Hierarchy-Guided Topology Latent Flow for Molecular Graph Generation
For drug discovery, HLTF improves the reliability of unconditional 3D molecular generation by explicitly controlling bond topology, reducing global failures from local bond errors.
HLTF generates 3D molecules with explicit bond topology, achieving 98.8% atom stability on QM9 and 85.5% validity on GEOM-DRUGS without post-processing, outperforming prior methods in validity and reducing false-valid samples.
Generating chemically valid 3D molecules is hindered by discrete bond topology: small local bond errors can cause global failures (valence violations, disconnections, implausible rings), especially for drug-like molecules with long-range constraints. Many unconditional 3D generators emphasize coordinates and then infer bonds or rely on post-processing, leaving topology feasibility weakly controlled. We propose Hierarchy-Guided Latent Topology Flow (HLTF), a planner-executor model that generates bond graphs with 3D coordinates, using a latent multi-scale plan for global context and a constraint-aware sampler to suppress topology-driven failures. On QM9, HLTF achieves 98.8% atom stability and 92.9% valid-and-unique, improving PoseBusters validity to 94.0% (+0.9 over the strongest reported baseline). On GEOM-DRUGS, HLTF attains 85.5%/85.0% validity/valid-unique-novel without post-processing and 92.2%/91.2% after standardized relaxation, within 0.9 points of the best post-processed baseline. Explicit topology generation also reduces "false-valid" samples that pass RDKit sanitization but fail stricter checks.