9 accepted papers
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…
Ensuring synthesizability in generative small molecule design remains a major challenge. While recent developments in synthesizable molecule generation have demonstrated promising results, these efforts have been largely confined to 2D molecular graph representations, limiting the ability to perform…
Generative Flow Networks (GFlowNets) is a new family of probabilistic samplers for generating objects under an unnormalized reward distribution. It has emerged as a promising framework for learning stochastic policies that generate high-quality and diverse discrete objects proportional to their rewa…
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…
We tackle the problem of sampling from intractable high-dimensional density functions, a fundamental task that often appears in machine learning and statistics. We extend recent sampling-based approaches that leverage controlled stochastic processes to model approximate samples from these target de…
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…
Generative models hold great promise for small molecule discovery, significantly increasing the size of search space compared to traditional in silico screening libraries. However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate com…
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---…
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++,…