Boltzmann Sampling

We present a transformer-based variational autoregressive network for sampling lattice systems with continuous degrees of freedom and apply it to the two-dimensional XY model near the Berezinskii-Kosterlitz-Thouless transition. The architecture is combined with physics-informed ingredients: locality-informed attention and approximate probabilities. The resulting sampler significantly outperforms existing neural samplers. We train the model on lattices up to $96\times96$, verify with a mode-dropping estimator that no parts of the configuration space are missed, and reproduce the energy, magnetization and helicity modulus obtained with the traditional Markov Chain Monte Carlo algorithm.

We propose a neural algorithm for sampling from distributions specified by unnormalized Boltzmann densities. Our approach is based on the Jordan--Kinderlehrer--Otto scheme for the Kullback--Leibler divergence in the Wasserstein--Fisher--Rao geometry (WFR JKO scheme). Our contributions are twofold. First, we prove that, for any fixed step size, the exact WFR JKO iterates converge exponentially fast to the target as the number of iterations tends to infinity. Notably, this result requires no structural assumptions on the target, such as log-concavity or a logarithmic Sobolev inequality. Second, we develop a neural implementation of the WFR JKO scheme that parametrizes its transport and reaction components using reweighted normalizing flows. Numerical experiments on challenging multimodal targets demonstrate the promising performance of the proposed method.

We introduce Grand Canonical Generators (GCG), a generative framework that extends Boltzmann generators to the grand canonical ensemble. We present two designs. The first conditions a variable-size generative model on the chemical potential, sampling particle number and configuration jointly. The second factorizes the grand canonical distribution into a particle-number distribution and the corresponding canonical Boltzmann density. This factorized formulation can use any existing Boltzmann generator for the canonical component, encodes the known linear chemical-potential dependence analytically, and yields a tractable likelihood that supports self-normalized importance sampling (SNIS). Empirically, GCG accurately reproduces grand canonical observables on a Lennard--Jones fluid and methane adsorption in a zeolite, demonstrating generalization across chemical potentials and correction via SNIS and grand canonical Monte Carlo.

Efficient sampling from Boltzmann distributions is central to modelling complex physical systems. Markov Chain Monte Carlo (MCMC) methods suffer from critical slowing down, high autocorrelation, and poor mode-mixing, limiting their scalability. Recent advances, like Boltzmann Generators, offer a promising alternative but remain constrained by costly MCMC-based training, inefficient sampling, and poor ergodicity. We introduce an algorithm for learning Boltzmann distributions that does not require any true samples for training. Our approach draws inspiration from flow matching but departs fundamentally from sample-trajectory matching to distribution-trajectory matching. The algorithm iteratively reshapes the target distribution, using model generated samples to guide learning and ensure comprehensive mode coverage. We validate our method on standard benchmarks, including a 2D Gaussian mixture, Many-Well distributions, and high-dimensional scalar $φ^4$ theory. The proposed approach not only improves sampling performance and accuracy over traditional MCMC and flow-based baselines but also establishes a new method for sample-free learning of complex physical distributions.

Generating independent, equilibrium samples of molecular systems at scale remains a central obstacle in computational statistical mechanics. Boltzmann Generators address this by pairing a generative model with importance sampling to obtain consistent samples from the target distribution. We introduce Normalizing Flow Flow Maps (NF$^2$M), which combines the strengths of recent stochastic flow maps with the tractability of classic normalizing flows to build a Boltzmann Generator. Unlike most methods, which correct the generative model only at the end, NF$^2$M reweighs each denoising transition as generation proceeds, avoiding wasted compute on trajectories that are ultimately discarded. At each denoising step, a conditional normalizing flow proposes clean configurations given the current noisy state (a simpler task than sampling directly from the target) and its exact likelihood enables correcting each proposal toward the true denoising transition of the target Boltzmann distribution. This is in contrast to most existing methods, whose likelihoods are approximate or expensive to evaluate, undermining the statistical reliability of the correction. We establish consistency of the corrected transitions and bound how approximation errors propagate through the sampling chain. We evaluate NF$^2$M on peptide systems, demonstrating improved sampling efficiency and sample quality.

