Related papers: Tiered Graph Autoencoders with PyTorch Geometric f…

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of…

The standard approach to representation learning on attributed graphs -- i.e., simultaneously reconstructing node attributes and graph structure -- is geometrically flawed, as it merges two potentially incompatible metric spaces. This…

While message passing graph neural networks result in informative node embeddings, they may suffer from describing the topological properties of graphs. To this end, node filtration has been widely used as an attempt to obtain the…

Graph embedding provides an efficient solution for graph analysis by converting the graph into a low-dimensional space which preserves the structure information. In contrast to the graph structure data, the i.i.d. node embedding can be…

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Although substantial efforts have been made using graph neural networks (GNNs) for AI-driven drug discovery (AIDD), effective molecular representation learning remains an open challenge, especially in the case of insufficient labeled…

Molecular Representation Learning is essential to solving many drug discovery and computational chemistry problems. It is a challenging problem due to the complex structure of molecules and the vast chemical space. Graph representations of…

We present a hierarchical neural message passing architecture for learning on molecular graphs. Our model takes in two complementary graph representations: the raw molecular graph representation and its associated junction tree, where nodes…

Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…

The goal of this work is to address two limitations in autoencoder-based models: latent space interpretability and compatibility with unstructured meshes. This is accomplished here with the development of a novel graph neural network (GNN)…

In this study, we present a graph neural network-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced…

We present PyTorch Geometric Temporal a deep learning framework combining state-of-the-art machine learning algorithms for neural spatiotemporal signal processing. The main goal of the library is to make temporal geometric deep learning…

A graph is a powerful concept for representation of relations between pairs of entities. Data with underlying graph structure can be found across many disciplines and there is a natural desire for understanding such data better. Deep…

Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…

Recently, there has been great success in applying deep neural networks on graph structured data. Most work, however, focuses on either node- or graph-level supervised learning, such as node, link or graph classification or node-level…

A wide variety of real-world data, such as sea measurements, e.g., temperatures collected by distributed sensors and multiple unmanned aerial vehicles (UAV) trajectories, can be naturally represented as graphs, often exhibiting…

The graph-based variational autoencoder represents an architecture that can handle the uncertainty of different geological scenarios, such as depositional or structural, through the concept of a lowerdimensional latent space. The main…

Graph representation learning is a fast-growing field where one of the main objectives is to generate meaningful representations of graphs in lower-dimensional spaces. The learned embeddings have been successfully applied to perform various…

Streets networks provide an invaluable source of information about the different temporal and spatial patterns emerging in our cities. These streets are often represented as graphs where intersections are modelled as nodes and streets as…

Representation learning for graphs enables the application of standard machine learning algorithms and data analysis tools to graph data. Replacing discrete unordered objects such as graph nodes by real-valued vectors is at the heart of…