Diffusion models are increasingly utilized for modeling molecular structures and conformational ensembles, yet the thermodynamic meaning of their learned representations and scores remains elusive. To resolve this ambiguity, we introduce a mathematically consistent action-operator framework natively compatible with diffusion models. By defining a fixed molecular environment as a base action S0(x) and an alchemical perturbation as an operator O(x), standard diffusion noising induces effective noised actions and operators whose gradients and alchemical derivatives are directly represented by the model's learned fields. This rigorous self-consistency enables a ``noisy operator bridge'' capable of reading out free-energy differences (ΔF) from endpoint ensembles and per-frame evaluations. In controlled experiments on alanine dipeptide systems, we show that incorporating physical inductive biases enables partial recovery of the base action and perturbation operator. When applied to a challenging C6-H to C6-F ligand-pocket nonbonded perturbation (185L/IND) with negligible phase-space overlap, our supervised bridge estimates the alchemical ΔF within approximately 1kBT of a stable 19-state MBAR reference. Finally, we demonstrate that endpoint coordinates and binary labels alone are sufficient to partially recover the operator shape and a centered free-energy scale without any force or action supervision. This work provides a rigorous path toward transforming generative molecular diffusion models from black-box coordinate samplers into auditable thermodynamic estimators.
The reverse process in score-based diffusion models is formally equivalent to overdamped Langevin dynamics in a time-dependent energy landscape. In our prior work we showed that a bilinearly-coupled analog substrate can physically realize this dynamics at a projected three-to-four orders of magnitude energy advantage over digital inference by replacing dense skip connections with low-rank inter-module couplings. Whether the \emph{training} loop can be closed on the same substrate -- without routing gradients through an external digital accelerator -- has remained open. We resolve this affirmatively: Equilibrium Propagation applied directly to the bilinear energy yields an unbiased estimator of the denoising score-matching gradient in the zero-nudge limit. For finite nudging we derive a sharp bias bound controlled solely by substrate stiffness, local curvature, and the norm of the loss-gradient signal, with a bilinear-specific corollary showing that one dominant bias term vanishes identically for coupling-parameter updates. Symmetric nudging further upgrades the leading bias from O(β) to O(β2) at negligible extra cost. Under realistic finite-relaxation budgets this upgrade is essential, as one-sided EqProp produces anti-correlated gradients while symmetric EqProp yields well-aligned updates. Bias-variance analysis determines the optimal operating point, and end-to-end physical-unit accounting projects a 103-104× energy advantage per training step over a matched GPU baseline. Symmetric bilinear EqProp is the first local, readout-only training rule that preserves the low-rank coupling enabling scalable thermodynamic diffusion models.
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), MetaDiff (a batchwise analogue for metadynamics), and ΔG-Diff (free-energy differences via tilted ensembles). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system-closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.
Diffusion models have seen wide adoption for 3D molecular generation, yet they offer no principled signal of when a generated molecule is likely to be of low quality. We propose a post-hoc method for estimating per-sample uncertainty in pretrained molecular diffusion models. Building on a Laplace approximation of the denoising network, we measure the variability of the noise prediction across the generation trajectory. Empirically, we show that the resulting uncertainty score is informative of sample quality, exhibiting a negative correlation with established sample-level quality metrics. We further study how the proposed uncertainty score can be used to filter generated samples, improving model performance via test-time scaling.
Paul Seij, Christian A. Naesseth, Stephan Mandt +1