Moyu Tang
Publications
PathMoG: A Pathway-Centric Modular Graph Neural Network for Multi-Omics Survival Prediction
Cancer survival prediction from multi-omics data remains challenging because prognostic signals are high-dimensional, heterogeneous, and distributed across interacting genes and pathways. We propose PathMoG, a pathway-centric modular graph neural network for multi-omics survival prediction. PathMoG reorganizes genome-scale inputs into 354 KEGG-informed pathway modules, introduces a Hierarchical Omics Modulation module to condition gene-expression representations on mutation, copy number variation, pathway, and clinical context, and uses dual-level attention to capture both intra-pathway driver signals and inter-pathway clinical relevance. We evaluated PathMoG on 5,650 patients across 10 TCGA cancer types and observed consistent improvements over representative survival baselines. The framework further provides gene-level, pathway-level, and patient-level interpretability, supporting biologically grounded and clinically relevant risk stratification.
An Integrated Deep-Learning Framework for Peptide-Protein Interaction Prediction and Target-Conditioned Peptide Generation with ConGA-PePPI and TC-PepGen
Motivation: Peptide-protein interactions (PepPIs) are central to cellular regulation and peptide therapeutics, but experimental characterization remains too slow for large-scale screening. Existing methods usually emphasize either interaction prediction or peptide generation, leaving candidate prioritization, residue-level interpretation, and target-conditioned expansion insufficiently integrated. Results: We present an integrated framework for early-stage peptide screening that combines a partner-aware prediction and localization model (ConGA-PepPI) with a target-conditioned generative model (TC-PepGen). ConGA-PepPI uses asymmetric encoding, bidirectional cross-attention, and progressive transfer from pair prediction to binding-site localization, while TC-PepGen preserves target information throughout autoregressive decoding via layerwise conditioning. In five-fold cross-validation, ConGA-PepPI achieved 0.839 accuracy and 0.921 AUROC, with binding-site AUPR values of 0.601 on the protein side and 0.950 on the peptide side, and remained competitive on external benchmarks. Under a controlled length-conditioned benchmark, 40.39% of TC-PepGen peptides exceeded native templates in AlphaFold 3 ipTM, and unconstrained generation retained evidence of target-conditioned signal.