5 papers
Bayesian Non-Negative Matrix Factorization with Correlated Mutation Type Probabilities for Mutational Signatures
Iris Lang, Jenna Landy, Giovanni Parmigiani
Somatic mutations, or alterations in DNA of a somatic cell, are key markers of cancer. In recent years, mutational signature analysis has become a prominent field of study within c…
Causal Inference for Latent Outcomes Learned with Factor Models
Jenna M. Landy, Dafne Zorzetto, Roberta De Vito +1
In many fields$\unicode{x2013}$including genomics, epidemiology, natural language processing, social and behavioral sciences, and economics$\unicode{x2013}$it is increasingly impor…
Multivariate Causal Effects: a Bayesian Causal Regression Factor Model
Dafne Zorzetto, Jenna Landy, Corwin Zigler +2
The impact of wildfire smoke on air quality is a growing concern, contributing to air pollution through a complex mixture of chemical species with important implications for public…
bayesNMF: Fast Bayesian Poisson NMF with Automatically Learned Rank Applied to Mutational Signatures
Jenna M. Landy, Nishanth Basava, Giovanni Parmigiani
Bayesian Poisson Non-Negative Matrix Factorization (NMF) is widely used to model count data, including in cancer mutational signature analysis. However, standard Gibbs samplers rel…
fdrSAFE: Selective Aggregation for Local False Discovery Rate Estimation
Jenna M. Landy, Giovanni Parmigiani
Estimating local false discovery rates (fdr) is central to large-scale multiple hypothesis testing, yet different methods often produce divergent results, and there is little guida…