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Learning the underlying distribution of molecular graphs and generating high-fidelity samples is a fundamental research problem in drug discovery and material science. However, accurately modeling distribution and rapidly generating novel…

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…

Column Generation (CG) is an effective method for solving large-scale optimization problems. CG starts by solving a sub-problem with a subset of columns (i.e., variables) and gradually includes new columns that can improve the solution of…

Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring…

The design of novel molecules with desired properties is a key challenge in drug discovery and materials science. Traditional methods rely on trial-and-error, while recent deep learning approaches have accelerated molecular generation.…

Graph Neural Networks (GNNs) have become a prominent approach to machine learning with graphs and have been increasingly applied in a multitude of domains. Nevertheless, since most existing GNN models are based on flat message-passing…

Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…

To design a drug given a biological molecule by using deep learning methods, there are many successful models published recently. People commonly used generative models to design new molecules given certain protein. LiGAN was regarded as…

Flow fields are often partitioned into data blocks for massively parallel computation and analysis based on blockwise relationships. However, most of the previous techniques only consider the first-order dependencies among blocks, which is…

Molecular optimization, which transforms a given input molecule X into another Y with desirable properties, is essential in molecular drug discovery. The traditional translating approaches, generating the molecular graphs from scratch by…

Deep generative models that produce novel molecular structures have the potential to facilitate chemical discovery. Flow matching is a recently proposed generative modeling framework that has achieved impressive performance on a variety of…

In this paper, we propose Continuous Graph Flow, a generative continuous flow based method that aims to model complex distributions of graph-structured data. Once learned, the model can be applied to an arbitrary graph, defining a…

Developing new molecular compounds is crucial to address pressing challenges, from health to environmental sustainability. However, exploring the molecular space to discover new molecules is difficult due to the vastness of the space. Here…

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on…

Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically…

Molecular machine learning (ML) has proven important for tackling various molecular problems, such as predicting molecular properties based on molecular descriptors or fingerprints. Since relatively recently, graph neural network (GNN)…

Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional…

The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early-stage drug discovery is de novo…

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from…