Adaptive Bayesian computation for efficient biobank-scale genomic inference
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866913071950200832 |
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| author | Li, Yiran Whittaker, John Richardson, Sylvia Ruffieux, Helene |
| author_facet | Li, Yiran Whittaker, John Richardson, Sylvia Ruffieux, Helene |
| contents | Motivation: Modern biobanks, with unprecedented sample sizes and phenotypic diversity, have become foundational resources for genomic studies, enabling powerful cross-phenotype and population-scale analyses. As studies grow in complexity, Bayesian hierarchical models offer a principled framework for jointly modeling multiple units such as cells, traits, and experimental conditions, increasing statistical power through information sharing. However, adoption of Bayesian hierarchical models in biobank-scale studies remains limited due to computational inefficiencies, particularly in posterior inference over high-dimensional parameter spaces. Deterministic approximations such as variational inference provide scalable alternatives to Markov Chain Monte Carlo, yet current implementations do not fully exploit the structure of genome-wide multi-unit modeling, especially when biological effects of interest are concentrated in a few units.
Results: We propose an adaptive focus (AF) strategy within a block coordinate ascent variational inference (CAVI) framework that selectively updates subsets of parameters at each iteration, corresponding to units deemed relevant based on current estimates. We illustrate this approach in protein quantitative trait locus (pQTL) mapping using a joint model of hierarchically linked regressions with shared parameters across traits. In both simulated data and real proteomic data from the UK Biobank, AF-CAVI achieves up to a 50\% reduction in runtime while maintaining statistical performance. We also provide a genome-wide pipeline for multi-trait pQTL mapping across thousands of traits, demonstrating AF-CAVI as an efficient scheme for large-scale, multi-unit Bayesian analysis in biobanks. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_10736 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Adaptive Bayesian computation for efficient biobank-scale genomic inference Li, Yiran Whittaker, John Richardson, Sylvia Ruffieux, Helene Applications Motivation: Modern biobanks, with unprecedented sample sizes and phenotypic diversity, have become foundational resources for genomic studies, enabling powerful cross-phenotype and population-scale analyses. As studies grow in complexity, Bayesian hierarchical models offer a principled framework for jointly modeling multiple units such as cells, traits, and experimental conditions, increasing statistical power through information sharing. However, adoption of Bayesian hierarchical models in biobank-scale studies remains limited due to computational inefficiencies, particularly in posterior inference over high-dimensional parameter spaces. Deterministic approximations such as variational inference provide scalable alternatives to Markov Chain Monte Carlo, yet current implementations do not fully exploit the structure of genome-wide multi-unit modeling, especially when biological effects of interest are concentrated in a few units. Results: We propose an adaptive focus (AF) strategy within a block coordinate ascent variational inference (CAVI) framework that selectively updates subsets of parameters at each iteration, corresponding to units deemed relevant based on current estimates. We illustrate this approach in protein quantitative trait locus (pQTL) mapping using a joint model of hierarchically linked regressions with shared parameters across traits. In both simulated data and real proteomic data from the UK Biobank, AF-CAVI achieves up to a 50\% reduction in runtime while maintaining statistical performance. We also provide a genome-wide pipeline for multi-trait pQTL mapping across thousands of traits, demonstrating AF-CAVI as an efficient scheme for large-scale, multi-unit Bayesian analysis in biobanks. |
| title | Adaptive Bayesian computation for efficient biobank-scale genomic inference |
| topic | Applications |
| url | https://arxiv.org/abs/2509.10736 |