Novel Molecules Generation Using Graph Generative Adversarial Networks

De novo molecular generation remains a central challenge in drug discovery due to the vastness of chemical space and the difficulty of generating molecules that are simultaneously valid, diverse, and property-aware. While graph-based generative models have improved structural validity over sequence-based approaches, many existing methods suffer from mode collapse, limited controllability, and unstable reinforcement learning dynamics. In this work, we propose NovMolG-GAN, a graph-based generative adversarial framework that integrates graph attention mechanisms, a learnable reward network, mode-seeking regularization, and proximal policy optimization-based reinforcement learning to address these limitations. The proposed model enables stable training while explicitly encouraging molecular validity, novelty, diversity, and drug-likeness. Experiments on the ChEMBL-35 dataset demonstrate that NovMolG-GAN achieves high validity (99.6%), high novelty (99.4%) strong uniqueness (88.5%), and competitive quantitative drug-likeness scores under unconstrained generation. Furthermore, a conditional generation ablation incorporating synthetic accessibility as an additional reward illustrates the controllability of the framework and its ability to steer generation toward synthesis-feasible regions of chemical space. These results highlight the potential of NovMolG-GAN as a flexible and extensible foundation for goal-directed molecular design.

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Publication Details

Journal
Molecular Informatics
Published
2026-05-01
DOI
https://doi.org/10.1002/minf.70031
Primary Topic
Machine Learning in Materials Science
Type
article
Field-Weighted Citation Impact
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article

Novel Molecules Generation Using Graph Generative Adversarial Networks

Chandra Mohan Dasari, Santhosh Amilpur, Amodini A. P.
Molecular Informatics
Machine Learning in Materials Science
article

Novel Molecules Generation Using Graph Generative Adversarial Networks

Chandra Mohan Dasari, Santhosh Amilpur, Amodini A. P.
article en

Abstract

De novo molecular generation remains a central challenge in drug discovery due to the vastness of chemical space and the difficulty of generating molecules that are simultaneously valid, diverse, and property-aware. While graph-based generative models have improved structural validity over sequence-based approaches, many existing methods suffer from mode collapse, limited controllability, and unstable reinforcement learning dynamics. In this work, we propose NovMolG-GAN, a graph-based generative adversarial framework that integrates graph attention mechanisms, a learnable reward network, mode-seeking regularization, and proximal policy optimization-based reinforcement learning to address these limitations. The proposed model enables stable training while explicitly encouraging molecular validity, novelty, diversity, and drug-likeness. Experiments on the ChEMBL-35 dataset demonstrate that NovMolG-GAN achieves high validity (99.6%), high novelty (99.4%) strong uniqueness (88.5%), and competitive quantitative drug-likeness scores under unconstrained generation. Furthermore, a conditional generation ablation incorporating synthetic accessibility as an additional reward illustrates the controllability of the framework and its ability to steer generation toward synthesis-feasible regions of chemical space. These results highlight the potential of NovMolG-GAN as a flexible and extensible foundation for goal-directed molecular design.

Molecular InformaticsVol. 45(5)
Rayalaseema University (IN), Kurnool Medical College (IN), Indian Institute of Technology Indore (IN)
Openalex Percentile: Top 9%
Machine Learning in Materials Science
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