Related papers: JTreeformer: Graph-Transformer via Latent-Diffusio…

We propose TD-GEN, a graph generation framework based on tree decomposition, and introduce a reduced upper bound on the maximum number of decisions needed for graph generation. The framework includes a permutation invariant tree generation…

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as…

Compared to sequential learning models, graph-based neural networks exhibit some excellent properties, such as ability capturing global information. In this paper, we investigate graph-based neural networks for text classification problem.…

Transformer-based models trained on large and general purpose datasets consisting of molecular strings have recently emerged as a powerful tool for successfully modeling various structure-property relations. Inspired by this success, we…

Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing. Recent studies have proposed…

The dynamic characterization of functional brain networks is of great significance for elucidating the mechanisms of human brain function. Although graph neural networks have achieved remarkable progress in functional network analysis,…

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility…

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation $z$, which is then decoded back to a molecule. The encoding process is easy, but the decoding…

Discovering new materials better suited to specific purposes is an important issue in improving the quality of human life. Here, a neural network that creates molecules that meet some desired conditions based on a deep understanding of…

Generating molecular graphs with desired chemical properties driven by deep graph generative models provides a very promising way to accelerate drug discovery process. Such graph generative models usually consist of two steps: learning…

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,…

Diffusion models have become a new SOTA generative modeling method in various fields, for which there are multiple survey works that provide an overall survey. With the number of articles on diffusion models increasing exponentially in the…

Learning distributions of graphs can be used for automatic drug discovery, molecular design, complex network analysis, and much more. We present an improved framework for learning generative models of graphs based on the idea of deep state…

The extraction of a scene graph with objects as nodes and mutual relationships as edges is the basis for a deep understanding of image content. Despite recent advances, such as message passing and joint classification, the detection of…

Recently, transformer architectures for graphs emerged as an alternative to established techniques for machine learning with graphs, such as (message-passing) graph neural networks. So far, they have shown promising empirical results, e.g.,…

Identifying molecules that exhibit some pre-specified properties is a difficult problem to solve. In the last few years, deep generative models have been used for molecule generation. Deep Graph Variational Autoencoders are among the most…

Self-supervised neural language models have recently found wide applications in generative design of organic molecules and protein sequences as well as representation learning for downstream structure classification and functional…

Generating as diverse molecules as possible with desired properties is crucial for drug discovery research, which invokes many approaches based on deep generative models today. Despite recent advancements in these models, particularly in…

Topological Deep Learning seeks to enhance the predictive performance of neural network models by harnessing topological structures in input data. Topological neural networks operate on spaces such as cell complexes and hypergraphs, that…

Graph Neural Networks (GNNs) have been widely applied to various fields due to their powerful representations of graph-structured data. Despite the success of GNNs, most existing GNNs are designed to learn node representations on the fixed…