arXiv subjects

Brian D. Athey

Publications and source records attributed to Brian D. Athey.

4 recordsLinked to original sources

arXiv2026

A Time-Varying and Covariate-Dependent Correlation Model for Multivariate Longitudinal Studies

In multivariate longitudinal studies, associations between outcomes often exhibit time-varying and individual level heterogeneity, motivating the modeling of correlations as an explicit function of time and covariates. However, most existing methods for correlation analysis fail to simultaneously capture the time-varying and covariate-dependent effects. We propose a Time-Varying and Covariate-Dependent (TiVAC) correlation model that jointly allows covariate effects on correlation to change flexibly and smoothly across time. TiVAC employs a bivariate Gaussian model where the covariate-dependent correlations are modeled semiparametrically using penalized splines. We develop a penalized maximum likelihood-based Newton-Raphson algorithm, and inference on time-varying effects is provided through simultaneous confidence bands. Simulation studies show that TiVAC consistently outperforms existing methods in accurately estimating correlations across a wide range of settings, including binary and continuous covariates, sparse to dense observation schedules, and across diverse correlation trajectory patterns. We apply TiVAC to a psychiatric case study of 291 bipolar I patients, modeling the time-varying correlation between depression and anxiety scores as a function of their clinical variables. Our analyses reveal significant heterogeneity associated with gender and nervous-system medication use, which varies with age, revealing the complex dynamic relationship between depression and anxiety in bipolar disorders.

stat.ME↗

arXiv2025

Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling

Microscopy enables direct observation of cellular morphology in 3D, with transmitted-light methods offering low-cost, minimally invasive imaging and fluorescence microscopy providing specificity and contrast. Virtual staining combines these strengths by using machine learning to predict fluorescence images from label-free inputs. However, training of existing methods typically relies on loss functions that treat all pixels equally, thus reproducing background noise and artifacts instead of focusing on biologically meaningful signals. We introduce Spotlight, a simple yet powerful virtual staining approach that guides the model to focus on relevant cellular structures. Spotlight uses histogram-based foreground estimation to mask pixel-wise loss and to calculate a Dice loss on soft-thresholded predictions for shape-aware learning. Applied to a 3D benchmark dataset, Spotlight improves morphological representation while preserving pixel-level accuracy, resulting in virtual stains better suited for downstream tasks such as segmentation and profiling.

cs.CV↗

arXiv2018

Pharmacogenomics in the Age of GWAS, Omics Atlases, and PheWAS

The search for causative pharmacogenomic loci is being transformed by integrative omics pipelines, but their outputs have only begun being applied to test design. We assess the direction of the field in light of Biobanks/PheWAS, omics atlases, and AI. We first assess the potential of recent epigenome and spatial genome concepts, datasets, and methods to improve the functionality of PIP-style pipelines. We then discuss new potential methods of genetic test design on the basis of the outputs of such pipelines. We conclude with a vision for a pharmacophenomic atlas, in which omics atlas data, PheWAS associations, and biobank data would be used with AI to design thousands of genetic tests for clinical deployment in an automated parallel process.

q-bio.GN↗

arXiv2018

Deep Learning in Pharmacogenomics: From Gene Regulation to Patient Stratification

This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) prediction of drugs, targets, and their interactions. Deep learning encapsulates a family of machine learning algorithms that over the last decade has transformed many important subfields of artificial intelligence (AI) and has demonstrated breakthrough performance improvements on a wide range of tasks in biomedicine. We anticipate that in the future deep learning will be widely used to predict personalized drug response and optimize medication selection and dosing, using knowledge extracted from large and complex molecular, epidemiological, clinical, and demographic datasets.

q-bio.QM↗