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Added supplementary data tables
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benjamin-james committed Jan 27, 2018
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13 changes: 13 additions & 0 deletions Tables/Align.csv
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Name,Data,Id,Realtime,Utime,Mem(MB),1-1,Intra,Inter,Sil,Clusters >= 5,avg size >= 5,median size >= 5,pct of clusters >= 5,Purity,NMI
MeShClust,15k,0.83,0:05.73,17.6,93.97265625,100%,96.403,39.606,0.933,200,74.965,74,99.502,1,1
MeShClust with Alignment,15k,0.83,11:00.77,2381.7,190.7578125,100%,93.569,39.677,0.880,200,74.965,74,99.502,1,1
MeShClust,15k,0.87,0:04.42,15.1,93.99609375,99.5%,96.400,39.602,0.918,201,74.582,74,99.015,1,1
MeShClust with Alignment,15k,0.87,8:35.88,1905.8,173,99.5%,93.474,39.684,0.873,201,74.582,74,98.529,1,1
MeShClust,15k,0.9,0:04.28,14.7,93.98046875,99.5%,96.413,39.602,0.918,201,74.572,74,99.015,1,1
MeShClust with Alignment,15k,0.9,6:47.68,1526.8,159.7890625,99.5%,93.464,39.653,0.870,201,74.562,74,97.101,1,1
MeShClust,15k,0.93,0:04.15,14.2,93.9453125,99.5%,96.404,39.600,0.918,201,74.592,74,99.505,1,1
MeShClust with Alignment,15k,0.93,6:02.54,1373.4,159.4765625,97.5%,93.654,39.650,0.802,212,69.925,72,60.399,1,0.993
MeShClust,15k,0.96,0:04.09,13.7,94.046875,98.5%,96.352,39.577,0.873,206,72.684,74,93.636,1,0.998
MeShClust with Alignment,15k,0.96,23:08.02,5382.1,305.0234375,64.5%,95.735,39.599,0.902,202,58.183,59,5.919,1,0.905
MeShClust,15k,0.97,0:05.56,15.1,96.609375,99%,96.483,39.576,0.874,205,70.927,71,31.202,1,0.984
MeShClust with Alignment,15k,0.97,40:38.75,9510.7,441.0390625,0%,96.795,39.635,0.940,200,40.245,41,2.812,1,0.821
20 changes: 20 additions & 0 deletions Tables/Align.org
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| Name | Data | Id | Realtime | Utime | Mem(MB) | 1-1 | Intra | Inter | Sil | Clusters >= 5 | avg size >= 5 | median size >= 5 | pct of clusters >= 5 | Purity | NMI |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
| MeShClust | 15k | 0.83 | 0:05.73 | 17.6 | 93.97265625 | 100% | 96.403 | 39.606 | 0.933 | 200 | 74.965 | 74 | 99.502 | 1 | 1 |
| MeShClust with Alignment | 15k | 0.83 | 11:00.77 | 2381.7 | 190.7578125 | 100% | 93.569 | 39.677 | 0.880 | 200 | 74.965 | 74 | 99.502 | 1 | 1 |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
| MeShClust | 15k | 0.87 | 0:04.42 | 15.1 | 93.99609375 | 99.5% | 96.400 | 39.602 | 0.918 | 201 | 74.582 | 74 | 99.015 | 1 | 1 |
| MeShClust with Alignment | 15k | 0.87 | 8:35.88 | 1905.8 | 173 | 99.5% | 93.474 | 39.684 | 0.873 | 201 | 74.582 | 74 | 98.529 | 1 | 1 |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
| MeShClust | 15k | 0.9 | 0:04.28 | 14.7 | 93.98046875 | 99.5% | 96.413 | 39.602 | 0.918 | 201 | 74.572 | 74 | 99.015 | 1 | 1 |
| MeShClust with Alignment | 15k | 0.9 | 6:47.68 | 1526.8 | 159.7890625 | 99.5% | 93.464 | 39.653 | 0.870 | 201 | 74.562 | 74 | 97.101 | 1 | 1 |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
