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Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

Unconditional generation -- the problem of modeling data distribution without relying on human-annotated labels -- is a long-standing and fundamental challenge in generative models, creating a potential of learning from large-scale…

Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely…

Generating novel molecules is challenging, with most representations leading to generative models producing many invalid molecules. Spanning Tree-based Graph Generation (STGG) is a promising approach to ensure the generation of valid…

Generating molecules with desired chemical properties presents a critical challenge in fields such as chemical synthesis and drug discovery. Recent advancements in artificial intelligence (AI) and deep learning have significantly…

Deep generative models have shown significant promise in generating valid 3D molecular structures, with the GEOM-Drugs dataset serving as a key benchmark. However, current evaluation protocols suffer from critical flaws, including incorrect…

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…

Predicting molecular conformations from molecular graphs is a fundamental problem in cheminformatics and drug discovery. Recently, significant progress has been achieved with machine learning approaches, especially with deep generative…

State-of-the-art models for 3D molecular generation are based on significant inductive biases, SE(3), permutation equivariance to respect symmetry and graph message-passing networks to capture local chemistry, yet the generated molecules…

Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage,…

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here,…

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph…

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…

Shape-based virtual screening is widely employed in ligand-based drug design to search chemical libraries for molecules with similar 3D shapes yet novel 2D chemical structures compared to known ligands. 3D deep generative models have the…

De novo 3D molecule generation is a pivotal task in drug discovery. However, many recent geometric generative models struggle to produce high-quality 3D structures, even if they maintain 2D validity and topological stability. To tackle this…

Recent advances in fast sampling methods for diffusion models have demonstrated significant potential to accelerate generation on image modalities. We apply these methods to 3-dimensional molecular conformations by building on the recently…

Molecule generation is advancing rapidly in chemical discovery and drug design. Flow matching methods have recently set the state of the art (SOTA) in unconditional molecule generation, surpassing score-based diffusion models. However,…

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…

With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…