Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning
Ján Kočí, Olga Flegontova, Piya Changmai, Leonid A. Vyazov, Leo R. Cooper, Hossein Ashrafi, Zeynep Şencan, Pavel Flegontov
Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.
bioRxiv · Aug 17, 2026 · PreprintGenetics✦ In-depth digest