14 accepted papers
Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico gold standard, its high computational cost limits scalabilit…
Personalization, while extensively studied in conventional autonomous driving pipelines, has been largely overlooked in the context of end-to-end autonomous driving (E2EAD), despite its critical role in fostering user trust, safety perception, and real-world adoption. A primary bottleneck is the abs
Multistate mechanisms underlie many of the complex functions observed in natural proteins. The ability to rationally design multistate proteins would have transformative implications for many areas of biotechnology, yet lies beyond the capabilities of existing deep learning frameworks for protein de…
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…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly accurate single-state predictors such as AlphaFold and ESMFol…
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…
Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with…
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…
Predicting the binding structure of a small molecule ligand to a protein---a task known as molecular docking---is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer…
"Score-based models generate samples by mapping noise to data (and vice versa) via a high-dimensional diffusion process. We question whether it is necessary to run this entire process at high dimensionality and incur all the inconveniences thereof. Instead, we restrict the diffusion via projections…
Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a novel diffusion framework that operates on the space of tor…
Computational methods that operate on three-dimensional (3D) molecular structure have the potential to solve important problems in biology and chemistry. Deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of eit…
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the geometric and relational aspects of the problem domain. To address this gap, we introduce geometric vector…