HEDGEHOG: Hierarchical Evaluation of Drug Generators Through Rigorous Filtration

arXiv:2607.13155 · cs.LG, cs.SE · Submitted 2026-07-14 · Read on arXiv

cs.LG, cs.SE

Submitted: 2026-07-14

Updated: 2026-09-29

Code: https://github.com/LigandPro/posecheck-fast

Terminology

• Benchmark — 1× in this paper · explained in 2 episodes

Sources

• Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
• Ergodicity and Algebraticity of the Fast and Slow Triangle Maps
• Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
• Matcha: Multi-Stage Riemannian Flow Matching for Accurate and Physically Valid Molecular Docking
• Learning to Extend Molecular Scaffolds with Structural Motifs
• Multi-domain Distribution Learning for De Novo Drug Design
• 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction
• Auto-Encoding Variational Bayes

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