arXiv subjects

Wenkai Xiang

Publications and source records attributed to Wenkai Xiang.

3 recordsLinked to original sources

arXiv2026

Learning Implicit Bias in Generative Spaces for Accelerating Protein Dynamics Emulation

Generative emulators of protein dynamics produce plausible trajectories at a fraction of the cost of molecular dynamics, but they inherit their training distribution and tend to revisit known states rather than reach rare ones under long-horizon extrapolation. Inspired by classical enhanced sampling, we introduce an implicit, history-dependent bias in the generative space of a pretrained emulator. Specifically, a history-aware score estimator augments the frozen emulator with a distance-weighted bias that steers reverse-time sampling away from previously generated structures, regularized by an environment-support term. To preserve structural validity at long horizons, a score-based refinement step re-projects drifted samples onto the data manifold using the frozen emulator. Our experiments demonstrate that the method (i) raises diversity by $35\%$ on DynamicPDB-80; (ii) on $12$ zero-shot Fast-Folding proteins, the learned bias alone reaches the unbiased emulator's coverage up to ${\sim}15\times$ faster, and pairing it with refinement reaches the coverage up to ${\sim}37\times$ faster while covering ${\sim}3\times$ as many low-energy states. Code will be released soon.

cs.LG↗

arXiv2025

MolPIF: A Parameter Interpolation Flow Model for Molecule Generation

Motivation: Structure-based drug design (SBDD) has advanced with deep generative models, but bridging the gap between continuous atomic coordinates and discrete atom types remains a challenge. Current approaches, such as diffusion and flow matching models, often fail to unify these heterogeneous modalities, relying on separate strategies or ill-fitting Euclidean metrics for discrete variables. This lack of a consistent framework limits generative models' ability to capture the geometric and chemical structure of protein-ligand complexes. Results: We present MolPIF, a parameter interpolation flow mechanism designed to unify the generation of continuous and discrete molecular variables. Unlike traditional flow models that operate in sample space, MolPIF interpolates between distributions in the parameter space, theoretically recovering Wasserstein-2 optimal transport for continuous coordinates and establishing Fisher-Rao geodesics for discrete atom types. We further incorporate a geometry-enhanced learning strategy to improve the capture of atomic contexts. Extensive evaluations on the CrossDocked2020 dataset demonstrate that MolPIF outperforms baselines in binding affinity, chemical validity, geometric fidelity and chemical space coverage. Additionally, MolPIF exhibits versatility in lead optimization and offers flexible prior distribution selection (such as Laplace), establishing a robust paradigm for SBDD. Availability: Source code is freely available at https://github.com/BLEACH366/MolPIF. Supplementary information: Supplementary data are available at Bioinformatics.

cs.LG↗

arXiv2023

SubAnom: Efficient Subgraph Anomaly Detection Framework over Dynamic Graphs

Given a dynamic graph, the efficient tracking of anomalous subgraphs via their node embeddings poses a significant challenge. Addressing this issue necessitates an effective scoring mechanism and an innovative anomalous subgraph strategy. Existing methods predominantly focus on designing scoring strategies or employing graph structures that consider nodes in isolation, resulting in ineffective capture of the anomalous subgraph structure information. In this paper, we introduce SUBANOM, a novel framework for subgraph anomaly detection that is adept at identifying anomalous subgraphs. SUBANOM has three key components: 1) We implement current state-of-the-art dynamic embedding methods to efficiently calculate node embeddings, thereby capturing all node-level anomalies successfully; 2) We devise novel subgraph identification strategies, which include k-hop and triadic-closure. These strategies form the crucial component that can proficiently differentiate between strong and weak neighbors, thus effectively capturing the anomaly structure information; 3) For qualifying the anomaly subgraphs, we propose using Lp-norm-based score aggregation functions. These iterative steps enable us to process large-scale dynamic graphs effectively. Experiments conducted on a real-world dynamic graph underscore the efficacy of our framework in detecting anomalous subgraphs, outperforming state-of-the-art methods. Experimental results further signify that our framework is a potent tool for identifying anomalous subgraphs in real-world scenarios. For instance, the F1 score under the optimal subgraph identification strategy, can peak at 0.6679, while the highest achievable score using the corresponding baseline method is 0.5677.

cs.SI↗