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Saeed Saremi

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11 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

Generative property enhancer: implicit guided generation through conditional density estimation

Pedro O. Pinheiro
Pan Kessel
Aya Ismail
Sai Pooja Mahajan
Kyunghyun Cho
Saeed Saremi
Nataša Tagasovska

Generative modeling is increasingly important for data-driven computational design. Conventional approaches pair a generative model with a discriminative model to select or guide samples toward optimized designs. Yet discriminative models often struggle in data-scarce settings, common in scientific applications, and are unreliable in the tails of the distribution where optimal designs typically lie. We introduce generative property enhancer (GPE), an approach that implicitly guides generation by matching samples with lower property values to higher-value ones. Formulated as conditional density estimation, our framework defines a target distribution with improved properties, compelling the generative model to produce enhanced, diverse designs without auxiliary predictors. GPE is simple, scalable, end-to-end, modality-agnostic, and integrates seamlessly with diverse generative model architectures and losses. We demonstrate competitive empirical results on standard in silico offline (non-sequential) protein fitness optimization benchmarks. Finally, we propose iterative training on a combination of limited real data and self-generated synthetic data, enabling extrapolation beyond the original property ranges.

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NeurIPS Conference 2025 Conference Paper

JAMUN: Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensemble Generation

Ameya Daigavane
Bodhi Vani
Darcy Davidson
Saeed Saremi
Joshua Rackers
Joseph Kleinhenz

Conformational ensembles of protein structures are immensely important both for understanding protein function and drug discovery in novel modalities such as cryptic pockets. Current techniques for sampling ensembles such as molecular dynamics (MD) are computationally inefficient, while many recent machine learning methods do not transfer to systems outside their training data. We propose JAMUN which performs MD in a smoothed, noised space of all-atom 3D conformations of molecules by utilizing the framework of walk-jump sampling. JAMUN enables ensemble generation for small peptides at rates of an order of magnitude faster than traditional molecular dynamics. The physical priors in JAMUN enables transferability to systems outside of its training data, even to peptides that are longer than those originally trained on. Our model, code and weights are available at https: //github. com/prescient-design/jamun.

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ICML Conference 2025 Conference Paper

Sampling Binary Data by Denoising through Score Functions

Francis R. Bach
Saeed Saremi

Gaussian smoothing combined with a probabilistic framework for denoising via the empirical Bayes formalism, i. e. , the Tweedie-Miyasawa formula (TMF), are the two key ingredients in the success of score-based generative models in Euclidean spaces. Smoothing holds the key for easing the problem of learning and sampling in high dimensions, denoising is needed for recovering the original signal, and TMF ties these together via the score function of noisy data. In this work, we extend this paradigm to the problem of learning and sampling the distribution of binary data on the Boolean hypercube by adopting Bernoulli noise, instead of Gaussian noise, as a smoothing device. We first derive a TMF-like expression for the optimal denoiser for the Hamming loss, where a score function naturally appears. Sampling noisy binary data is then achieved using a Langevin-like sampler which we theoretically analyze for different noise levels. At high Bernoulli noise levels sampling becomes easy, akin to log-concave sampling in Euclidean spaces. In addition, we extend the sequential multi-measurement sampling of Saremi et al. (2024) to the binary setting where we can bring the "effective noise" down by sampling multiple noisy measurements at a fixed noise level, without the need for continuous-time stochastic processes. We validate our formalism and theoretical findings by experiments on synthetic data and binarized images.

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NeurIPS Conference 2025 Conference Paper

Unified all-atom molecule generation with neural fields

Matthieu Kirchmeyer
Pedro O. Pinheiro
Emma Willett
Karolis Martinkus
Joseph Kleinhenz
Emily Makowski
Andrew Watkins
Vladimir Gligorijevic

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation.

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ICLR Conference 2024 Conference Paper

Chain of Log-Concave Markov Chains

Saeed Saremi
Ji Won Park
Francis R. Bach

We introduce a theoretical framework for sampling from unnormalized densities based on a smoothing scheme that uses an isotropic Gaussian kernel with a single fixed noise scale. We prove one can decompose sampling from a density (minimal assumptions made on the density) into a sequence of sampling from log-concave conditional densities via accumulation of noisy measurements with equal noise levels. Our construction is unique in that it keeps track of a history of samples, making it non-Markovian as a whole, but it is lightweight algorithmically as the history only shows up in the form of a running empirical mean of samples. Our sampling algorithm generalizes walk-jump sampling (Saremi & Hyvärinen, 2019). The "walk" phase becomes a (non-Markovian) chain of (log-concave) Markov chains. The "jump" from the accumulated measurements is obtained by empirical Bayes. We study our sampling algorithm quantitatively using the 2-Wasserstein metric and compare it with various Langevin MCMC algorithms. We also report a remarkable capacity of our algorithm to "tunnel" between modes of a distribution.

