Parallel Tempering

Bayesian inference increasingly uses informative but implicit priors represented only by samples, such as historical ensembles, simulator outputs, and pretrained generative models. The same computational problem appears in the test-time guidance task (generalized Bayes), where an explicit positive weight, e.g., an exponentiated reward, tilts an implicit prior. We develop a framework for source-space generalized Bayesian inference that combines inexpensive few-step prior transports with posterior stability guarantees. Specifically, we represent the prior using a one- or few-step improved MeanFlow (iMF) map and perform posterior sampling in its Gaussian source space. We establish Wasserstein error bounds between the exact and learned posteriors in terms of the joint population iMF and auxiliary-velocity loss, decomposed into training suboptimality and model-class approximation error. In the iMF source space, we adopt parallel tempering with preconditioned Crank-Nicolson updates and introduce a hybrid variant that incorporates split Hamiltonian Monte Carlo to improve sampling efficiency. Synthetic experiments show that the proposed framework can approximate posterior distributions accurately and efficiently, while CLIP-guided ImageNet experiments demonstrate its ability to steer a pretrained iMF image prior toward text-specified preferences.

For a Markov kernel $T$ with an invariant probability measure $π$, we give a self-contained proof of the Markov chain convergence theorem via a criterion called asymptotic equivalence with the target. It assumes two parts about the Lebesgue decompositions of $T^{n}_{x}$ and $π$ for every starting point $x$: 1.) asymptotic absolute continuity: the singular mass sing$(T^{n}_{x}\midπ)$ tends to $0$; 2.) asymptotic domination of the target: the singular mass sing$(π\mid T^{n}_{x})$ tends to $0$, as $n \to \infty$. This criterion, on countably generated measurable spaces, is both sufficient and necessary for the Markov chain convergence. A density version of this criterion is verified on general measurable spaces in three cases: (i) $T$ has a positive transition density wrt $π$; (ii) $T$ consists of an absolutely continuous part with positive transition density together with an atom at the starting point, which covers the Metropolis--Hastings algorithm; (iii) the transition density is positive only after a finite number of steps that may depend on the starting point $x$. To demonstrate our general criterion, we investigate the Gibbs sampler with random scan and the parallel tempering algorithm. Furthermore, we show that in all mentioned settings Birkhoff's ergodic theorem applies, so as to obtain the strong law of large numbers. Throughout this paper, neither irreducibility, nor aperiodicity, nor recurrence, nor couplings, nor splitting constructions, nor small sets are used. In most results, the state space is a general measurable space, which carries no structure beyond a $σ$-algebra. Countable generation is only assumed where the density-free form of the criterion is stated. None of the theorems proved here is new; what is offered is a short route to a single, widely applicable Markov chain convergence criterion, which is both sufficient and necessary.

Energy-Based Models (EBMs) provide an interpretable framework for generative modeling of scientific data, but poor Markov Chain Monte Carlo mixing often limits their reliability. We introduce a training algorithm based on Parallel Trajectory Tempering (PTT), which exploits the continuity of the optimization path to maintain equilibrium sampling throughout learning. This enables stable and fast training on highly multimodal and data-scarce scientific datasets. Combined with reservoir sampling and adaptive optimization, PTT has a computational cost comparable to Persistent Contrastive Divergence, making it a practical replacement for standard training methods. It also provides direct estimates of thermalization times, equilibrium samples from trained models, and accurate log-likelihoods at essentially no additional cost. Experiments on Restricted Boltzmann Machines show that PTT consistently outperforms existing EBM training approaches. On discrete tabular data, it also surpasses state-of-the-art deep generative models, yielding higher-quality samples and greater robustness to overfitting and limited data. Our results make equilibrium maximum-likelihood training of EBMs practical and computationally efficient.

