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apid growth of high-dimensional datasets in fields such as single-cell RNA sequencing and spatial genomics has led to unprecedented opportunities for scientific discovery, but it also presents unique computational and statistical challenges. Traditional methods struggle with geometry-aware data generation, interpolation along meaningful trajectories, and transporting populations via feasible paths. To address these issues, we introduce Geometry-Aware Generative Autoencoder (GAGA), a novel framework that combines extensible manifold learning with generative modeling. GAGA constructs a neural network embedding space that respects the intrinsic geometries discovered by manifold learning and learns a novel warped Riemannian metric on the data space. This warped metric is derived from both the points on the data manifold and negative samples off the manifold, allowing it to characterize a meaningful geometry across the entire latent space. Using this metric, GAGA can uniformly sample points on the manifold, generate points along geodesics, and interpolate between populations across the learned manifold. GAGA shows competitive performance in simulated and real-world datasets, including a 30% improvement over SOTA in single-cell population-level trajectory inference. 

Adversarial examples have been shown to cause neural networks to fail on a wide range of vision and language tasks, but recent work has claimed that {\em Bayesian} neural networks (BNNs) are inherently robust to adversarial perturbations. In this work, we examine this claim. To study the adversarial robustness of BNNs, we investigate whether it is possible to successfully break state-of-the-art BNN inference methods and prediction pipelines using even relatively unsophisticated attacks for three tasks: (1) label prediction under the posterior predictive mean, (2) adversarial example detection with Bayesian predictive uncertainty, and (3) semantic shift detection. We find that BNNs trained with state-of-the-art approximate inference methods, and even BNNs trained with Hamiltonian Monte Carlo, are highly susceptible to adversarial attacks. We also identify various conceptual and experimental errors in previous works that claimed inherent adversarial robustness of BNNs and conclusively demonstrate that BNNs and uncertainty-aware Bayesian prediction pipelines are {\em not} inherently robust against adversarial attacks. 

Bayesian optimization is a highly efficient approach to optimizing objective functions which are expensive to query. These objectives are typically represented by Gaussian process (GP) surrogate models which are easy to optimize and support exact inference. While standard GP surrogates have been well-established in Bayesian optimization, Bayesian neural networks (BNNs) have recently become practical function approximators, with many benefits over standard GPs such as the ability to naturally handle non-stationarity and learn representations for high-dimensional data. In this paper, we study BNNs as alternatives to standard GP surrogates for optimization. We consider a variety of approximate inference procedures for finite-width BNNs, including high-quality Hamiltonian Monte Carlo, low-cost stochastic MCMC, and heuristics such as deep ensembles. We also consider infinite-width BNNs, linearized Laplace approximations, and partially stochastic models such as deep kernel learning. We evaluate this collection of surrogate models on diverse problems with varying dimensionality, number of objectives, non-stationarity, and discrete and continuous inputs. We find: (i) the ranking of methods is highly problem dependent, suggesting the need for tailored inductive biases; (ii) HMC is the most successful approximate inference procedure for fully stochastic BNNs; (iii) full stochasticity may be unnecessary as deep kernel learning is relatively competitive; (iv) deep ensembles perform relatively poorly; (v) infinite-width BNNs are particularly promising, especially in high dimensions. 

Machine learning models often perform poorly under subpopulation shifts in the data distribution. Developing methods that allow machine learning models to better generalize to such shifts is crucial for safe deployment in real-world settings. In this paper, we develop a family of group-aware prior (GAP) distributions over neural network parameters that explicitly favor models that generalize well under subpopulation shifts. We design a simple group-aware prior that only requires access to a small set of data with group information and demonstrate that training with this prior yields state-of-the-art performance -- even when only retraining the final layer of a previously trained non-robust model. Group aware-priors are conceptually simple, complementary to existing approaches, such as attribute pseudo labeling and data reweighting, and open up promising new avenues for harnessing Bayesian inference to enable robustness to subpopulation shifts. 

Standard regularized training procedures correspond to maximizing a posterior distribution over parameters, known as maximum a posteriori (MAP) estimation. However, model parameters are of interest only insomuch as they combine with the functional form of a model to provide a function that can make good predictions. Moreover, the most likely parameters under the parameter posterior do not generally correspond to the most likely function induced by the parameter posterior. In fact, we can re-parametrize a model such that any setting of parameters can maximize the parameter posterior. As an alternative, we investigate the benefits and drawbacks of directly estimating the most likely function implied by the model and the data. We show that this procedure leads to pathological solutions when using neural networks and prove conditions under which the procedure is well-behaved, as well as a scalable approximation. Under these conditions, we find that function-space MAP estimation can lead to flatter minima, better generalization, and improved robustness to overfitting. 

A popular approach to protein design is to combine a generative model with a discriminative model for conditional sampling. The generative model samples plausible sequences while the discriminative model guides a search for sequences with high fitness. Given its broad success in conditional sampling, classifier-guided diffusion modeling is a promising foundation for protein design, leading many to develop guided diffusion models for structure with inverse folding to recover sequences. In this work, we propose diffusioN Optimized Sampling (NOS), a guidance method for discrete diffusion models that follows gradients in the hidden states of the denoising network. NOS makes it possible to perform design directly in sequence space, circumventing significant limitations of structure-based methods, including scarce data and challenging inverse design. Moreover, we use NOS to generalize LaMBO, a Bayesian optimization procedure for sequence design that facilitates multiple objectives and edit-based constraints. The resulting method, LaMBO-2, enables discrete diffusions and stronger performance with limited edits through a novel application of saliency maps. We apply LaMBO-2 to a real-world protein design task, optimizing antibodies for higher expression yield and binding affinity to several therapeutic targets under locality and developability constraints, attaining a 99% expression rate and 40% binding rate in exploratory in vitro experiments.