Related papers: GraphEBM: Molecular Graph Generation with Energy-B…

It is common practice for chemists to search chemical databases based on substructures of compounds for finding molecules with desired properties. The purpose of de novo molecular generation is to generate instead of search. Existing…

Learning distributions over graph-structured data is a challenging task with many applications in biology and chemistry. In this work we use an energy-based model (EBM) based on multi-channel graph neural networks (GNN) to learn permutation…

Learning generative models for graph-structured data is challenging because graphs are discrete, combinatorial, and the underlying data distribution is invariant to the ordering of nodes. However, most of the existing generative models for…

Optimizing chemical properties is a challenging task due to the vastness and complexity of chemical space. Here, we present a generative energy-based architecture for implicit chemical property optimization, designed to efficiently generate…

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…

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

Energy-based models for discrete domains, such as graphs, explicitly capture relative likelihoods, naturally enabling composable probabilistic inference tasks like conditional generation or enforcing constraints at test-time. However,…

Deep generative models have emerged as a popular machine learning-based approach for inverse design problems in the life sciences. However, these problems often require sampling new designs that satisfy multiple properties of interest in…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…

Generating novel molecules with optimal properties is a crucial step in many industries such as drug discovery. Recently, deep generative models have shown a promising way of performing de-novo molecular design. Although graph generative…

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab-initio calculations) and at speeds suitable for molecular dynam- ics simulation. Best…

Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from.…

Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…

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…

Graph generation poses a significant challenge as it involves predicting a complete graph with multiple nodes and edges based on simply a given label. This task also carries fundamental importance to numerous real-world applications,…

We propose GraphNVP, the first invertible, normalizing flow-based molecular graph generation model. We decompose the generation of a graph into two steps: generation of (i) an adjacency tensor and (ii) node attributes. This decomposition…

A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…

Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

In domains with interdependent data, such as graphs, quantifying the epistemic uncertainty of a Graph Neural Network (GNN) is challenging as uncertainty can arise at different structural scales. Existing techniques neglect this issue or…

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…