Related papers: Scaling Graph Neural Networks to Large Proteins
Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to…
Training graph neural networks on large datasets has long been a challenge. Traditional approaches include efficiently representing the whole graph in-memory, designing parameter efficient and sampling-based models, and graph partitioning…
Neural forecasting of spatiotemporal time series drives both research and industrial innovation in several relevant application domains. Graph neural networks (GNNs) are often the core component of the forecasting architecture. However, in…
Graph neural network (GNN) is an efficient neural network model for graph data and is widely used in different fields, including wireless communications. Different from other neural network models, GNN can be implemented in a decentralized…
We present GERN, a novel scalable framework for training GNNs in node classification tasks, based on effective resistance, a standard tool in spectral graph theory. Our method progressively refines the GNN weights on a sequence of random…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic…
Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs…
Graph structured data, specifically text-attributed graphs (TAG), effectively represent relationships among varied entities. Such graphs are essential for semi-supervised node classification tasks. Graph Neural Networks (GNNs) have emerged…
Graph neural networks (GNNs) have received tremendous attention due to their power in learning effective representations for graphs. Most GNNs follow a message-passing scheme where the node representations are updated by aggregating and…
Despite the omnipresence of tensors and tensor operations in modern deep learning, the use of tensor mathematics to formally design and describe neural networks is still under-explored within the deep learning community. To this end, we…
We present a Graph Neural Network (GNN) that accurately simulates a multidisperse suspension of interacting spherical particles. Our machine learning framework is built upon the recent work of Sanchez-Gonzalez et al. ICML, PMLR, 119,…
Condense phase molecular systems organize in wide range of distinct molecular configurations, including amorphous melt and glass as well as crystals often exhibiting polymorphism, that originate from their intricate intra- and…
Molecular activity prediction is critical in drug design. Machine learning techniques such as kernel methods and random forests have been successful for this task. These models require fixed-size feature vectors as input while the molecules…
Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented…
The recent rapid growth in mobile data traffic entails a pressing demand for improving the throughput of the underlying wireless communication networks. Network node deployment has been considered as an effective approach for throughput…
Networks are a powerful tool to model complex systems, and the definition of many Graph Neural Networks (GNN), Deep Learning algorithms that can handle networks, has opened a new way to approach many real-world problems that would be hardly…
Graph Neural Networks (GNNs) have emerged as powerful tools for learning representations from structured data. Despite their growing popularity and success across various applications, GNNs encounter several challenges that limit their…
Graph neural networks (GNNs) build on the success of deep learning models by extending them for use in graph spaces. Transfer learning has proven extremely successful for traditional deep learning problems: resulting in faster training and…
Graph neural networks (GNNs) have attracted much attention due to their ability to leverage the intrinsic geometries of the underlying data. Although many different types of GNN models have been developed, with many benchmarking procedures…
Graph neural networks (GNNs) have become the standard learning architectures for graphs. GNNs have been applied to numerous domains ranging from quantum chemistry, recommender systems to knowledge graphs and natural language processing. A…