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Bias mitigation in graph diffusion models

About

Most existing graph diffusion models have significant bias problems. We observe that the forward diffusion's maximum perturbation distribution in most models deviates from the standard Gaussian distribution, while reverse sampling consistently starts from a standard Gaussian distribution, which results in a reverse-starting bias. Together with the inherent exposure bias of diffusion models, this results in degraded generation quality. This paper proposes a comprehensive approach to mitigate both biases. To mitigate reverse-starting bias, we employ a newly designed Langevin sampling algorithm to align with the forward maximum perturbation distribution, establishing a new reverse-starting point. To address the exposure bias, we introduce a score correction mechanism based on a newly defined score difference. Our approach, which requires no network modifications, is validated across multiple models, datasets, and tasks, achieving state-of-the-art results.Code is at https://github.com/kunzhan/spp

Meng Yu, Kun Zhan• 2026

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TaskDatasetResultRank
Graph generationENZYMES
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Molecular Generationparp1
Top-Hit 5% Docking Score (kcal/mol)-10.961
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Molecular Generation5ht1b
Docking Score (Top-Hit 5%, kcal/mol)-11.231
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Molecular Generationjak2
Top-Hit 5% Docking Score (kcal/mol)-10.163
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Molecular Generationfa7
Top-Hit 5% Docking Score (kcal/mol)-8.182
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Molecular Generationbraf
Top-Hit 5% Docking Score (kcal/mol)-11.143
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Graph generationCommunity small
MMD (Degree)0.011
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Molecular GenerationZINC 250K
FCD12.7
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Graph generationGRID
Degree Similarity1.996
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