2 citations · 4 across the 9 of their papers we have counts for
11 papers
Nonparametric Estimation of Event-Free Survival for Data with Left-Truncated Death and Intermittently Assessed Nonfatal Events
Han Lu, Xianghua Luo, Yifei Sun +6
In certain clinical settings, patients diagnosed with a disease of interest are at risk for death as well as a serious nonfatal event, and interest lies in event-free survival (EFS…
MERLIN-SUITE: Probabilistic modular GRN inference from multi-omics data integrating regulatory priors and transcription factor activity
Suvojit Hazra, Marina Kotvanova, Kirstan Gimse +1
Accurately reconstructing gene regulatory networks (GRNs) is essential for understanding transcriptional processes in development and disease. MERLIN-SUITE (https://github.com/Roy-…
scMTNI: Leveraging cellular trajectory and context to infer dynamic GRNs from single-cell multi-omics data
Suvojit Hazra, Chandrani Kumari, Sushmita Roy
Transcriptional gene regulatory networks (GRNs) depict the directed relationships between regulators and target genes, determining gene expression patterns in a cell-type-specific…
Modeling Dynamics, Cell Type Specificity, and Perturbations in Gene Regulatory Networks
Junha Shin, Spencer Halberg-Spencer, Yuda Liu +3
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role…
The Target Polish: A New Approach to Outlier-Resistant Non-Negative Matrix Factorization
Paul Fogel, Christophe Geissler, George Luta
This paper introduces the "Target Polish," a robust and computationally efficient framework for Non-Negative Matrix Factorization (NMF). Although conventional weighted NMF approach…
Bayesian Regression Analysis with the Drift-Diffusion Model
Zekai Jin, Yaakov Stern, Seonjoo Lee
The Drift-Diffusion Model (DDM) is widely used in neuropsychological studies to understand the decision process by incorporating both reaction times and subjects' responses. Variou…
Demographic Parity-aware Individualized Treatment Rules
Wenhai Cui, Wen Su, Xiaodong Yan +2
There has been growing interest in developing optimal individualized treatment rules (ITRs) in various fields, such as precision medicine, business decision-making, and social welf…
Comparing Lasso and Adaptive Lasso in High-Dimensional Data: A Genetic Survival Analysis in Triple-Negative Breast Cancer
Pilar González-Barquero, Rosa E. Lillo, Álvaro Méndez-Civieta
In high-dimensional survival analysis, effective variable selection is crucial for both model interpretation and predictive performance. This paper investigates Cox regression with…
Bayesian Nonparametric Clustering with Feature Selection for Spatially Resolved Transcriptomics Data
Bencong Zhu, Guanyu Hu, Yang Xie +3
The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profilin…
Sequential monitoring using the Second Generation P-Value with Type I error controlled by monitoring frequency
Jonathan J. Chipman, Robert A. Greevy, Lindsay Mayberry +1
Many adaptive monitoring schemes adjust the required evidence toward a hypothesis to control Type I error. This shifts focus away from determining scientific relevance with an unco…
Inferring high-resolution human mixing patterns for disease modeling
Dina Mistry, Maria Litvinova, Ana Pastore y Piontti +12
Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for…