CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data
This work addresses the challenge of simultaneously preserving local neighborhoods, global structure, and population coherence when reducing the dimensionality of high-dimensional, sparse omics and lineage data. To this end, the authors propose a graph-based unsupervised dimensionality reduction method that constructs an initial neighborhood graph using cosine similarity and optimizes an attraction–repulsion objective in the embedding space via temperature-normalized contrastive affinities. A two-stage optimization strategy is introduced: first, an intermediate high-dimensional representation is used to refine the neighborhood graph and initialize the embedding; second, the final low-dimensional representation is fine-tuned. Evaluated on single-cell RNA-seq, handwritten digit, and large-scale lineage datasets, the method consistently outperforms existing approaches, yielding more coherent visualizations, superior neighborhood preservation, and clearer global structural organization.