Related papers: Tiered Graph Autoencoders with PyTorch Geometric f…

Tiered graph autoencoders provide the architecture and mechanisms for learning tiered latent representations and latent spaces for molecular graphs that explicitly represent and utilize groups (e.g., functional groups). This enables the…

Molecular graphs generally contain subgraphs (known as groups) that are identifiable and significant in composition, functionality, geometry, etc. Flat latent representations (node embeddings or graph embeddings) fail to represent, and…

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…

We propose a combination of a variational autoencoder and a transformer based model which fully utilises graph convolutional and graph pooling layers to operate directly on graphs. The transformer model implements a novel node encoding…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

Molecular dynamics simulations produce data with complex nonlinear dynamics. If the timestep behavior of such a dynamic system can be represented by a linear operator, future states can be inferred directly without expensive simulations.…

Contemporary graph learning algorithms are not well-defined for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determine the molecular properties of macromolecules. In this…

Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…

We propose a novel dynamic network model to capture evolving latent communities within temporal networks. To achieve this, we decompose each observed dynamic edge between vertices using a Poisson-gamma edge partition model, assigning each…

We present Geo2DR (Geometric to Distributed Representations), a GPU ready Python library for unsupervised learning on graph-structured data using discrete substructure patterns and neural language models. It contains efficient…

Nowadays, the coupling of electronic structure and machine learning techniques serves as a powerful tool to predict chemical and physical properties of a broad range of systems. With the aim of improving the accuracy of predictions, a large…

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…

Graphs provide a powerful means for representing complex interactions between entities. Recently, deep learning approaches are emerging for representing and modeling graph-structured data, although the conventional deep learning methods…

Autoencoders are effective deep learning models that can function as generative models and learn latent representations for downstream tasks. The use of graph autoencoders - with both encoder and decoder implemented as message passing…

Deep learning on graphs has become a popular research topic with many applications. However, past work has concentrated on learning graph embedding tasks, which is in contrast with advances in generative models for images and text. Is it…

Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…

The geometry of three-dimensional (3D) graphs, consisting of nodes and edges, plays a crucial role in many important applications. An excellent example is molecular graphs, whose geometry influences important properties of a molecule…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…

Automatic labelling of anatomical structures, such as coronary arteries, is critical for diagnosis, yet existing (non-deep learning) methods are limited by a reliance on prior topological knowledge of the expected tree-like structures. As…