Transport-Coupled Bayesian Flows for Molecular Graph Generation

arXiv:2510.10211 · cs.LG · Submitted 2025-10-11 · Read on arXiv

cs.LG

Submitted: 2025-10-11

Updated: 2026-09-22

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Diffusion Model — 14× in this paper · explained in 8 episodes
• Diffusion Models — 13× in this paper · explained in 6 episodes
• Optimal Transport — 9× in this paper · explained in 5 episodes
• Accuracy — 6× in this paper · explained in 1 episode
• Core — 6× in this paper · explained in 2 episodes
• Fidelity — 5× in this paper · explained in 2 episodes
• Generative Model — 5× in this paper · explained in 2 episodes
• Generative Models — 4× in this paper · explained in 2 episodes
• Ablation — 3× in this paper · explained in 1 episode
• Embeddings — 3× in this paper · explained in 2 episodes
• Generalization — 3× in this paper · explained in 13 episodes
• Generative Modeling — 3× in this paper · explained in 3 episodes
• Regularization — 3× in this paper · explained in 3 episodes
• Unified Framework — 3× in this paper · explained in 5 episodes
• Ablation study — 2× in this paper · explained in 1 episode
• Alignment — 2× in this paper · explained in 1 episode
• Benchmark — 2× in this paper · explained in 2 episodes
• Diffusion Process — 2× in this paper · explained in 2 episodes
• Flow Matching — 2× in this paper · explained in 8 episodes
• Structural Constraints — 2× in this paper · explained in 2 episodes
• Transformer — 2× in this paper · explained in 2 episodes
• AdamW Optimizer — 1× in this paper · explained in 1 episode
• Adjacency Matrix — 1× in this paper · explained in 1 episode
• Aggregation — 1× in this paper · explained in 1 episode
• Contrastive Learning — 1× in this paper · explained in 5 episodes
• Diffusion Processes — 1× in this paper · explained in 2 episodes
• Downstream Tasks — 1× in this paper · explained in 2 episodes
• Exponential Moving Average (EMA) — 1× in this paper · explained in 2 episodes
• Interpretability — 1× in this paper · explained in 15 episodes
• Neighborhood Subgraph Pairwise Distance Kernel — 1× in this paper
• Optimal Transport (OT) — 1× in this paper · explained in 4 episodes

Sources

• Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding
• A Generalization of Transformer Networks to Graphs
• Bayesian Flow Networks
• Regressor-free Molecule Generation to Support Drug Response Prediction

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