Saifuddin Syed

Charlie B. Tan, Majdi Hassan, Leon Klein et al.

Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Classical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in-full for each system of interest. The widespread success of generative models has inspired interest into overcoming this limitation through learning sampling algorithms. Despite performing on par with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We prove that deep learning enables the design of scalable and transferable samplers by introducing Prose, a 280 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Prose draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Prose as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based finetuning procedure to achieve superior performance to established methods such as sequential Monte Carlo on unseen tetrapeptides. We open-source the Prose codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and finetuning objectives.

Francisco M. Castro-Macías, Pablo Morales-Álvarez, Saifuddin Syed et al.

Sampling from unnormalized multimodal distributions with limited density evaluations remains a fundamental challenge in machine learning and natural sciences. Successful approaches construct a bridge between a tractable reference and the target distribution. Parallel Tempering (PT) serves as the gold standard, while recent diffusion-based approaches offer a continuous alternative at the cost of neural training. In this work, we introduce Conditional Diffusion Sampling (CDS), a framework that combines these two paradigms. To this end, we derive Conditional Interpolants, a class of stochastic processes whose transport dynamics are governed by an exact, closed-form stochastic differential equation (SDE), requiring no neural approximation. Although these dynamics require sampling from a non-trivial initialization distribution, we show both theoretically and empirically that the cost of this initialization diminishes for sufficiently short diffusion times. CDS leverages this by a two-stage procedure: (1) PT is used to efficiently sample the initial distribution, and then (2) samples are transported via the transport SDE. This combination couples the robust global exploration of PT with efficient local transport. Experiments suggest that CDS has the potential to achieve a superior trade-off between sample quality and density evaluation cost compared to state-of-the-art samplers.

Christopher Williams, Andrew Campbell, Arnaud Doucet et al.

Denoising diffusion models (DDMs) offer a flexible framework for sampling from high dimensional data distributions. DDMs generate a path of probability distributions interpolating between a reference Gaussian distribution and a data distribution by incrementally injecting noise into the data. To numerically simulate the sampling process, a discretisation schedule from the reference back towards clean data must be chosen. An appropriate discretisation schedule is crucial to obtain high quality samples. However, beyond hand crafted heuristics, a general method for choosing this schedule remains elusive. This paper presents a novel algorithm for adaptively selecting an optimal discretisation schedule with respect to a cost that we derive. Our cost measures the work done by the simulation procedure to transport samples from one point in the diffusion path to the next. Our method does not require hyperparameter tuning and adapts to the dynamics and geometry of the diffusion path. Our algorithm only involves the evaluation of the estimated Stein score, making it scalable to existing pre-trained models at inference time and online during training. We find that our learned schedule recovers performant schedules previously only discovered through manual search and obtains competitive FID scores on image datasets.

Leo Zhang, Saifuddin Syed

In this work, we study the problem of choosing the discretisation schedule for sampling from masked discrete diffusion models in terms of the information geometry of the induced probability path. Specifically, we show that the optimal schedule under the Fisher-Rao geometry recovers the popularly-used cosine schedule.

Leo Zhang, Peter Potaptchik, Jiajun He et al. · cambridge

Markov Chain Monte Carlo (MCMC) algorithms are essential tools in computational statistics for sampling from unnormalised probability distributions, but can be fragile when targeting high-dimensional, multimodal, or complex target distributions. Parallel Tempering (PT) enhances MCMC's sample efficiency through annealing and parallel computation, propagating samples from tractable reference distributions to intractable targets via state swapping across interpolating distributions. The effectiveness of PT is limited by the often minimal overlap between adjacent distributions in challenging problems, which requires increasing the computational resources to compensate. We introduce a framework that accelerates PT by leveraging neural samplers -- including normalising flows, diffusion models, and controlled diffusions -- to reduce the required overlap. Our approach utilises neural samplers in parallel, circumventing the computational burden of neural samplers while preserving the asymptotic consistency of classical PT. We demonstrate theoretically and empirically on a variety of multimodal sampling problems that our method improves sample quality, reduces the computational cost compared to classical PT, and enables efficient free energy/normalising constant estimation.

Jiajun He, Paul Jeha, Peter Potaptchik et al. · cambridge

Inference-time control of diffusion models aims to steer model outputs to satisfy new constraints without retraining. Previous approaches have mostly relied on heuristic guidance or have been coupled with Sequential Monte Carlo (SMC) for bias correction. In this paper, we propose a flexible alternative based on replica exchange, an algorithm designed initially for sampling problems. We refer to this method as the CREPE (Controlling with REPlica Exchange). Unlike SMC, CREPE: (1) generates particles sequentially, (2) maintains high diversity in the generated samples after a burn-in period, and (3) enables online refinement or early termination. We demonstrate its versatility across various tasks, including temperature annealing, reward-tilting, model composition and classifier-free guidance debiasing, with competitive performance compared to prior SMC methods.

Christopher Williams, Fabian Falck, George Deligiannidis et al.

U-Nets are a go-to, state-of-the-art neural architecture across numerous tasks for continuous signals on a square such as images and Partial Differential Equations (PDE), however their design and architecture is understudied. In this paper, we provide a framework for designing and analysing general U-Net architectures. We present theoretical results which characterise the role of the encoder and decoder in a U-Net, their high-resolution scaling limits and their conjugacy to ResNets via preconditioning. We propose Multi-ResNets, U-Nets with a simplified, wavelet-based encoder without learnable parameters. Further, we show how to design novel U-Net architectures which encode function constraints, natural bases, or the geometry of the data. In diffusion models, our framework enables us to identify that high-frequency information is dominated by noise exponentially faster, and show how U-Nets with average pooling exploit this. In our experiments, we demonstrate how Multi-ResNets achieve competitive and often superior performance compared to classical U-Nets in image segmentation, PDE surrogate modelling, and generative modelling with diffusion models. Our U-Net framework paves the way to study the theoretical properties of U-Nets and design natural, scalable neural architectures for a multitude of problems beyond the square.