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ICLR Conference 2024 Conference Paper

Protein Discovery with Discrete Walk-Jump Sampling

Nathan C. Frey
Daniel Berenberg
Karina Zadorozhny
Joseph Kleinhenz
Julien Lafrance-Vanasse
Isidro Hötzel
Yan Wu 0027
Stephen Ra

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our $\textit{Discrete Walk-Jump Sampling}$ formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the $\textit{distributional conformity score}$ to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100\% of generated samples are successfully expressed and purified and 70\% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

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NeurIPS Conference 2024 Conference Paper

Score-based 3D molecule generation with neural fields

Matthieu Kirchmeyer
Pedro O. Pinheiro
Saeed Saremi

We introduce a new representation for 3D molecules based on their continuous atomic density fields. Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous space using neural fields. Our model, FuncMol, encodes molecular fields into latent codes using a conditional neural field, samples noisy codes from a Gaussian-smoothed distribution with Langevin MCMC (walk), denoises these samples in a single step (jump), and finally decodes them into molecular fields. FuncMol performs all-atom generation of 3D molecules without assumptions on the molecular structure and scales well with the size of molecules, unlike most approaches. Our method achieves competitive results on drug-like molecules and easily scales to macro-cyclic peptides, with at least one order of magnitude faster sampling. The code is available at https: //github. com/prescient-design/funcmol.

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ICML Conference 2024 Conference Paper

Structure-based drug design by denoising voxel grids

Pedro O. Pinheiro
Arian Rokkum Jamasb
Omar Mahmood
Vishnu Sresht
Saeed Saremi

We presents VoxBind, a new score-based generative model for 3D molecules conditioned on protein structures. Our approach represents molecules as 3D atomic density grids and leverages a 3D voxel-denoising network for learning and generation. We extend the neural empirical Bayes formalism (Saremi & Hyvärinen, 2019) to the conditional setting and generate structure-conditioned molecules with a two-step procedure: (i) sample noisy molecules from the Gaussian-smoothed conditional distribution with underdamped Langevin MCMC using the learned score function and (ii) estimate clean molecules from the noisy samples with single-step denoising. Compared to the current state of the art, our model is simpler to train, significantly faster to sample from, and achieves better results on extensive in silico benchmarks—the generated molecules are more diverse, exhibit fewer steric clashes, and bind with higher affinity to protein pockets.

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NeurIPS Conference 2023 Conference Paper

3D molecule generation by denoising voxel grids

Pedro O. O. Pinheiro
Joshua Rackers
Joseph Kleinhenz
Michael Maser
Omar Mahmood
Andrew Watkins
Stephen Ra
Vishnu Sresht

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the "clean" molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (ie, diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. Our experiments show that VoxMol captures the distribution of drug-like molecules better than state of the art, while being faster to generate samples.

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ICLR Conference 2022 Conference Paper

Multimeasurement Generative Models

Saeed Saremi
Rupesh Kumar Srivastava

We formally map the problem of sampling from an unknown distribution with a density in $\mathbb{R}^d$ to the problem of learning and sampling a smoother density in $\mathbb{R}^{Md}$ obtained by convolution with a fixed factorial kernel: the new density is referred to as M-density and the kernel as multimeasurement noise model (MNM). The M-density in $\mathbb{R}^{Md}$ is smoother than the original density in $\mathbb{R}^d$, easier to learn and sample from, yet for large $M$ the two problems are mathematically equivalent since clean data can be estimated exactly given a multimeasurement noisy observation using the Bayes estimator. To formulate the problem, we derive the Bayes estimator for Poisson and Gaussian MNMs in closed form in terms of the unnormalized M-density. This leads to a simple least-squares objective for learning parametric energy and score functions. We present various parametrization schemes of interest including one in which studying Gaussian M-densities directly leads to multidenoising autoencoders—this is the first theoretical connection made between denoising autoencoders and empirical Bayes in the literature. Samples in $\mathbb{R}^d$ are obtained by walk-jump sampling (Saremi & Hyvarinen, 2019) via underdamped Langevin MCMC (walk) to sample from M-density and the multimeasurement Bayes estimation (jump). We study permutation invariant Gaussian M-densities on MNIST, CIFAR-10, and FFHQ-256 datasets, and demonstrate the effectiveness of this framework for realizing fast-mixing stable Markov chains in high dimensions.

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JMLR Journal 2019 Journal Article

Neural Empirical Bayes

Saeed Saremi
Aapo Hyvärinen

We unify kernel density estimation and empirical Bayes and address a set of problems in unsupervised machine learning with a geometric interpretation of those methods, rooted in the concentration of measure phenomenon. Kernel density is viewed symbolically as $X\rightharpoonup Y$ where the random variable $X$ is smoothed to $Y= X+N(0,\sigma^2 I_d)$, and empirical Bayes is the machinery to denoise in a least-squares sense, which we express as $X \leftharpoondown Y$. A learning objective is derived by combining these two, symbolically captured by $X \rightleftharpoons Y$. Crucially, instead of using the original nonparametric estimators, we parametrize the energy function with a neural network denoted by $\phi$; at optimality, $\nabla \phi \approx -\nabla \log f$ where $f$ is the density of $Y$. The optimization problem is abstracted as interactions of high-dimensional spheres which emerge due to the concentration of isotropic Gaussians. We introduce two algorithmic frameworks based on this machinery: (i) a “walk-jump” sampling scheme that combines Langevin MCMC (walks) and empirical Bayes (jumps), and (ii) a probabilistic framework for associative memory, called NEBULA, defined a la Hopfield by the gradient flow of the learned energy to a set of attractors. We finish the paper by reporting the emergence of very rich “creative memories” as attractors of NEBULA for highly-overlapping spheres. [abs] [ pdf ][ bib ] &copy JMLR 2019. ( edit, beta )

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