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.

Effective data-driven PDE forecasting methods often rely on fixed spatial and / or temporal discretizations. This raises limitations in real-world applications like weather prediction where flexible extrapolation at arbitrary spatiotemporal locations is required. We address this problem by introducing a new data-driven approach, DINo, that models a PDE's flow with continuous-time dynamics of spatially continuous functions. This is achieved by embedding spatial observations independently of their discretization via Implicit Neural Representations in a small latent space temporally driven by a learned ODE. This separate and flexible treatment of time and space makes DINo the first data-driven model to combine the following advantages. It extrapolates at arbitrary spatial and temporal locations; it can learn from sparse irregular grids or manifolds; at test time, it generalizes to new grids or resolutions. DINo outperforms alternative neural PDE forecasters in a variety of challenging generalization scenarios on representative PDE systems.

Standard neural networks struggle to generalize under distribution shifts in computer vision. Fortunately, combining multiple networks can consistently improve out-of-distribution generalization. In particular, weight averaging (WA) strategies were shown to perform best on the competitive DomainBed benchmark; they directly average the weights of multiple networks despite their nonlinearities. In this paper, we propose Diverse Weight Averaging (DiWA), a new WA strategy whose main motivation is to increase the functional diversity across averaged models. To this end, DiWA averages weights obtained from several independent training runs: indeed, models obtained from different runs are more diverse than those collected along a single run thanks to differences in hyperparameters and training procedures. We motivate the need for diversity by a new bias-variance-covariance-locality decomposition of the expected error, exploiting similarities between WA and standard functional ensembling. Moreover, this decomposition highlights that WA succeeds when the variance term dominates, which we show occurs when the marginal distribution changes at test time. Experimentally, DiWA consistently improves the state of the art on DomainBed without inference overhead.

In recent years, impressive progress has been made in the design of implicit probabilistic models via Generative Adversarial Networks (GAN) and its extension, the Conditional GAN (CGAN). Excellent solutions have been demonstrated mostly in image processing applications which involve large, continuous output spaces. There is almost no application of these powerful tools to problems having small dimensional output spaces. Regression problems involving the inductive learning of a map, $y=f(x,z)$, $z$ denoting noise, $f:\mathbb{R}^n\times \mathbb{R}^k \rightarrow \mathbb{R}^m$, with $m$ small (e.g., $m=1$ or just a few) is one good case in point. The standard approach to solve regression problems is to probabilistically model the output $y$ as the sum of a mean function $m(x)$ and a noise term $z$; it is also usual to take the noise to be a Gaussian. These are done for convenience sake so that the likelihood of observed data is expressible in closed form. In the real world, on the other hand, stochasticity of the output is usually caused by missing or noisy input variables. Such a real world situation is best represented using an implicit model in which an extra noise vector, $z$ is included with $x$ as input. CGAN is naturally suited to design such implicit models. This paper makes the first step in this direction. Through several artificial and real world datasets, we demonstrate CGAN to be an effective approach for solving regression problems. We compare against Gaussian Processes and show that CGAN has excellent output likelihood properties and possesses the ability to model complex noise forms in a better way.