Genomic Dimensionality
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Related Articles from SNS
Genomic Dimensionality Bounds Mixed-Model Association Power and Fine-Mapping Resolution
Mixed-model genome-wide association studies (GWAS) behave differently in livestock than in humans, yet a unified explanation is lacking. Analyses using the full genomic relationship matrix (full-GRM; from genome-wide SNPs) yield only a few significant peaks even with hundreds of thousands of animals, whereas leave-one-chromosome-out (LOCO), numerator-relationship-matrix, and sparse-GRM approaches report many broad associations over similar data. Here we develop a framework that traces these...
An interpretable machine learning framework for dog breed inference and ancestry decomposition
The over 300 currently recognized breeds of domesticated dogs are the culmination of centuries of intense artificial selection and recurrent population bottlenecks. While breed labels are widely used in genetic and veterinary studies, inferring breed identity from genomic data remains challenging due to the high dimensionality of genotype data, uneven sampling across breeds, and admixture resulting in mixed-breed individuals. Here, we present an interpretable machine learning framework to...
GPU accelerated population genetics statistics using pg_gpu
Population genetics summary statistics-- diversity, divergence, linkage disequilibrium, selection scans, and dimensionality reduction-- are fundamental across human, agricultural, and ecological genomics. As whole-genome sequencing datasets have grown to hundreds of thousands of individuals, the cost of computing these statistics on conventional CPU implementations has become a major bottleneck: windowed scans of a single chromosome arm can take hours to days, and computation of pairwise...
Rethinking Genomic Modeling Through Optical Character Recognition
arXiv:2602.02014v2 Announce Type: replace Abstract: Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic semantics, leading to wasted computation on low-information background and preventing understanding-driven compression for long contexts. Here, we present OpticalDNA, a vision-based framework that reframes...
Radiomic Feature Selection Using Gradient Loss of Deep Neural Network for Lung Cancer Stage Detection
arXiv:2606.04453v1 Announce Type: new Abstract: Radiomics enables extraction of quantitative imaging biomarkers from medical images and has become an important tool for computer-aided cancer diagnosis. However, radiomics datasets are typically high-dimensional with limited samples, making feature selection a critical step for building reliable predictive models. This study proposes a Gradient-Loss Recursive Feature Elimination (GL-RFE) framework that integrates gradient sensitivity analysis...
Nuclear confinement from matrix stiffness drives epigenomic reprogramming of gingival fibroblasts
Periodontal disease is characterized by progressive degradation of the gingival extracellular matrix and loss of the physical confinement it imposes on resident stromal cells. In human periodontal tissue, ECM collagen integrity is inversely correlated with facultative nuclear histone acetylation in stromal cells. We hypothesized that matrix stiffness directly coordinates an epigenomic shift in stromal cells.
QPredSGG: Hybrid Quantum Predicate Learning for Long-Tailed Scene Graph Generation
arXiv:2606.04689v1 Announce Type: cross Abstract: Scene Graph Generation (SGG) requires relational reasoning over objects and their interactions, but performance is often limited by severe long-tail predicate imbalance. Classical SGG models frequently rely on dataset statistics, leading to biased predictions toward frequent relations rather than fine-grained semantic predicates. Although existing debiasing strategies improve mean recall, predicate classification in current frameworks still...
A Pan-Cancer Multi-Omic SuperLearner for Regulated Cell Death Survival Topologies
Introduction: Regulated cell death (RCD) pathways profoundly influence tumor progression and immune modulation. In prior work, we constructed a comprehensive database mapping 25 forms of RCD across seven multi-omic layers encompassing 33 tumor types (CancerRCDShiny). Despite their robust ability to identify risk populations, translating these prognostic signatures into personalized clinical workflows requires a shift from generalized cohort stratification to individualized risk mapping.
SHERLOC: An interpretable deep learning model for longitudinal circulating tumor DNA data in survival analysis
Longitudinal circulating tumor DNA (ctDNA) measurements offer a noninvasive means to monitor treatment response, but clinical trial data present substantial methodological challenges due to high-dimensional short longitudinal ctDNA sequences and limited sample sizes. We introduce SHERLOC, a deep learning framework specifically designed for survival analysis using longitudinal on-treatment ctDNA data, which integrates shared temporal representations of gene-level variant allele frequencies,...
A Fast Screening Approach for High-dimensional Outcomes and High-dimensional Predictors
Announce Type: cross Abstract: Modeling interactions among multimodal, high-dimensional data is intrinsically challenging due to ultra-high dimensionality and complex dependence structure with high level noise. Screening methods are effective for reducing dimensionality, but most existing approaches shrink only the predictor space while retaining all outcomes. In cross-modal analyses, different outcomes often select different predictor subsets, so the union remains large and the response...