GeneticsbioRxivPreprint
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Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning
Ján Kočí, Olga Flegontova, Piya Changmai…·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.
DOI 10.64898/2026.08.11.744230