Sampling from Boltzmann distributions of molecular systems is an inference problem that has seen significant recent developments fuelled by advances in neural density estimation. We develop a novel sampling algorithm, Neural Transport Nested Sampling (NTNS), which combines the classical strengths of nested sampling with modern neural flow-based methods. NTNS uses a flow matching velocity as the drift in a Metropolis--Hastings corrected Langevin kernel inside a nested sampling outer loop, requiring only evaluations of the target energy function and providing scalable estimation of the full partition function of high-dimensional particle systems. We benchmark NTNS on challenging molecular sampling benchmarks, scaling up to Lennard--Jones clusters of 55 interacting particles, where it reduces both interatomic distance and energy Wasserstein errors to reference MCMC by over an order of magnitude relative to the strongest neural baselines at lower wall-clock cost. To our knowledge, NTNS is also the first neural sampler to return a calibrated, temperature resolved partition function estimate at this scale, recovering the phase structure across temperature from a single run.

Learned dynamical proposals can generate configurations without providing a tractable endpoint density. Nonequilibrium path probabilities offer a way to correct such proposals, but correction alone does not determine their ability to connect separated regions. We introduce Neural Non-Equilibrium Hamiltonian Monte Carlo (NHMC), which combines conditional momentum distributions with reversible, volume preserving dynamics. The forward--reverse path ratio gives the work used for training, importance weighting, normalizer estimation, and Metropolis correction. We then construct a configuration space round-trip kernel whose reverse and forward paths share an intermediate configuration. Conditional on that configuration, its path record update is independence Metropolis--Hastings. We compare its stationary inter-region flow with the flow obtained under exact conditional matching and bound their difference by the conditional path mismatch. This separates errors in the conditional proposal from dependence between the endpoint region and the intermediate configuration. Many well calculations test normalizers and mode probabilities; a controlled lattice $φ^4$ calculation compares ideal and accepted inter-sector flows and measures sector relaxation. In two dimensional $U(1)$, $\mathrm{SU}(2)$, and $\mathrm{SU}(3)$ gauge theories, corrected path weight estimates reproduce finite volume Wilson loops; $U(1)$ topological susceptibilities are also compared with analytic predictions across several lattice volumes.

We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution at a fraction of the cost of molecular dynamics (MD). This is in contrast with existing generative models that remove degrees of freedom by operating on coarse-grained, vacuum, or implicit solvent systems. Operating at this resolution allows for post-processing through force field energy evaluations and MD simulations, and enables the prediction of relevant properties in a gray-box manner (as ensemble averages of potential energy evaluations over generated samples). We demonstrate the utility of this paradigm on absolute hydration free energy (AHFE), producing estimates 4-10x faster and with comparable accuracy to standard GPU-based MD. By generating uncorrelated samples from alchemical Boltzmann distributions, we create more accurate, interpretable, and refinable ensemble predictions with calibrated uncertainty estimates, unlike regression methods which are entirely black-box predictors. Our approach also yields predictable benefits from increasing train- and test-time compute, realized by scaling model size and generating more samples, respectively. We believe that this approach demonstrates the utility of high-resolution ensemble generation for free energy estimation, with future potential to replace MD in tasks such as the prediction of lipophilicity, membrane permeability, or absolute binding free energy (ABFE) -- whose grounding and interpretability may be critical for the development of new drugs and materials.

Modern engineering workflows increasingly rely on massive parallel simulation, driving the need for scalable, large-batch Bayesian Optimization (BO). Existing batch BO methods, however, incur large computational cost or rely on approximations that erode batch diversity. We propose B3O (Boltzmann Batch Bayesian Optimization), a framework that reframes batch generation as a pure sampling problem: drawing samples directly from the Boltzmann distribution defined by the acquisition function avoids the bottlenecks of existing large-batch methods. Theoretically, we prove that queries sampled from this distribution incur only negligible additional regret. Empirically, B3O outperforms existing batch BO methods on standard synthetic benchmarks and adapts robustly across complex applied tasks, including multi-objective electrode design and mixed-variable race car configuration.