Neural Markov Logic Networks (NMLNs) are a flexible neurosymbolic relational model. Previous work has shown that, although NMLNs achieve strong performance as generative models for small relational structures, they underperform diffusion-based generative graph models on larger structures. In this paper, we strengthen NMLNs along two main dimensions: (i) we increase the expressive capacity of their potential functions using graph neural networks, and (ii) we develop a new training and inference algorithm inspired by parallel-tempering Markov chain Monte Carlo methods, which we name parallel noising. Together, these enhancements enable NMLNs to attain strong performance in graph generation relative to general diffusion-based generative graph models. Furthermore, they allow NMLNs to match the performance of specialized text-based recurrent models when generating small molecular structures.

Prompt optimization adapts large language models (LLMs) without updating model parameters, but many automatic prompt optimizers remain heuristic search procedures over candidate instructions. This paper studies prompt optimization as Bayesian posterior sampling over discrete prompt tokens. We define a posterior distribution by combining a task likelihood term, which rewards prompts that explain input-output examples, with a language-model prior, which favors fluent instructions. This converts prompt optimization into an energy-based posterior sampling problem, for which gradients can be used to guide discrete Markov chain Monte Carlo (MCMC) proposals over vocabulary tokens. We refer to our framework as BayesPO, short for Bayesian Prompt Optimization. In this paper, BayesPO is instantiated with Markov chain Monte Carlo: it uses a Metropolis-Hastings corrected Gibbs-with-Langevin (GwL) proposal and integrates parallel tempering for global exploration of rugged LLM-induced energy landscapes. The concrete sampler further adapts the GwL sampler to the practical constraints of non-weight-tied LLM embeddings. Experiments with Qwen2.5 models show that the sampler discovers semantically meaningful prompts on diagnostic tasks, that parallel tempering helps escape a local optimum in a poetry completion task, and that post-optimizing APE prompts on 24 instruction-induction subtasks improves average accuracy from 60.04% to 63.23%. The study also reveals two main limitations: energy minimization may overfit small optimization sets, and the current sampler remains computationally expensive. These findings position Bayesian prompt sampling as a principled post-optimization tool and point to a promising direction for probabilistic prompt optimization.

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.

Inference-time reward alignment steers pretrained diffusion and flow-based generative models to satisfy user-specified rewards without retraining. Recently, Sequential Monte Carlo (SMC) has emerged as a powerful framework for this task by iteratively filtering and propagating multiple particles. However, we show that standard SMC-based methods often suffer from poor performance because they initialize particles from a standard prior, whereas high-reward regions in complex reward landscapes are extremely rare. Further, we show that even recent reward-aware initial sampling approaches remain vulnerable to getting trapped in local modes, as complex reward landscapes are often multi-modal. To overcome these limitations, we propose PATHS (PArallel Tempering for High-complexity reward Sampling), a novel initialization method that couples multiple sampling chains through parallel tempering. PATHS maintains a ladder of reward-tempered chains and periodically performs Metropolis swaps, enabling efficient exploration across flattened reward landscapes, thereby mitigating the mode-trapping issues. Our analysis reveals that this mechanism substantially enhances the finite-budget exploration of rare, high-reward regions that are typically challenging to sample. Experiments on layout-to-image and quantity-aware generation show that PATHS achieves consistent gains in alignment quality, particularly on complex prompts.

Integer Linear Programming (ILP) serves as a versatile framework for modeling a wide range of combinatorial optimization problems, typically addressed by sophisticated exact solvers or heuristics. While learning-based approaches have recently shown their effectiveness, they suffer from poor generalization to out-of-distribution instances and inherent dependence on external solvers. In this work, we propose a solver-free, sampling-based optimization framework for ILP that directly explores discrete feasible regions without training or external solvers. Exploiting the linear structure of ILP, we employ a Locally-Balanced Proposal to construct a transition kernel, thereby avoiding the gradient approximation. To overcome the highly multimodal nature of ILP energy landscapes, we integrate Parallel Tempering. In addition to standard temperature tempering, we introduce penalty tempering, which modulates constraint barriers while preserving the objective landscape over feasible solutions. Empirically, our method consistently outperforms SCIP across all four benchmarks, matches or exceeds Gurobi on two of four tasks within a 200-second budget, and is substantially more robust to distribution shift than learning-based methods. Furthermore, on MIPLIB 2017 instances, our framework remains competitive with classical solvers without any problem-specific tuning.