| MeShClust | 15k | 0.93 | 0:04.15 | 14.2 | 93.9453125 | 99.5% | 96.404 | 39.600 | 0.918 | 201 | 74.592 | 74 | 99.505 | 1 | 1 |
| MeShClust with Alignment | 15k | 0.93 | 6:02.54 | 1373.4 | 159.4765625 | 97.5% | 93.654 | 39.650 | 0.802 | 212 | 69.925 | 72 | 60.399 | 1 | 0.993 |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
| MeShClust | 15k | 0.96 | 0:04.09 | 13.7 | 94.046875 | 98.5% | 96.352 | 39.577 | 0.873 | 206 | 72.684 | 74 | 93.636 | 1 | 0.998 |
| MeShClust with Alignment | 15k | 0.96 | 23:08.02 | 5382.1 | 305.0234375 | 64.5% | 95.735 | 39.599 | 0.902 | 202 | 58.183 | 59 | 5.919 | 1 | 0.905 |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
| MeShClust | 15k | 0.97 | 0:05.56 | 15.1 | 96.609375 | 99% | 96.483 | 39.576 | 0.874 | 205 | 70.927 | 71 | 31.202 | 1 | 0.984 |
| MeShClust with Alignment | 15k | 0.97 | 40:38.75 | 9510.7 | 441.0390625 | 0% | 96.795 | 39.635 | 0.940 | 200 | 40.245 | 41 | 2.812 | 1 | 0.821 |
|--------------------------+------+------+----------+--------+-------------+-------+--------+--------+-------+---------------+---------------+------------------+----------------------+--------+-------|
76 changes: 76 additions & 0 deletions Tables/Real.csv
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Name,Data,Id,Realtime,Utime,Mem(MB),1-1,Intra,Inter,Sil,Clusters >= 5,avg size >= 5,median size >= 5,pct of clusters >= 5,Purity,NMI
CD-HIT,15k,0.83,0:01.94,1.9,41.05859375,100%,92.673,39.643,0.864,200,74.965,74,99.502,1,1
DNACLUST,15k,0.83,0:21.58,78.3,401.48046875,92%,92.941,39.703,0.612,228,63.754,69,37.438,1,0.981
MeShClust,15k,0.83,0:05.73,17.6,93.97265625,100%,96.403,39.606,0.933,200,74.965,74,99.502,1,1
UCLUST,15k,0.83,0:01.48,1.4,10.05078125,90%,92.848,39.541,0.660,233,64.258,69,94.715,1,0.991
CD-HIT,15k,0.87,0:01.91,1.9,41.109375,100%,92.673,39.643,0.864,200,74.965,74,99.502,1,1
DNACLUST,15k,0.87,1:06.79,231.1,401.484375,29%,93.593,39.559,0.480,323,36.576,37,10.720,1,0.893
MeShClust,15k,0.87,0:04.42,15.1,93.99609375,99.5%,96.400,39.602,0.918,201,74.582,74,99.015,1,1
UCLUST,15k,0.87,0:01.69,1.6,10.328125,80.5%,92.908,39.545,0.548,275,54.095,63,80.645,1,0.979
CD-HIT,15k,0.9,0:01.87,1.8,41.171875,100%,92.673,39.643,0.864,200,74.965,74,99.502,1,1
DNACLUST,15k,0.9,1:37.91,328.9,401.484375,0%,94.982,39.631,0.370,423,17.381,14,5.877,1,0.795
MeShClust,15k,0.9,0:04.28,14.7,93.98046875,99.5%,96.413,39.602,0.918,201,74.572,74,99.015,1,1
UCLUST,15k,0.9,0:01.01,0.9,11.3515625,53%,93.148,39.604,0.362,394,36.977,33,62.342,1,0.950
CD-HIT,15k,0.93,0:01.38,1.3,41.16796875,95%,92.575,39.633,0.759,223,66.906,71,82.900,1,0.993
DNACLUST,15k,0.93,1:12.26,229.8,401.46875,0%,96.632,39.737,0.709,262,9.893,8,2.219,1,0.735
MeShClust,15k,0.93,0:04.15,14.2,93.9453125,99.5%,96.404,39.600,0.918,201,74.592,74,99.505,1,1
UCLUST,15k,0.93,0:01.31,1.3,15.48828125,9.5%,93.930,39.601,0.209,639,20.343,14,34.709,1,0.885
