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

As a classical generative modeling approach, energy-based models have the natural advantage of flexibility in the form of the energy function. Recently, energy-based models have achieved great success in modeling high-dimensional data in…

In this work, we provide a theoretical understanding of the framelet-based graph neural networks through the perspective of energy gradient flow. By viewing the framelet-based models as discretized gradient flows of some energy, we show it…

Graph generation is a crucial task in many fields, including network science and bioinformatics, as it enables the creation of synthetic graphs that mimic the properties of real-world networks for various applications. Graph Generative…

The design of molecules and materials with tailored properties is challenging, as candidate molecules must satisfy multiple competing requirements that are often difficult to measure or compute. While molecular structures, produced through…

It is challenging for generative models to learn a distribution over graphs because of the lack of permutation invariance: nodes may be ordered arbitrarily across graphs, and standard graph alignment is combinatorial and notoriously…

This work addresses one-shot set and graph generation, and, more specifically, the parametrization of probabilistic decoders that map a vector-shaped prior to a distribution over sets or graphs. Sets and graphs are most commonly generated…

Graph is a prevalent discrete data structure, whose generation has wide applications such as drug discovery and circuit design. Diffusion generative models, as an emerging research focus, have been applied to graph generation tasks.…

In materials science, the challenge of rapid prototyping materials with desired properties often involves extensive experimentation to find suitable microstructures. Additionally, finding microstructures for given properties is typically an…

Generative models based on static scalar energy functions represent an emerging paradigm in which a single time independent potential drives sample generation through its gradient field, eliminating the need for time conditioning entirely.…

Recent advancements in graph representation learning have shifted attention towards dynamic graphs, which exhibit evolving topologies and features over time. The increased use of such graphs creates a paramount need for generative models…

We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and…

Traditional molecule generation methods often rely on sequence- or graph-based representations, which can limit their expressive power or require complex permutation-equivariant architectures. This paper introduces a novel paradigm for…

Generative deep learning has become pivotal in molecular design for drug discovery, materials science, and chemical engineering. A widely used paradigm is to pretrain neural networks on string representations of molecules and fine-tune them…

Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and…

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs…

We present a novel approach to tackle explainability of deep graph networks in the context of molecule property prediction tasks, named MEG (Molecular Explanation Generator). We generate informative counterfactual explanations for a…

Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE)…

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…

Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient…

Energy-based models (EBMs) are versatile density estimation models that directly parameterize an unnormalized log density. Although very flexible, EBMs lack a specified normalization constant of the model, making the likelihood of the model…