GraphEBM: Molecular Graph Generation with Energy-Based Models

Meng Liu, Keqiang Yan, Bora Oztekin, Shuiwang Ji

Molecular graph generation is an emerging area of research with numerous applications. This problem remains challenging as molecular graphs are discrete, irregular, and permutation invariant to node order. Notably, most existing approaches fail to guarantee the intrinsic property of permutation invariance, resulting in unexpected bias in generative models. In this work, we propose GraphEBM to generate molecular graphs using energy-based models. In particular, we parameterize the energy function in a permutation invariant manner, thus making GraphEBM permutation invariant. We apply Langevin dynamics to train the energy function by approximately maximizing likelihood and generate samples with low energies. Furthermore, to generate molecules with a specific desirable property, we propose a simple yet effective strategy, which pushes down energies with flexible degrees according to the properties of corresponding molecules. Finally, we explore the use of GraphEBM for generating molecules with multiple objectives in a compositional manner. Comprehensive experimental results on random, goal-directed, and compositional generation tasks demonstrate the effectiveness of our proposed method.

Knowledge Graph

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