Efficient sampling of the Boltzmann distribution in frustrated spin glasses is central to statistical mechanics and combinatorial optimization. Despite advances in machine-learning-based approaches, two issues persist: limited understanding of why variational models fail to benefit from increased scale, unlike the monotonic scaling law of large language models; and high computational cost on large systems that negates advantages over classical sampling methods. Here, we develop a physics-inspired transformer with interpretable sparse attention and spin-tailored positional embeddings to address these challenges. By further leveraging FlashAttention for parallel ancestral sampling, it achieves up to two orders of magnitude speedup over vanilla variational autoregressive networks, enabling neural-network simulations of spin-glass systems to unprecedented sizes on a single GPU. It can resolve full probability distributions, free energies, and overlap statistics across temperatures, for Sherrington-Kirkpatrick and 2D or 3D Edwards-Anderson models, where existing machine-learning methods encounter limitations at certain temperatures. This framework thus establishes a scalable paradigm for frustrated spin-glass systems.

A long standing challenge in computational chemistry and biophysics is efficiently sampling the Boltzmann distribution of molecules. Advances in generative modeling have been proposed to address the limitations of conventional sampling techniques by eliminating the computational cost of simulation. A promising direction is iteratively finetuning diffusion models along a temperature ladder whereby training data is generated via importance sampling during inference-time annealing. Unfortunately, these methods require computing a divergence over the score field to estimate importance weights, rendering them intractable for larger systems. Here we present scalable inference-time annealing (SITA), which retrains flow-based models to generate samples at progressively lower temperatures using an energy-based model to facilitate fast surrogate likelihoods. We demonstrate state-of-the-art performance on both Alanine Dipeptide and Alanine Tripeptide while avoiding costly divergence terms. Our code is available at https://github.com/countrsignal/sita.git

Sampling physical systems with rough energy landscapes is hindered by rare events and metastable trapping. While Boltzmann generators already offer a solution, their reliance on the reverse Kullback--Leibler divergence frequently induces catastrophic mode collapse, missing specific modes in multi-modal distributions. Here, we introduce the Jeffreys Flow, a robust generative framework that mitigates this failure by distilling empirical sampling data from Parallel Tempering trajectories using the symmetric Jeffreys divergence. This formulation effectively balances local target-seeking precision with global modes coverage. We show that minimizing Jeffreys divergence suppresses mode collapse and structurally corrects inherent inaccuracies via distillation of the empirical reference data. We demonstrate the framework's scalability and accuracy on highly non-convex multidimensional benchmarks, including the systematic correction of stochastic gradient biases in Replica Exchange Stochastic Gradient Langevin Dynamics and the massive acceleration of exact importance sampling in Path Integral Monte Carlo for quantum thermal states.

We present a drifting-based framework for amortized sampling of Boltzmann distributions defined by energy functions. The method trains a one-step neural generator by projecting samples along a Gaussian-smoothed score field from the current model distribution toward the target Boltzmann distribution. For targets specified only up to an unknown normalization constant, we derive a practical target-side drift from a smoothed energy and use two estimators: a local importance-sampling mean-shift estimator and a second-order curvature-corrected approximation. Combined with a mini-batch Gaussian mean-shift estimate of the sampler-side smoothed score, this yields a simple stop-gradient objective for stable one-step training. On a four-mode Gaussian-mixture Boltzmann target, our sampler achieves mean error $0.0754$, covariance error $0.0425$, and RBF MMD $0.0020$. Additional double-well and banana targets show that the same formulation also handles nonconvex and curved low-energy geometries. Overall, the results support drifting as an effective way to amortize iterative sampling from Boltzmann distributions into a single forward pass at test time.

