Benchmark of BINN, GraphPath, and PATH on 2622 TCGA patients shows PATH best for targeted therapy, BINN for survival, none useful for radiation, with GraphPath at 0.92 AUROC on prostate targeted therapy.
Mootha, Sayan Mukherjee, Benjamin L
2 Pith papers cite this work. Polarity classification is still indexing.
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ORBIT uses an intervention-consistent self-supervised objective in a transformer to infer asymmetric gene program influences from observational scRNA-seq data, recovering Alzheimer's vulnerability patterns and achieving 0.984 macro F1 cell-type classification from 220 pathway scores.
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TRAPS: Therapeutic Response Analysis via Pathway-informed Stratification
Benchmark of BINN, GraphPath, and PATH on 2622 TCGA patients shows PATH best for targeted therapy, BINN for survival, none useful for radiation, with GraphPath at 0.92 AUROC on prostate targeted therapy.
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ORBIT: Learning Gene Program Co-Activation Structure for Cell-Type-Stratified Pathway Rewiring Analysis in Single-Cell Transcriptomics
ORBIT uses an intervention-consistent self-supervised objective in a transformer to infer asymmetric gene program influences from observational scRNA-seq data, recovering Alzheimer's vulnerability patterns and achieving 0.984 macro F1 cell-type classification from 220 pathway scores.