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O. Deniz Akyildiz

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4 papers

1 author row

NeurIPS Conference 2025 Conference Paper

Learning Latent Variable Models via Jarzynski-adjusted Langevin Algorithm

James Cuin
Davide Carbone
O. Deniz Akyildiz

We utilise a sampler originating from nonequilibrium statistical mechanics, termed here Jarzynski-adjusted Langevin algorithm (JALA), to build statistical estimation methods in latent variable models. We achieve this by leveraging Jarzynski’s equality and developing algorithms based on a weighted version of the unadjusted Langevin algorithm (ULA) with recursively updated weights. Adapting this for latent variable models, we develop a sequential Monte Carlo (SMC) method that provides the maximum marginal likelihood estimate of the parameters, termed JALA-EM. Under suitable regularity assumptions on the marginal likelihood, we provide a nonasymptotic analysis of the JALA-EM scheme implemented with stochastic gradient descent and show that it provably converges to the maximum marginal likelihood estimate. We demonstrate the performance of JALA-EM on a variety of latent variable models and show that it performs comparably to existing methods in terms of accuracy and computational efficiency. Importantly, the ability to recursively estimate marginal likelihoods—an uncommon feature among scalable methods—makes our approach particularly suited for model selection, which we validate through dedicated experiments.

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TMLR Journal 2025 Journal Article

On diffusion posterior sampling via sequential Monte Carlo for zero-shot scaffolding of protein motifs

James Matthew Young
O. Deniz Akyildiz

With the advent of diffusion models, new proteins can be generated at an unprecedented rate. The motif scaffolding problem requires steering this generative process to yield proteins with a desirable functional substructure called a motif. While models have been trained to take the motif as conditional input, recent techniques in diffusion posterior sampling can be leveraged as zero-shot alternatives whose approximations can be corrected with sequential Monte Carlo (SMC) algorithms. In this work, we introduce a new set of guidance potentials for describing scaffolding tasks and solve them by adapting SMC-aided diffusion posterior samplers with an unconditional model, Genie, as a prior. In single motif problems, we find that (i) the proposed potentials perform comparably, if not better, than the conventional masking approach, (ii) samplers based on reconstruction guidance outperform their replacement method counterparts, and (iii) measurement tilted proposals and twisted targets improve performance substantially. Furthermore, as a demonstration, we provide solutions to two multi-motif problems by pairing reconstruction guidance with an SE(3)-invariant potential. We also produce designable internally symmetric monomers with a guidance potential for point symmetry constraints. Our code is available at: https://github.com/matsagad/mres-project.

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NeurIPS Conference 2025 Conference Paper

Sampling by averaging: A multiscale approach to score estimation

Paula Cordero-Encinar
Andrew Duncan
Sebastian Reich
O. Deniz Akyildiz

We introduce a novel framework for efficient sampling from complex, unnormalised target distributions by exploiting multiscale dynamics. Traditional score-based sampling methods either rely on learned approximations of the score function or involve computationally expensive nested Markov chain Monte Carlo (MCMC) loops. In contrast, the proposed approach leverages stochastic averaging within a slow-fast system of stochastic differential equations (SDEs) to estimate intermediate scores along a diffusion path without training or inner-loop MCMC. Two algorithms are developed under this framework: MultALMC, which uses multiscale annealed Langevin dynamics, and MultCDiff, based on multiscale controlled diffusions for the reverse-time Ornstein-Uhlenbeck process. Both overdamped and underdamped variants are considered, with theoretical guarantees of convergence to the desired diffusion path. The framework is extended to handle heavy-tailed target distributions using Student’s t-based noise models and tailored fast-process dynamics. Empirical results across synthetic and real-world benchmarks, including multimodal and high-dimensional distributions, demonstrate that the proposed methods are competitive with existing samplers in terms of accuracy and efficiency, without the need for learned models.

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JMLR Journal 2024 Journal Article

Nonasymptotic analysis of Stochastic Gradient Hamiltonian Monte Carlo under local conditions for nonconvex optimization

O. Deniz Akyildiz
Sotirios Sabanis

We provide a nonasymptotic analysis of the convergence of the stochastic gradient Hamiltonian Monte Carlo (SGHMC) to a target measure in Wasserstein-2 distance without assuming log-concavity. Our analysis quantifies key theoretical properties of the SGHMC as a sampler under local conditions which significantly improves the findings of previous results. In particular, we prove that the Wasserstein-2 distance between the target and the law of the SGHMC is uniformly controlled by the step-size of the algorithm, therefore demonstrate that the SGHMC can provide high-precision results uniformly in the number of iterations. The analysis also allows us to obtain nonasymptotic bounds for nonconvex optimization problems under local conditions and implies that the SGHMC, when viewed as a nonconvex optimizer, converges to a global minimum with the best known rates. We apply our results to obtain nonasymptotic bounds for scalable Bayesian inference and nonasymptotic generalization bounds. [abs] [ pdf ][ bib ] &copy JMLR 2024. ( edit, beta )

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