Conformal Graph Prediction with Z-Gromov Wasserstein Distances

Supervised graph prediction addresses regression problems where the outputs are structured graphs. Although several approaches exist for graph-valued prediction, principled uncertainty quantification remains limited. We propose a conformal prediction framework for graph-valued outputs, providing distribution-free coverage guarantees in structured output spaces. Our method defines nonconformity via the Z-Gromov-Wasserstein distance, instantiated in practice through Fused Gromov-Wasserstein (FGW), enabling permutation invariant comparison between predicted and candidate graphs. To obtain adaptive prediction sets, we introduce Score Conformalized Quantile Regression (SCQR), an extension of Conformalized Quantile Regression (CQR) to handle complex output spaces such as graph-valued outputs. We evaluate the proposed approach on a synthetic task and a real problem of molecule identification.

The quest for the GRAph Level autoEncoder (GRALE)

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.