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Life sciences · Preprint
arXiv · November 7, 2026
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Widely used dimensionality reduction methods prioritize neighborhood or distance 1 preservation, yet planar coordinates alone cannot certify the homological type or 2 sample-level support of higher-order structures. Obtaining this evidence directly 3 is costly because simplicial complexes grow rapidly with dimension. We propose 4 Certified Homology-Aware Reverse-scale Mapping (CHARM), which combines 5 two-dimensional coordinates with certified homology records and sample-level 6 localization. Diffusion coordinates guide cover proposals; safe contractions and a 7 Cover Quotient Tower reduce the domain of structural computation; exact algebra 8 certifies and tracks homology representatives; and reverse-scale layout places their 9 supports in shared coordinates. Safe contraction preserves the homotopy type of 10 the input flag complex. The quotient tower is multiplicatively 3-interleaved with 11 the coarse-graph hop-distance Rips filtration. Verifiable distance-distortion bounds 12 give an additive guarantee between the original Euclidean and coarse-graph Rips 13 filtrations, and composite multiplicative guarantees for the tower on positive scales. 14 Across 22 datasets and 41,637 samples under a fixed configuration, CHARM 15 ranks among the top two on all 15 sample-weighted metrics for nonsynthetic data, 16 including the smallest values on all four Euclidean persistence-diagram distances. 17 It also provides 957 traceable support records across the full benchmark. On a 18 spherical shell, one certified H2 record identifies 1,578 original samples in the 19 two-dimensional view. CHARM thus combines geometric exploration with explicit 20 evidence of homological type and location.