Related papers: Multi-Scale Protein Structure Modelling with Geome…

3D meshes are fundamental data representations for capturing complex geometric shapes in computer vision and graphics applications. While Convolutional Neural Networks (CNNs) have excelled in structured data like images, extending them to…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Graph neural networks (GNN) represent an emerging line of deep learning models that operate on graph structures. It is becoming more and more popular due to its high accuracy achieved in many graph-related tasks. However, GNN is not as well…

The recurrent geometric network (RGN), the first end-to-end differentiable neural architecture for protein structure prediction, is a competitive alternative to existing models. However, the RGN's use of recurrent neural networks (RNNs) as…

Pattern recognition problems in high energy physics are notably different from traditional machine learning applications in computer vision. Reconstruction algorithms identify and measure the kinematic properties of particles produced in…

Graph neural networks (GNNs) based on message passing between neighboring nodes are known to be insufficient for capturing long-range interactions in graphs. In this project we study hierarchical message passing models that leverage a…

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making…

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model…

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes…

This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…

In this contribution, we demonstrate that Graph Neural Networks and Transformers can learn to reason about geometric constraints. We train them to predict spatial position of points in a discrete 2D grid from a set of constraints that…

Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…

Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using…

Recently, graph neural networks (GNNs) have proved to be suitable in tasks on unstructured data. Particularly in tasks as community detection, node classification, and link prediction. However, most GNN models still operate with static…

Graph Neural Networks operate through bottom-up message-passing, fundamentally differing from human visual perception, which intuitively captures global structures first. We investigate the underappreciated potential of vision models for…

In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically --…

We introduce ProteinWorkshop, a comprehensive benchmark suite for representation learning on protein structures with Geometric Graph Neural Networks. We consider large-scale pre-training and downstream tasks on both experimental and…

Graph neural networks (GNNs) learn representations from network data with naturally distributed architectures, rendering them well-suited candidates for decentralized learning. Oftentimes, this decentralized graph support changes with time…

Many recent efforts have been devoted to designing sophisticated deep learning structures, obtaining revolutionary results on benchmark datasets. The success of these deep learning methods mostly relies on an enormous volume of labeled…

Many scientific fields study data with an underlying structure that is a non-Euclidean space. Some examples include social networks in computational social sciences, sensor networks in communications, functional networks in brain imaging,…