7 papers
A Joint Bayesian Boolean Matrix Factorization with Application to Chromosomal Copy Number Alterations in Multiple Myeloma
Adolphus Wagala, Samur Mehmet, Giovanni Parmigiani
Boolean matrix factorization provides an interpretable framework for discovering latent binary patterns in high-dimensional data, yet existing methods typically analyze a single bi…
A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer
Adolphus Wagala, Mehmet Samur, Giovanni Parmigiani
Binary data factorization is common, but real-valued methods ignore discreteness and yield hard-to-interpret factors. Boolean Matrix Factorization (BooMF) instead decomposes a bina…
Poisson process factorization for modeling mutational processes along cancer genomes
Alessandro Zito, Giovanni Parmigiani, Jeffrey W. Miller
Cancer cells acquire DNA mutations through many processes, such as environmental exposures and dysregulated repair mechanisms, and each process consistently produces distinct mutat…
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…
Bayesian Probit Multi-Study Non-negative Matrix Factorization for Mutational Signatures
Blake Hansen, Isabella N. Grabski, Giovanni Parmigiani +1
Mutational signatures are patterns of somatic mutations in tumor genomes that provide insights into underlying mutagenic processes and cancer origin. Developing reliable methods fo…