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arXiv AI

DMT-Dens: Density-preserving manifold visualization for biological data

DMT‑Dens is a parametric manifold‑visualization technique that uses a latent‑token Transformer encoder to produce two‑dimensional embeddings of high‑dimensional biological data. It preserves sampling density by aligning rank‑based manifold structures and optimizing a Pearson‑correlation loss on k‑nearest‑neighbor log‑radius estimates. Benchmark tests show that DMT‑Dens maintains density fidelity while achieving competitive label separability on biological datasets.

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arXiv AI
6d ago

LapDDPM: Spectral Perturbation Diffusion for Robust Single-Cell Manifold Generation

LapDDPM is a conditional Graph Diffusion Probabilistic Model that generates high‑fidelity, biologically plausible single‑cell RNA sequencing data. It incorporates graph‑based inductive biases and a spectral adversarial perturbation mechanism to enforce robustness against structural noise, effectively acting as a Distributionally Robust Optimization framework. The model extends to spatial transcriptomics and multi‑modal data, and experimental results on datasets such as PBMC3K, Dentate Gyrus, HLCA, Visium, and 10x Multiome show it outperforms state‑of‑the‑art baselines in distribution matching, manifold preservation, and downstream utility.

By Lorenzo Bini, Stephane Marchand-Maillet
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arXiv Machine Learning
Sep 17

A General Kernel Framework for Non-CND Distance Measures Using |D|-Dimensional Sparse Landmark Embeddings

The paper introduces the Sparse Landmark Embedding (SLE) kernel, a new framework that removes the need for conditionally negative definite (CND) distance measures in kernel methods and Gaussian Processes. By embedding each input into a sparse feature vector using compactly supported bump functions centered at all training points, any standard positive semi-definite (PSD) kernel can be applied in this embedding space, guaranteeing PSD for arbitrary distance measures. The authors provide theoretical guarantees on PSD, sparsity, stability, and universal approximation, and show through experiments with geodesic and Wasserstein distances that the SLE kernel matches or surpasses domain-specific baselines in predictive accuracy and uncertainty quantification.

By Marcus M. Noack, Maher B. Alghalayini, Mark D. Risser
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arXiv Machine Learning
Sep 25

SpaFactor: Lightweight Spatial Context-Aware Gene Program Modeling for Histology-to-Transcriptomics Inference

SpaFactor is a lightweight framework that predicts spatial gene expression from hematoxylin and eosin images by fusing central spot visuals with multiscale neighborhood context. It uses a residual MLP to map tissue microenvironment to low‑dimensional latent gene programs, which are decoded into coordinated multi‑gene predictions. Across five public cohorts, SpaFactor outperforms existing methods, especially for spatially variable genes, and better recovers biologically organized spatial patterns.

By Shiting Ruan, Xitong Ling, Qiming He, Ziyou Yan, Huaitian Yuan, Tian Guan, Ying Xiao, Xu Guan, Yonghong He
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Hugging Face Trending Papers
Aug 5

Intrinsic-Hybrid Latent Diffusion Models for Generative Modeling on Unknown Manifolds

We introduce the Intrinsic Hybrid Latent Diffusion Model (ILDM), a generative framework that integrates probabilistic dimensionality reduction with geometry-aware diffusion on unknown manifolds. While diffusion models (DMs) have achieved state-of-the-art results in high-dimensional data synthesis, they rely on large training datasets and ignore intrinsic geometric structure.

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