CD-HIT,15k,0.96,0:01.41,1.3,55.8671875,4.5%,94.370,39.627,0.282,493,20.744,15,11.251,1,0.843
DNACLUST,15k,0.96,0:28.71,73.4,401.44140625,0%,98.214,44.197,0.889,34,5.765,5,0.237,1,0.713
MeShClust,15k,0.96,0:04.09,13.7,94.046875,98.5%,96.352,39.577,0.873,206,72.684,74,93.636,1,0.998
UCLUST,15k,0.96,0:02.34,2.3,31.90625,0%,95.643,39.633,0.210,650,10.766,8,9.884,1,0.784
WCD,15k,0.96,0:04.70,18.13,22.914,66.5%,96.848,39.975,0.941,135,73.970,74,2.624,1,0.879
CD-HIT,15k,0.97,0:01.26,1.2,71.84765625,0%,95.889,39.658,0.370,448,11.891,9,5,1,0.765
DNACLUST,15k,0.97,0:18.03,40.0,401.453125,0%,98.787,100,0.988,5,5.200,5,0.034,1,0.712
MeShClust,15k,0.97,0:05.56,15.1,96.609375,99%,96.483,39.576,0.874,205,70.927,71,31.202,1,0.984
UCLUST,15k,0.97,0:02.67,2.6,43.5078125,0%,96.421,39.692,0.373,459,8.669,7,4.888,1,0.752
CD-HIT,150k,0.83,0:59.29,59.1,106.05078125,100%,92.592,39.393,0.859,2000,75.147,75,99.950,1,1
DNACLUST,150k,0.83,35:06.76,7892.5,489.19140625,90.05%,93.031,39.302,0.579,2353,61.605,68,35.004,1,0.984
MeShClust,150k,0.83,1:36.63,327.3,230.171875,100%,96.369,39.373,0.930,2001,75.104,75,99.503,1,1
UCLUST,150k,0.83,0:21.28,21.0,60.30078125,90.3%,92.721,39.314,0.654,2330,64.385,70,94.218,1,0.994
CD-HIT,150k,0.87,0:59.56,59.4,105.8984375,100%,92.592,39.393,0.859,2000,75.147,75,99.950,1,1
DNACLUST,150k,0.87,1:40:27,22709.3,489.19140625,27.95%,93.568,39.357,0.443,3532,33.367,31,11.439,1,0.919
MeShClust,150k,0.87,1:21.26,279.5,230.19921875,100%,96.368,39.374,0.930,2001,75.104,75,99.552,1,1
UCLUST,150k,0.87,0:25.66,25.4,60.30078125,79.45%,92.787,39.337,0.536,2795,53.325,62,80.524,1,0.985
CD-HIT,150k,0.9,0:58.85,58.6,105.8984375,99.8%,92.584,39.383,0.856,2006,74.922,75,99.851,1,1
DNACLUST,150k,0.9,2:18:32,30863.9,489.19140625,0.3%,95.001,39.409,0.394,4135,17.639,14,5.752,1,0.848
MeShClust,150k,0.9,1:17.54,253.0,230.3515625,100%,96.367,39.373,0.929,2001,75.106,75,99.751,1,1
UCLUST,150k,0.9,0:10.44,10.2,60.296875,51.15%,93.077,39.330,0.337,4032,36.185,31,62.280,1,0.963
CD-HIT,150k,0.93,0:14.18,14.0,105.89453125,92.9%,92.495,39.314,0.723,2311,64.693,70,83.070,1,0.994
DNACLUST,150k,0.93,1:41:11,21792.5,489.19140625,0%,96.638,39.336,0.707,2572,9.524,8,2.164,1,0.798
MeShClust,150k,0.93,1:01.88,208.9,231.12109375,100%,96.365,39.374,0.929,2001,75.103,75,99.503,1,1
UCLUST,150k,0.93,0:14.05,13.8,87.5078125,8.15%,93.891,39.383,0.195,6780,19.319,13,36.615,1,0.914
CD-HIT,150k,0.96,0:18.00,17.7,199.2265625,4.2%,94.337,39.388,0.278,4961,20.685,15,11.349,1,0.885
DNACLUST,150k,0.96,37:00.99,7067.7,489.52734375,0%,98.176,40.704,0.966,278,6.151,6,0.193,1,0.781
MeShClust,150k,0.96,0:55.82,187.6,231.90234375,100%,96.373,39.372,0.930,2001,75.054,75,95.195,1,1
UCLUST,150k,0.96,0:26.88,26.4,282.81640625,0%,95.643,39.407,0.226,6497,10.597,8,9.716,1,0.838
WCD,150k,0.96,5:21.11,1229.33,45.867,31.2%,96.915,39.452,0.941,631,74.633,75,0.607,1,0.836