In a celebrated paper \cite{noe2019boltzmann}, Noé, Olsson, Köhler and Wu introduced an efficient method for sampling high-dimensional Boltzmann distributions arising in molecular dynamics via normalizing flow approximation of transport maps. Here, we place this approach on a firm mathematical foundation. We prove the existence of a normalizing flow between the reference measure and the true Boltzmann distribution up to an arbitrarily small error in the Wasserstein distance. This result covers general Boltzmann distributions from molecular dynamics, which have low regularity due to the presence of interatomic Coulomb and Lennard-Jones interactions. The proof is based on a rigorous construction of the Moser transport map for low-regularity endpoint densities and approximation theorems for neural networks in Sobolev spaces. Numerical simulations for a simple model system and for the alanine dipeptide molecule confirm that the true and generated distributions are close in the Wasserstein distance. Moreover we observe that the RealNVP architecture does not just successfully capture the equilibrium Boltzmann distribution but also the metastable dynamics.

Sampling from unnormalized probability densities is a central challenge in computational science. Boltzmann generators are generative models that enable independent sampling from the Boltzmann distribution of physical systems at a given temperature. However, their practical success depends on data-efficient training, as both simulation data and target energy evaluations are costly. To this end, we propose off-policy log-dispersion regularization (LDR), a novel regularization framework that builds on a generalization of the log-variance objective. We apply LDR in the off-policy setting in combination with standard data-based training objectives, without requiring additional on-policy samples. LDR acts as a shape regularizer of the energy landscape by leveraging additional information in the form of target energy labels. The proposed regularization framework is broadly applicable, supporting unbiased or biased simulation datasets as well as purely variational training without access to target samples. Across all benchmarks, LDR improves both final performance and data efficiency, with sample efficiency gains of up to one order of magnitude.

Sampling configurations in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators address this problem by employing generative models to propose independent configurations, which are then reweighted via importance sampling using exact likelihood evaluations. Recent Boltzmann Generators based on continuous normalizing flows and flow matching have achieved significant success for particle systems and biomolecules. However, these approaches have not been extended to amorphous materials (glasses), for which equilibrium sampling is notoriously slow. Because of their disordered structure, the invariances and geometrical constraints of amorphous materials differ from those of crystals and biomolecules, preventing the direct use of existing generative models. Here, we develop Boltzmann Generators tailored to amorphous materials by building the required equivariances directly into Riemannian stochastic interpolants. Our framework incorporates periodic boundary conditions and particle symmetries using equivariant graph neural networks. Numerical experiments demonstrate that enforcing physical symmetries significantly improves the accuracy of Boltzmann Generators, but also reveal an intrinsic limitation of the continuous-flow formulation: accumulated numerical errors during likelihood integration break time-reversibility, compromising exact thermodynamic reweighting. These results reveal a fundamental challenge for continuous-flow generative models in statistical mechanics and call for alternative approaches that preserve exact thermodynamic consistency.

Efficient sampling from Boltzmann distributions over discrete variables is a fundamental operation in a wide range of applications. While fast non-MCMC samplers have recently emerged as promising alternatives to conventional MCMC methods, their practical use for probabilistic learning remains hindered by the difficulty of estimating the effective temperature of the generated samples. In this work, we begin by introducing Langevin simulated bifurcation (LSB), a Boltzmann sampler that enables fast and parallel sampling with accuracy comparable to sequential MCMC methods. To address the challenge of unknown effective temperature, we propose conditional expectation matching (CEM), an efficient estimation method applicable to energy-based models (EBMs) with exploitable conditional independence structures. Building on these components, we further develop a learning framework, termed sampler adaptive learning (SAL), which adaptively adjusts the model temperature to match that of the distribution induced by fast non-MCMC sampling. We demonstrate the effectiveness of LSB, CEM, and SAL on semi-restricted Boltzmann machines (SRBMs), a class of EBMs that are difficult to train using conventional approaches. LSB achieves orders-of-magnitude acceleration over Gibbs sampling while maintaining comparable or higher accuracy, and CEM enables accurate temperature estimation of the resulting distribution with negligible computational overhead. As a consequence, SAL enables efficient training of SRBMs and outperforms conventional Boltzmann machine learning methods on synthetic spin-glass datasets. In addition, the trained models achieve strong performance across multiple tasks. These results establish LSB as a fast and accurate Boltzmann sampler and provide key insights that enable practical applications of fast non-MCMC sampling methods via efficient temperature estimation with CEM.