Unsupervised Thermodynamics of Molecular Diffusion Models: Action-Operator Semantics and Auditable Free-Energy Readout

arXiv:2606.30687 · physics.chem-ph, cond-mat.stat-mech, cs.AI · Submitted 2026-06-28 · Read on arXiv

physics.chem-ph, cond-mat.stat-mech, cs.AI

Submitted: 2026-06-28

Updated: 2026-09-06

Code: https://github.com/openforcefield/openff-forcefields

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

Terminology

• Diffusion Model — 17× in this paper · explained in 8 episodes
• Diffusion Models — 15× in this paper · explained in 6 episodes
• Consistency — 8× in this paper · explained in 3 episodes
• Degeneracy — 3× in this paper · explained in 3 episodes
• Generative Model — 2× in this paper · explained in 2 episodes
• Generative Models — 2× in this paper · explained in 2 episodes
• Self-consistency — 2× in this paper · explained in 2 episodes
• Accuracy — 1× in this paper · explained in 1 episode
• Alignment — 1× in this paper · explained in 1 episode
• Computational Biology — 1× in this paper · explained in 2 episodes
• Core — 1× in this paper · explained in 2 episodes
• Embeddings — 1× in this paper · explained in 2 episodes
• Flow Matching — 1× in this paper · explained in 8 episodes
• Generalization — 1× in this paper · explained in 13 episodes
• Generative Modeling — 1× in this paper · explained in 3 episodes
• Hysteresis — 1× in this paper · explained in 3 episodes
• Representation Learning — 1× in this paper · explained in 2 episodes

Sources

• Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models
• Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models
• Autonomous Emergence of Hamiltonian in Deep Generative Models

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