TreeRef-BFN: Equivariance-Free De Novo Molecule Generation based on 2D Topology and Internal 3D Geometry

arXiv:2609.32502 · cs.AI, cs.LG · Submitted 2026-09-26 · Read on arXiv

cs.AI, cs.LG

Submitted: 2026-09-26

Updated: 2026-09-26

Terminology

• Transformer — 20× in this paper · explained in 2 episodes
• Consistency — 16× in this paper · explained in 3 episodes
• Alignment — 6× in this paper · explained in 1 episode
• Inverse Design — 6× in this paper · explained in 2 episodes
• Accuracy — 5× in this paper · explained in 1 episode
• Diffusion Model — 5× in this paper · explained in 8 episodes
• Flow Matching — 5× in this paper · explained in 8 episodes
• In International Conference on Machine Learning — 5× in this paper
• Diffusion Models — 4× in this paper · explained in 6 episodes
• Embeddings — 4× in this paper · explained in 2 episodes
• Ablation — 3× in this paper · explained in 1 episode
• Core — 3× in this paper · explained in 2 episodes
• Decode — 3× in this paper · explained in 2 episodes
• Fidelity — 3× in this paper · explained in 2 episodes
• Geometric Distribution — 2× in this paper · explained in 2 episodes
• In International Conference on Learning Representations — 2× in this paper
• Pruning — 2× in this paper · explained in 4 episodes
• Cosine Similarity — 1× in this paper · explained in 3 episodes
• Downstream Tasks — 1× in this paper · explained in 2 episodes
• Exponential Moving Average (EMA) — 1× in this paper · explained in 2 episodes
• Foundation Model — 1× in this paper · explained in 3 episodes
• Generalization — 1× in this paper · explained in 13 episodes
• Generative AI — 1× in this paper · explained in 2 episodes
• Generative Modeling — 1× in this paper · explained in 3 episodes
• Reconstruction Error — 1× in this paper · explained in 2 episodes
• Redundancy — 1× in this paper · explained in 2 episodes
• Regularization — 1× in this paper · explained in 3 episodes
• Robustness — 1× in this paper · explained in 5 episodes
• Transformer Architecture — 1× in this paper · explained in 2 episodes

Sources

• FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generation
• Bayesian Flow Networks
• Classifier-Free Diffusion Guidance
• Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation
• Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition
• Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials

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