7 accepted papers
Generalization beyond training data remains a central challenge in machine learning for biology. A common way to enhance generalization is self-supervised pre-training on large datasets. However, aiming to perform well on all possible proteins can limit a model’s capacity to excel on any specific on…
We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from…
Discrete diffusion has achieved state-of-the-art performance, outperforming or approaching autoregressive models on standard benchmarks. In this work, we introduce *Discrete Diffusion with Planned Denoising* (DDPD), a novel framework that separates the generation process into two models: a planner a…
Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that naive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To…
Predicting low-energy molecular conformations given a molecular graph is an important but challenging task in computational drug discovery. Existing state- of-the-art approaches either resort to large scale transformer-based models that diffuse over conformer fields, or use computationally expensiv…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible mu…
A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy storage. Towards this goal, we first develop HarmonicFlow, an impr…