Extended Data Fig. 3: Multi-head Neural ADMIXTURE results on a dataset consisting of closely related groups.
To qualitatively assess the performance of Neural ADMIXTURE on related groups, we ran multi-head Neural ADMIXTURE on a subset of the dataset All-Chms containing 504 East Asian (EAS) individuals from neighboring regions. The self-reported ancestry of these individuals are Chinese Dai in Xishuangbanna, China (CDX, 93), Han Chinese in Beijing, China (CHB, 103), Han Chinese South (CHS, 105), Japanese in Tokyo, Japan (JPT, 104) and Kinh in Ho Chi Minh City, Vietnam (KHV, 99). The network was trained in its multi-head version from K=3 to K=7 using the PCK-Means initialization. The Japanese samples (JPT) are differentiated and clearly assigned their own cluster (blue), which is present only marginally in other populations. CDX (Chinese Dai) and KHV (Vietnamese Kinh) initially share the same cluster (K=3, green), reflecting their common Southeast Asian lineage, but are split into different groups at K=4 (purple and green). As expected CHB (Han Chinese in Beijing) and CHS (Han Chinese from South China) samples share the same cluster at first (red) and are only differentiated last (at K=5, red and orange). Further structure (yellow and brown) is seen within some populations at higher K.
