arXiv subjects

Dan Teng

Publications and source records attributed to Dan Teng.

4 recordsLinked to original sources

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

P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

physics.bio-ph↗

arXiv2019

Continual Learning via Online Leverage Score Sampling

In order to mimic the human ability of continual acquisition and transfer of knowledge across various tasks, a learning system needs the capability for continual learning, effectively utilizing the previously acquired skills. As such, the key challenge is to transfer and generalize the knowledge learned from one task to other tasks, avoiding forgetting and interference of previous knowledge and improving the overall performance. In this paper, within the continual learning paradigm, we introduce a method that effectively forgets the less useful data samples continuously and allows beneficial information to be kept for training of the subsequent tasks, in an online manner. The method uses statistical leverage score information to measure the importance of the data samples in every task and adopts frequent directions approach to enable a continual or life-long learning property. This effectively maintains a constant training size across all tasks. We first provide mathematical intuition for the method and then demonstrate its effectiveness in avoiding catastrophic forgetting and computational efficiency on continual learning of classification tasks when compared with the existing state-of-the-art techniques.

cs.LG↗

arXiv2017

A Fast Frequent Directions Algorithm for Low Rank Approximation

Recently a deterministic method, frequent directions (FD) is proposed to solve the high dimensional low rank approximation problem. It works well in practice, but experiences high computational cost. In this paper, we establish a fast frequent directions algorithm for the low rank approximation problem, which implants a randomized algorithm, sparse subspace embedding (SpEmb) in FD. This new algorithm makes use of FD's natural block structure and sends more information through SpEmb to each block in FD. We prove that our new algorithm produces a good low rank approximation with a sketch of size linear on the rank approximated. Its effectiveness and efficiency are demonstrated by the experimental results on both synthetic and real world datasets, as well as applications in network analysis.

math.NA↗