Lanzhou
Publications
MEDNA-DFM: A Dual-View FiLM-MoE Model for Explainable DNA Methylation Prediction
Accurate computational identification of DNA methylation is essential for understanding epigenetic regulation. Although deep learning excels in this binary classification task, its "black-box" nature impedes biological insight. We address this by introducing a high-performance model MEDNA-DFM, alongside mechanism-inspired signal purification algorithms. Our investigation demonstrates that MEDNA-DFM effectively captures conserved methylation patterns, achieving robust distinction across diverse species. Validation on external independent datasets confirms that the model's generalization is driven by conserved intrinsic motifs (e.g., GC content) rather than phylogenetic proximity. Furthermore, applying our developed algorithms extracted motifs with significantly higher reliability than prior studies. Finally, empirical evidence from a Drosophila 6mA case study prompted us to propose a "sequence-structure synergy" hypothesis, suggesting that the GAGG core motif and an upstream A-tract element function cooperatively. We further validated this hypothesis via in silico mutagenesis, confirming that the ablation of either or both elements significantly degrades the model's recognition capabilities. This work provides a powerful tool for methylation prediction and demonstrates how explainable deep learning can drive both methodological innovation and the generation of biological hypotheses.
Lagged backward-compatible physics-informed neural networks for unsaturated soil consolidation analysis
This study develops a Lagged Backward-Compatible Physics-Informed Neural Network (LBC-PINN) for simulating and inverting one-dimensional unsaturated soil consolidation under long-term loading. To address the challenges of coupled air and water pressure dissipation across multi-scale time domains, the framework integrates logarithmic time segmentation, lagged compatibility loss enforcement, and segment-wise transfer learning. In forward analysis, the LBC-PINN with recommended segmentation schemes accurately predicts pore air and pore water pressure evolution. Model predictions are validated against finite element method (FEM) results, with mean absolute errors below 1e-2 for time durations up to 1e10 seconds. A simplified segmentation strategy based on the characteristic air-phase dissipation time improves computational efficiency while preserving predictive accuracy. Sensitivity analyses confirm the robustness of the framework across air-to-water permeability ratios ranging from 1e-3 to 1e3.