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.

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.

Machine learning models have recently shown promise in predicting molecular quantum chemical properties. However, the path to real-life adoption requires (1) learning under low-resource constraints and (2) out-of-distribution generalization to unseen, structurally diverse molecules. We observe that these two challenges can be addressed via abundant labels, which is often not the case in quantum chemistry. We hypothesize that pseudo-labeling on a vast array of unlabeled molecules can serve as gold-label proxies to expand the training labeled dataset significantly. The challenge in pseudo-labeling is to prevent the bad pseudo-labels from biasing the model. Motivated by the entropy minimization framework, we develop a simple and effective strategy Pseudo that can assign pseudo-labels, detect bad pseudo-labels through evidential uncertainty, and prevent them from biasing the model using adaptive weighting. Empirically, Pseudo improves quantum calculations accuracy in full data, low data, and out-of-distribution settings.