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Graph generation has emerged as a crucial task in machine learning, with significant challenges in generating graphs that accurately reflect specific properties. Existing methods often fall short in efficiently addressing this need as they…

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…

Graph generation is a fundamental task with broad applications, such as drug discovery. Recently, discrete flow matching-based graph generation, \aka, graph flow model (GFM), has emerged due to its superior performance and flexible…

Modern microelectronic devices are composed of interfaces between a large number of materials, many of which are in amorphous or polycrystalline phases. Modeling such non-crystalline materials using first-principles methods such as density…

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and…

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…

Graphs are ubiquitous in social networks and biochemistry, where Graph Neural Networks (GNN) are the state-of-the-art models for prediction. Graphs can be evolving and it is vital to formally model and understand how a trained GNN responds…

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…

Existing graph generative models often face a critical trade-off between sample quality and generation speed. We introduce Autoregressive Noisy Filtration Modeling (ANFM), a flexible autoregressive framework that addresses both challenges.…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

In this paper, we propose a proof-of-concept Graph Neural Network model that can successfully predict network flow-level traffic (NetFlow) by accurately modelling the graph structure and the connection features. We use sliding-windows to…

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…

Graph generative models are essential across diverse scientific domains by capturing complex distributions over relational data. Among them, graph diffusion models achieve superior performance but face inefficient sampling and limited…

Most previous work on neural text generation from graph-structured data relies on standard sequence-to-sequence methods. These approaches linearise the input graph to be fed to a recurrent neural network. In this paper, we propose an…

Molecular generation plays an important role in drug discovery and materials science, especially in data-scarce scenarios where traditional generative models often struggle to achieve satisfactory conditional generalization. To address this…

We show theoretically and empirically that the linear Transformer, when applied to graph data, can implement algorithms that solve canonical problems such as electric flow and eigenvector decomposition. The Transformer has access to…

Diffusion-based models decompose sampling into many small Gaussian denoising steps -- an assumption that breaks down when generation is compressed to a few coarse transitions. Existing few-step methods address this through distillation,…

How can we analyze enormous networks including the Web and social networks which have hundreds of billions of nodes and edges? Network analyses have been conducted by various graph mining methods including shortest path computation,…

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…

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…