11 papers
AI-Augmented Statistical Network Estimation with Proxy Gene Embeddings
Yan Chen, Weijing Tang, Jin-Hong Du
Gene--gene networks are often observed only on a restricted target set, while modern biomedical foundation models provide proxy gene embeddings over substantially larger gene unive…
Beyond Importance: Interchange-Sobol Sensitivity Reveals Task-Specific Content Channels in Transformer Components
Yifeng Guo, Jin-Hong Du, Xiang Chen
Mechanistic interpretability methods summarize a transformer component by a single importance score, conflating two distinct roles: a component may matter because it transports tas…
Distance-Preserving Representations for Genomic Spatial Reconstruction
Wenbin Zhou, Jin-Hong Du
The spatial context of single-cell gene expression data is crucial for many downstream analyses, yet often remains inaccessible due to practical and technical limitations, restrict…
Precise Asymptotics of Bagging Regularized M-estimators
Takuya Koriyama, Pratik Patil, Jin-Hong Du +2
We characterize the squared prediction risk of ensemble estimators obtained through subagging (subsample bootstrap aggregating) regularized M-estimators and construct a consistent…
Causal Inference for Genomic Data with Multiple Heterogeneous Outcomes
Jin-Hong Du, Zhenghao Zeng, Edward H. Kennedy +2
With the evolution of single-cell RNA sequencing techniques into a standard approach in genomics, it has become possible to conduct cohort-level causal inferences based on single-c…
Network-based Neighborhood regression
Yaoming Zhen, Jin-Hong Du
Given the ubiquity of modularity in biological systems, module-level regulation analysis is vital for understanding biological systems across various levels and their dynamics. Cur…