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.

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.

They are not well characterized as single structures as has traditionally been the case, but rather as ensembles of structures with an ergodic probability distribution(Henzler-Wildman & Kern, 2007). Protein motion is required for myglobin to bind oxygen and move it around the body (Miller & Phillips, 2021). Drug discovery on protein kinases depends on characterizing kinase conforma-tional ensembles (Gough & Kalodimos, 2024). The search for druggable'cryptic pockets' requires understanding protein dynamics, and antibody design is deeply affected by conformational ensembles (Colombo, 2023). However, while machine learning (ML) methods for molecular structure prediction have experienced enormous success recently, ML methods for dynamics have yet to have similar impact. ML models for generating molecular ensembles are widely considered the'next frontier' (Bowman, 2024; Miller & Phillips, 2021; Zheng et al., 2023).

We present NEBULA, the first latent 3D generative model for scalable generation of large molecular libraries around a seed compound of interest. Such libraries are crucial for scientific discovery, but it remains challenging to generate large numbers of high quality samples efficiently. 3D-voxel-based methods have recently shown great promise for generating high quality samples de novo from random noise (Pinheiro et al., 2023). However, sampling in 3D-voxel space is computationally expensive and use in library generation is prohibitively slow. Here, we instead perform neural empirical Bayes sampling (Saremi & Hyvarinen, 2019) in the learned latent space of a vector-quantized variational autoencoder. NEBULA generates large molecular libraries nearly an order of magnitude faster than existing methods without sacrificing sample quality. Moreover, NEBULA generalizes better to unseen drug-like molecules, as demonstrated on two public datasets and multiple recently released drugs. We expect the approach herein to be highly enabling for machine learning-based drug discovery. The code is available at https://github.com/prescient-design/nebula

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 & Hyv\"arinen, 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.

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 (i.e., 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. VoxMol achieves comparable results to state of the art on unconditional 3D molecule generation while being simpler to train and faster to generate molecules.

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 Discrete Walk-Jump Sampling formalism combines the maximum likelihood 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 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 35% 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.

We consider the problem of generative modeling based on smoothing an unknown density of interest in $\mathbb{R}^d$ using factorial kernels with $M$ independent Gaussian channels with equal noise levels introduced by Saremi and Srivastava (2022). First, we fully characterize the time complexity of learning the resulting smoothed density in $\mathbb{R}^{Md}$, called M-density, by deriving a universal form for its parametrization in which the score function is by construction permutation equivariant. Next, we study the time complexity of sampling an M-density by analyzing its condition number for Gaussian distributions. This spectral analysis gives a geometric insight on the "shape" of M-densities as one increases $M$. Finally, we present results on the sample quality in this class of generative models on the CIFAR-10 dataset where we report Fr\'echet inception distances (14.15), notably obtained with a single noise level on long-run fast-mixing MCMC chains.

We formally map the problem of sampling from an unknown distribution with density $p_X$ in $\mathbb{R}^d$ to the problem of learning and sampling $p_\mathbf{Y}$ in $\mathbb{R}^{Md}$ obtained by convolving $p_X$ with a fixed factorial kernel: $p_\mathbf{Y}$ is referred to as M-density and the factorial kernel as multimeasurement noise model (MNM). The M-density is smoother than $p_X$, easier to learn and sample from, yet for large $M$ the two problems are mathematically equivalent since $X$ can be estimated exactly given $\mathbf{Y}=\mathbf{y}$ using the Bayes estimator $\widehat{x}(\mathbf{y})=\mathbb{E}[X\vert\mathbf{Y}=\mathbf{y}]$. To formulate the problem, we derive $\widehat{x}(\mathbf{y})$ for Poisson and Gaussian MNMs expressed in closed form in terms of unnormalized $p_\mathbf{Y}$. 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 from $p_X$ are obtained by walk-jump sampling (Saremi & Hyvarinen, 2019) via underdamped Langevin MCMC (walk) to sample from $p_\mathbf{Y}$ and the multimeasurement Bayes estimation of $X$ (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.

With the goal of designing novel inhibitors for SARS-CoV-1 and SARS-CoV-2, we propose the general molecule optimization framework, Molecular Neural Assay Search (MONAS), consisting of three components: a property predictor which identifies molecules with specific desirable properties, an energy model which approximates the statistical similarity of a given molecule to known training molecules, and a molecule search method. In this work, these components are instantiated with graph neural networks (GNNs), Deep Energy Estimator Networks (DEEN) and Monte Carlo tree search (MCTS), respectively. This implementation is used to identify 120K molecules (out of 40-million explored) which the GNN determined to be likely SARS-CoV-1 inhibitors, and, at the same time, are statistically close to the dataset used to train the GNN.