26 accepted papers
Efficient sampling of molecular systems at thermodynamic equilibrium is a hallmark challenge in statistical physics. This challenge has driven the development of Boltzmann Generators (BGs), which allow rapid generation of uncorrelated equilibrium samples by combining a generative model with exact li…
Simulation-free training frameworks have been at the forefront of the generative modelling revolution in continuous spaces, leading to large-scale diffusion and flow matching models. However, such modern generative models suffer from expensive inference, inhibiting their use in numerous scientific a…
Geometric data and purpose-built generative models on them have become ubiquitous in high-impact deep learning application domains, ranging from protein backbone generation and computational chemistry to geospatial data. Current geometric generative models remain computationally expensive at infer…
Accurately predicting experimentally-realizable $3\textrm{D}$ molecular crystal structures from their $2\textrm{D}$ chemical graphs is a long-standing open challenge in computational chemistry called $\textit{crystal structure prediction}$ (CSP). Efficiently solving this problem has implications ran…
Diffusion language models have emerged as a powerful alternative to autoregressive models, enabling fast inference through more flexible and parallel generation paths. This flexibility of sampling is unlocked by new engineered sampling strategies, or *planners*, that select more favorable generation…
Modeling the transport dynamics of natural processes from population-level observations is a ubiquitous problem in the natural sciences. Such models rely on key assumptions about the underlying process in order to enable faithful learning of governing dynamics that mimic the actual system behavior.…
Sampling efficiently from a target unnormalized probability density remains a core challenge, with relevance across countless high-impact scientific applications. A promising approach towards this challenge is the design of amortized samplers that borrow key ideas, such as probability path design, f…
A fundamental challenge in organic chemistry is identifying and predicting the sequence of reactions that synthesize a desired target molecule. Due to the combinatorial nature of the chemical search space, single-step reactant prediction—i.e., single-step retrosynthesis—remains difficult, even for s…
Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing normalizing flows with importance sampling to obtain uncorrelated samples under the target distribution. In this paper, we exten…
Generative modeling of discrete data underlies important applications spanning text-based agents like ChatGPT to the design of the very building blocks of life in protein sequences. However, application domains need to exert control over the generated data by steering the generative process—typicall…
The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of com…
Generative modeling over discrete data has recently seen numerous success stories, with applications spanning language modeling, biological sequence design, and graph-structured molecular data. The predominant generative modeling paradigm for discrete data is still autoregressive, with more recent a…
Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising Energy Matching (iDEM), an iterative algorithm that uses a nove…
Matching objectives underpin the success of modern generative models and rely on constructing conditional paths that transform a source distribution into a target distribution. Despite being a fundamental building block, conditional paths have been designed principally under the assumption of $\text…
Deep generative models have made tremendous progress in modeling complex data, often exhibiting generation quality that surpasses a typical human's ability to discern the authenticity of samples. Undeniably, a key driver of this success is enabled by the massive amounts of web-scale data consumed by…
The computational design of novel protein structures has the potential to impact numerous scientific disciplines greatly. Toward this goal, we introduce \foldflow, a series of novel generative models of increasing modeling power based on the flow-matching paradigm over $3\mathrm{D}$ rigid motions---…
The rapid progress in generative models has resulted in impressive leaps in generation quality, blurring the lines between synthetic and real data. Web-scale datasets are now prone to the inevitable contamination by synthetic data, directly impacting the training of future generated models. Alre…
Proteins are essential for almost all biological processes and derive their diverse functions from complex $3 \rm D$ structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive bias of amino acid sequences and introduce FoldFlow++,…
The Strong Lottery Ticket Hypothesis (SLTH) stipulates the existence of a subnetwork within a sufficiently overparameterized (dense) neural network that---when initialized randomly and without any training---achieves the accuracy of a fully trained target network. Recent works by Da Cunha et. al 202…
Embodied agents operate in a structured world, often solving tasks with spatial, temporal, and permutation symmetries. Most algorithms for planning and model-based reinforcement learning (MBRL) do not take this rich geometric structure into account, leading to sample inefficiency and poor generaliza…
The past few years have seen impressive progress in the development of deep generative models capable of producing high-dimensional, complex, and photo-realistic data. However, current methods for evaluating such models remain incomplete: standard likelihood-based metrics do not always apply and rar…
Continuous Normalizing Flows (CNFs) are a class of generative models that transform a prior distribution to a model distribution by solving an ordinary differential equation (ODE). We propose to train CNFs on manifolds by minimizing probability path divergence (PPD), a novel family of divergences be…
Adversarial attacks expose important vulnerabilities of deep learning models, yet little attention has been paid to settings where data arrives as a stream. In this paper, we formalize the online adversarial attack problem, emphasizing two key elements found in real-world use-cases: attackers must o…
Diffusion models are recent state-of-the-art methods for image generation and likelihood estimation. In this work, we generalize continuous-time diffusion models to arbitrary Riemannian manifolds and derive a variational framework for likelihood estimation. Computationally, we propose new methods fo…
The existence of adversarial examples capable of fooling trained neural network classifiers calls for a much better understanding of possible attacks to guide the development of safeguards against them. This includes attack methods in the challenging {\em non-interactive blackbox} setting, where adv…
The choice of approximate posterior distributions plays a central role in stochastic variational inference (SVI). One effective solution is the use of normalizing flows \cut{defined on Euclidean spaces} to construct flexible posterior distributions. However, one key limitation of existing normalizin…