Yufan Tang | Searcharxiv

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↗

arXiv2024

A Consistency-Aware Spot-Guided Transformer for Versatile and Hierarchical Point Cloud Registration

Deep learning-based feature matching has shown great superiority for point cloud registration in the absence of pose priors. Although coarse-to-fine matching approaches are prevalent, the coarse matching of existing methods is typically sparse and loose without consideration of geometric consistency, which makes the subsequent fine matching rely on ineffective optimal transport and hypothesis-and-selection methods for consistency. Therefore, these methods are neither efficient nor scalable for real-time applications such as odometry in robotics. To address these issues, we design a consistency-aware spot-guided Transformer (CAST), which incorporates a spot-guided cross-attention module to avoid interfering with irrelevant areas, and a consistency-aware self-attention module to enhance matching capabilities with geometrically consistent correspondences. Furthermore, a lightweight fine matching module for both sparse keypoints and dense features can estimate the transformation accurately. Extensive experiments on both outdoor LiDAR point cloud datasets and indoor RGBD point cloud datasets demonstrate that our method achieves state-of-the-art accuracy, efficiency, and robustness.

cs.CV↗