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GraViti introduces a transformer-based graph-level variational autoencoder that achieves state-of-the-art reconstruction on molecular datasets by relaxing permutation invariance requirements in the loss function. This architectural shift eliminates the computationally expensive cubic-cost matching step, reducing complexity to quadratic while preserving generalization through an invariant encoder. The resulting latent space enables efficient property-guided search and controlled molecular editing, offering a practical advance for generative chemistry tasks.
GraViti: Graph-Level Variational Autoencoders with Relaxed Permutation Invariance
arXiv:2605.16668v2 Announce Type: replace-cross Abstract: We introduce GraViti, a transformer-based graph-level variational autoencoder that encodes entire graphs into single, fixed-dimensional latent vectors rather than per-node embeddings, yielding a graph-level latent space that supports smooth interpolation, property-guided search, and other downstream tasks beyond the reach of node-level approaches. GraViti achieves state-of-the-art reconstruction accuracy on large molecular graph datasets while offering competitive single-step generative performance. Our central finding concerns where permutation invariance is needed in such a model, and where it is not. The encoder remains permutation-invariant throughout, ensuring the model generalizes to graphs regardless of input order. The reconstruction loss, however, does not need to be: when training data is provided in a consistent node order, comparing predictions to targets directly in that order, without a graph-matching step, is sufficient. Relaxing invariance in the loss alone lets GraViti avoid the cubic-cost matching step required by prior graph-level autoencoders, reducing complexity to quadratic while improving reconstruction fidelity. We show the resulting latent space is chemically meaningful, supporting controlled molecular editing and property optimization, recovering established chemical trends, and enabling direct regression of graph-level properties from latent embeddings.
Abstract:We introduce GraViti, a transformer-based graph-level variational autoencoder that encodes entire graphs into single, fixed-dimensional latent vectors rather than per-node embeddings, yielding a graph-level latent space that supports smooth interpolation, property-guided search, and other downstream tasks beyond the reach of node-level approaches. GraViti achieves state-of-the-art reconstruction accuracy on large molecular graph datasets while offering competitive single-step generative performance. Our central finding concerns where permutation invariance is needed in such a model, and where it is not. The encoder remains permutation-invariant throughout, ensuring the model generalizes to graphs regardless of input order. The reconstruction loss, however, does not need to be: when training data is provided in a consistent node order, comparing predictions to targets directly in that order, without a graph-matching step, is sufficient. Relaxing invariance in the loss alone lets GraViti avoid the cubic-cost matching step required by prior graph-level autoencoders, reducing complexity to quadratic while improving reconstruction fidelity. We show the resulting latent space is chemically meaningful, supporting controlled molecular editing and property optimization, recovering established chemical trends, and enabling direct regression of graph-level properties from latent embeddings.
Machine Learning (cs.LG); Artificial Intelligence (cs.AI)
arXiv:2605.16668 [cs.LG]
(or arXiv:2605.16668v2 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2605.16668 Focus to learn more arXiv-issued DOI via DataCite
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