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

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.

AdapDISCOM: An Adaptive Sparse Regression Method for High-Dimensional Multimodal Data With Block-Wise Missingness and Measurement Errors

Multimodal high-dimensional data are increasingly prevalent in biomedical research, yet they are often compromised by block-wise missingness and measurement errors, posing significant challenges for statistical inference and prediction. We propose AdapDISCOM, a novel adaptive direct sparse regression method that simultaneously addresses these two pervasive issues. Building on the DISCOM framework, AdapDISCOM introduces modality-specific weighting schemes to account for heterogeneity in data structures and error magnitudes across modalities. We establish the theoretical properties of AdapDISCOM, including model selection consistency and convergence rates under sub-Gaussian and heavy-tailed settings, and develop robust and computationally efficient variants (AdapDISCOM-Huber and Fast-AdapDISCOM). Extensive simulations demonstrate that AdapDISCOM consistently outperforms existing methods such as DISCOM, SCOM, and CoCoLasso, particularly under heterogeneous contamination and heavy-tailed distributions. Finally, we apply AdapDISCOM to Alzheimers Disease Neuroimaging Initiative (ADNI) data, demonstrating improved prediction of cognitive scores and reliable selection of established biomarkers, even with substantial missingness and measurement errors. AdapDISCOM provides a flexible, robust, and scalable framework for high-dimensional multimodal data analysis under realistic data imperfections.