CD-HIT,150k,0.97,0:18.56,18.2,334.578125,0%,95.861,39.393,0.362,4388,12.182,9,4.911,1,0.824
DNACLUST,150k,0.97,21:36.88,3882.7,489.19140625,0%,98.680,44.850,0.976,42,5.619,5,0.029,1,0.780
MeShClust,150k,0.97,1:27.05,274.9,256.46875,96.2%,96.291,39.361,0.926,2006,71.457,72,22.486,1,0.984
UCLUST,150k,0.97,0:32.39,32.0,390.3828125,0%,96.416,39.356,0.367,4543,8.799,7,4.812,1,0.813
CD-HIT,Costello,0.83,10:17.57,616.4,491.36328125,NA,84.643,62.627,0.320,568,1885.092,74,63.111,NA,NA
DNACLUST,Costello,0.83,2:26.16,425.1,1127.2734375,NA,85.109,62.942,0.306,615,1740.629,52,57.584,NA,NA
MeShClust,Costello,0.83,6:18.42,591.5,927.1171875,NA,88.611,65.021,0.437,341,3139.625,20,43.550,NA,NA
UCLUST,Costello,0.83,2:18.56,136.1,412.37890625,NA,87.247,63.451,0.363,962,1112.932,55,72.824,NA,NA
CD-HIT,Costello,0.87,10:16.83,615.7,492.328125,NA,85.965,64.089,0.247,1077,993.171,35,54.421,NA,NA
DNACLUST,Costello,0.87,3:32.53,613.8,1123.4296875,NA,86.102,64.214,0.218,1197,893.310,31,51.395,NA,NA
MeShClust,Costello,0.87,6:57.30,723.5,1079.828125,NA,91.162,65.312,0.530,403,2653.918,12,25.362,NA,NA
UCLUST,Costello,0.87,3:30.73,209.4,412.37890625,NA,88.611,64.469,0.310,1668,641.192,34,63.835,NA,NA
CD-HIT,Costello,0.9,11:40.13,699.0,494.1015625,NA,88.258,64.704,0.246,1746,611.727,24,48.581,NA,NA
DNACLUST,Costello,0.9,4:22.61,707.4,1115.68359375,NA,88.395,64.936,0.197,1927,553.852,23,45.664,NA,NA
MeShClust,Costello,0.9,9:25.28,1181.2,941.80859375,NA,91.911,65.225,0.437,922,1159.304,19,37.388,NA,NA
UCLUST,Costello,0.9,1:08.47,67.2,412.3828125,NA,90.672,65.308,0.302,2605,409.837,27,56.594,NA,NA
CD-HIT,Costello,0.93,9:05.19,544.1,497.96875,NA,90.610,65.585,0.228,2832,375.775,19,41.163,NA,NA
DNACLUST,Costello,0.93,5:08.55,742.4,1130.90625,NA,91.155,65.828,0.194,3120,340.554,18,37.896,NA,NA
MeShClust,Costello,0.93,9:22.34,1193.9,950.96875,NA,92.950,65.553,0.445,1204,886.146,18,30.130,NA,NA
UCLUST,Costello,0.93,1:32.25,90.9,412.37890625,NA,92.612,66.343,0.246,4388,242.153,20,47.941,NA,NA
CD-HIT,Costello,0.96,14:06.25,844.3,510.43359375,NA,93.447,66.501,0.207,4722,223.110,14,30.086,NA,NA
DNACLUST,Costello,0.96,4:16.88,558.2,1122.30859375,NA,94.014,66.866,0.179,4946,212.043,13,25.644,NA,NA
MeShClust,Costello,0.96,9:28.71,1208.5,931.26953125,NA,94.448,66.255,0.453,1735,612.986,15,25.545,NA,NA
UCLUST,Costello,0.96,2:09.83,124.8,412.37890625,NA,94.985,67.037,0.157,7560,138.613,15,35.615,NA,NA
WCD,Costello,0.96,39:11.69,9089.53,204.906,NA,90.704,63.989,0.681,24,44596.583,10,2.424,NA,NA
CD-HIT,Costello,0.97,17:27.64,1046.4,520.4140625,NA,94.462,66.806,0.189,5630,185.592,13,25.158,NA,NA
DNACLUST,Costello,0.97,3:36.42,455.6,1123.41796875,NA,94.958,67.185,0.156,5731,181.083,12,20.561,NA,NA
MeShClust,Costello,0.97,9:47.09,1294.5,999.23828125,NA,95.281,66.370,0.464,2029,523.007,15,23.073,NA,NA
UCLUST,Costello,0.97,2:43.78,162.3,412.37890625,NA,95.905,67.304,0.073,9770,106.043,15,31.340,NA,NA
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