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 source and reconstructed graphs and leverages a differentiable 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.

We propose Any2graph, a generic framework for end-to-end Supervised Graph Prediction (SGP) i.e. a deep learning model that predicts an entire graph for any kind of input. The framework is built on a novel Optimal Transport loss, the Partially-Masked Fused Gromov-Wasserstein, that exhibits all necessary properties (permutation invariance, differentiability and scalability) and is designed to handle any-sized graphs. Numerical experiments showcase the versatility of the approach that outperform existing competitors on a novel challenging synthetic dataset and a variety of real-world tasks such as map construction from satellite image (Sat2Graph) or molecule prediction from fingerprint (Fingerprint2Graph).