT | 80.0 | 85.39 | 71.10 | 64.08 | 100.00 | 75.94 | 0:01.66 | |
85.0 | 77.87 | 60.19 | 51.56 | 100.00 | 67.23 | 0:02.76 | ||
90.0 | 65.62 | 48.89 | 39.54 | 100.00 | 57.13 | 0:04.93 | ||
95.0 | 45.10 | 28.76 | 20.16 | 100.00 | 46.40 | 0:07.29 | ||
UCLUST | 80.0 | 70.56 | 55.00 | 43.23 | 100.00 | 60.60 | 0:01.13 | |
85.0 | 60.71 | 44.25 | 32.51 | 100.00 | 53.79 | 0:01.56 | ||
90.0 | 46.99 | 30.48 | 20.19 | 100.00 | 47.03 | 0:02.12 | ||
95.0 | 30.91 | 18.12 | 10.80 | 100.00 | 41.81 | 0:02.50 | ||
HycDemux | - | 98.77 | 97.43 | 95.90 | 99.99 | 97.61 | 0:29.50 | |
S6 | MeShClust | 80.0 | 87.66 | 79.22 | 83.36 | 93.81 | 83.40 | 0:49.57 |
85.0 | 83.44 | 76.77 | 77.05 | 95.24 | 76.69 | 1:01.72 | ||
90.0 | 76.70 | 71.47 | 68.35 | 96.18 | 68.72 | 1:03.75 | ||
95.0 | 70.43 | 64.56 | 56.08 | 98.07 | 62.35 | 1:05.74 | ||
CD-HIT | 80.0 | 92.46 | 86.29 | 82.23 | 100.00 | 86.44 | 0:01.58 | |
85.0 | 86.30 | 77.45 | 72.41 | 100.00 | 77.51 | 0:02.80 | ||
90.0 | 74.23 | 61.01 | 52.30 | 100.00 | 64.25 | 0:05.54 | ||
95.0 | 52.12 | 32.98 | 24.42 | 100.00 | 49.34 | 0:09.23 | ||
UCLUST | 80.0 | 78.99 | 67.27 | 57.71 | 100.00 | 68.73 | 0:01.27 | |
85.0 | 69.14 | 54.09 | 44.34 | 100.00 | 59.75 | 0:01.73 | ||
90.0 | 53.36 | 34.91 | 25.64 | 100.00 | 49.81 | 0:02.39 | ||
95.0 | 31.74 | 15.71 | 9.68 | 100.00 | 41.86 | 0:03.07 | ||
HycDemux | - | 99.40 | 99.11 | 98.93 | 100.00 | 98.82 | 0:33.77 |