13 papers
Hi-GMAE: Hierarchical Graph Masked Autoencoders
Chuang Liu, Zelin Yao, Xueqi Ma +4
Graph Masked Autoencoders (GMAEs) have emerged as a notable self-supervised learning approach for graph-structured data. Existing GMAE models primarily focus on reconstructing node…
Variational Bayesian Flow Network for Graph Generation
Yida Xiong, Jiameng Chen, Xiuwen Gong +3
Graph generation aims to sample discrete node and edge attributes while satisfying coupled structural constraints. Diffusion models for graphs often adopt largely factorized forwar…
PCEvo: Path-Consistent Molecular Representation via Virtual Evolutionary
Kun Li, Longtao Hu, Yida Xiong +6
Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific appl…
Transport-Coupled Bayesian Flows for Molecular Graph Generation
Yida Xiong, Jiameng Chen, Kun Li +4
Molecular graph generation (MGG) is essentially a multi-class generative task, aimed at predicting categories of atoms and bonds under strict chemical and structural constraints. H…
Text-guided multi-property molecular optimization with a diffusion language model
Yida Xiong, Kun Li, Jiameng Chen +4
Molecular optimization (MO) is a crucial stage in drug discovery in which task-oriented generated molecules are optimized to meet practical industrial requirements. Existing mainst…
FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation
Jiameng Chen, Yida Xiong, Kun Li +4
Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynami…