9 accepted papers
Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBi…
In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously…
We propose a new self-explainable Graph Neural Network (GNN) model: GraphChef. GraphChef integrates decision trees into the GNN message passing framework. Given a dataset, GraphChef returns a set of rules (a recipe) that explains each class in the dataset unlike existing GNNs and explanation methods…
We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel architecture for aligned proteins, and utilizes strong diffusion p…
We present a novel graph neural network we call AgentNet, which is designed specifically for graph-level tasks. AgentNet is inspired by sublinear algorithms, featuring a computational complexity that is independent of the graph size. The architecture of AgentNet differs fundamentally from the archit…
Rigid origami has shown potential in large diversity of practical applications. However, current rigid origami crease pattern design mostly relies on known tessellations. This strongly limits the diversity and novelty of patterns that can be created. In this work, we build upon the recently develope…
We approach the graph generation problem from a spectral perspective by first generating the dominant parts of the graph Laplacian spectrum and then building a graph matching these eigenvalues and eigenvectors. Spectral conditioning allows for direct modeling of the global and local graph structure…
This paper studies Dropout Graph Neural Networks (DropGNNs), a new approach that aims to overcome the limitations of standard GNN frameworks. In DropGNNs, we execute multiple runs of a GNN on the input graph, with some of the nodes randomly and independently dropped in each of these runs. Then, we c…
Learning system dynamics directly from observations is a promising direction in machine learning due to its potential to significantly enhance our ability to understand physical systems. However, the dynamics of many real-world systems are challenging to learn due to the presence of nonlinear potent…