12 accepted papers
Diffusion models have emerged as a successful approach for molecular docking, but they often cannot model protein flexibility or generate nonphysical poses. We argue that both these challenges can be tackled by framing the problem as a transport between distributions. Still, existing paradigms lack…
Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark ba…
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…
Diffusion models (DMs) have revolutionized generative learning. They utilize a diffusion process to encode data into a simple Gaussian distribution. However, encoding a complex, potentially multimodal data distribution into a single *continuous* Gaussian distribution arguably represents an unnecessa…
In light of the widespread success of generative models, a significant amount of research has gone into speeding up their sampling time. However, generative models are often sampled multiple times to obtain a diverse set incurring a cost that is orthogonal to sampling time. We tackle the question of…
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…
Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Although the 3D molecular graph structure is necessary for models to achieve strong performance on many tasks, it is infeasible to obtain 3D structures at the scale required by…
"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…
The lack of anisotropic kernels in graph neural networks (GNNs) strongly limits their expressiveness, contributing to well-known issues such as over-smoothing. To overcome this limitation, we propose the first globally consistent anisotropic kernels for GNNs, allowing for graph convolutions that are…
The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete com…
Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features---whic…