# CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data

arXiv: https://arxiv.org/abs/2608.11269 · HTML: https://mlsanity.com/paper/2608.11269/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 79 references that are in the map.
- First posted on arXiv 11 Aug 2026.

## Builds on (most cited first, 14 of 14)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Understanding How Dimension Reduction Tools Work: An Empirical Approach to Deciphering t-SNE, UMAP, TriMAP, and PaCMAP for Data Visualization](https://mlsanity.com/paper/2012.04456/) (2020)
- [Visualizing Large-scale and High-dimensional Data](https://mlsanity.com/paper/1602.00370/) (2016)
- [TriMap: Large-scale Dimensionality Reduction Using Triplets](https://mlsanity.com/paper/1910.00204/) (2019)
- [A survey of dimensionality reduction techniques](https://mlsanity.com/paper/1403.2877/) (2014)
- [On UMAP's true loss function](https://mlsanity.com/paper/2103.14608/) (2021)
- [From t-SNE to UMAP with contrastive learning](https://mlsanity.com/paper/2206.01816/) (2022)
- [Unsupervised visualization of image datasets using contrastive learning](https://mlsanity.com/paper/2210.09879/) (2022)
- [Hierarchical Nearest Neighbor Graph Embedding for Efficient Dimensionality Reduction](https://mlsanity.com/paper/2203.12997/) (2022)
- [NCVis: Noise Contrastive Approach for Scalable Visualization](https://mlsanity.com/paper/2001.11411/) (2020)
- [Surpassing Cosine Similarity for Multidimensional Comparisons: Dimension Insensitive Euclidean Metric](https://mlsanity.com/paper/2407.08623/) (2024)
- [Dimension Reduction with Locally Adjusted Graphs](https://mlsanity.com/paper/2412.15426/) (2024)
- [The Shape of Attraction in UMAP: Exploring the Embedding Forces in Dimensionality Reduction](https://mlsanity.com/paper/2503.09101/) (2025)

## Abstract (arXiv)

Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging. Existing dimensionality-reduction methods may distort local neighbourhoods, global organization, or the cohesion of meaningful populations, with similar limitations arising in genealogical data. We introduce Contrastive Manifold Approximation and Projection (CosMAP), a graph-based unsupervised dimensionality-reduction method for producing faithful and interpretable embeddings. CosMAP extends the graph-based framework of UMAP by combining cosine-similarity neighbourhoods with temperature-normalized contrastive affinities, which are optimized in the embedding space using an attractive--repulsive objective. It further employs a two-phase refinement strategy: an intermediate higher-dimensional representation is first learned and then used to reconstruct the neighbourhood graph and initialize the final low-dimensional embedding. We evaluate CosMAP on MNIST and USPS handwritten-digit datasets, mouse retina and cortex single-cell RNA-sequencing datasets, and a large genealogical kinship dataset derived from BALSAC-CARTaGENE. Compared with state-of-the-art dimensionality-reduction methods, CosMAP produces more coherent visual representations, improves neighbourhood preservation, and provides clearer global organization of digit classes, biological cell populations, and regional genealogical patterns. These results indicate that CosMAP offers a robust framework for exploratory analysis of complex, sparse, high-dimensional data. The implementation is publicly available at https://github.com/FenosoaRandrianjatovo/CosMAP-dr.