Table 2 10 times repeated 5-fold cross-validated F1 score for 19 population classes from 1000 Genomes Project using SVM, PCA or GTM
From: Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics
Ancestry | 1000G code | Population | PCA 8-NN | SVM 10 PCs | GTM 3 PCs | GTM 10 PCs |
|---|---|---|---|---|---|---|
EAS | CHB | Han Chinese | 0.20±0.01 | 0.78±0.01 | 0.45±0.04 | 0.75±0.01 |
EAS | JPT | Japanese | 0.37±0.02 | 1.00±0.00 | 0.80±0.01 | 1.00±0.00 |
EAS | CHS | Southern Han Chinese | 0.34±0.02 | 0.80±0.01 | 0.54±0.02 | 0.80±0.01 |
EAS | CDX | Chinese Dai | 0.24±0.02 | 0.10±0.02 | 0.51±0.03 | 0.44±0.08 |
EAS | KHV | Kinh in Vietnam | 0.44±0.01 | 0.68±0.00 | 0.63±0.01 | 0.71±0.01 |
EUR | CEU+GBR | Northern/Western Eur. | 0.75±0.01 | 0.99±0.00 | 0.79±0.01 | 0.99±0.00 |
EUR | TSI | Toscani | 0.46±0.01 | 0.74±0.02 | 0.58±0.01 | 0.54±0.06 |
EUR | FIN | Finnish | 0.95±0.01 | 0.99±0.00 | 0.91±0.01 | 0.99±0.01 |
EUR | IBS | Iberian | 0.35±0.03 | 0.81±0.01 | 0.35±0.04 | 0.74±0.02 |
AFR | YRI | Yoruba in Nigeria | 0.30±0.02 | 0.69±0.00 | 0.15±0.03 | 0.66±0.03 |
AFR | LWK | Luhya | 0.67±0.01 | 1.00±0.00 | 0.59±0.01 | 1.00±0.00 |
AFR | GWD | Gambian | 0.26±0.02 | 0.94±0.02 | 0.23±0.02 | 0.78±0.07 |
AFR | MSL | Mende | 0.25±0.03 | 0.93±0.02 | 0.35±0.03 | 0.81±0.04 |
AFR | ESN | Esan in Nigeria | 0.28±0.02 | 0.00±0.01 | 0.19±0.05 | 0.28±0.13 |
AMR | PUR | Puerto Ricans | 0.90±0.01 | 0.86±0.02 | 0.90±0.01 | 0.87±0.03 |
AMR | CLM | Colombians | 0.69±0.01 | 0.85±0.01 | 0.84±0.01 | 0.82±0.02 |
AMR | PEL | Peruvians | 0.88±0.01 | 0.97±0.01 | 0.94±0.01 | 0.95±0.01 |
SAS | PJL | Punjabi | 0.89±0.01 | 0.96±0.01 | 0.96±0.01 | 0.96±0.00 |
SAS | BEB | Bengali | 0.95±0.01 | 0.96±0.01 | 0.96±0.01 | 0.96±0.01 |
Overall | 0.54±0.00 | 0.80±0.00 | 0.61±0.01 | 0.80±0.01 |