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.

End-to-end Supervised Prediction of Arbitrary-size Graphs with Partially-Masked Fused Gromov-Wasserstein Matching

We present a novel end-to-end deep learning-based approach for Supervised Graph Prediction (SGP). We introduce an original Optimal Transport (OT)-based loss, the Partially-Masked Fused Gromov-Wasserstein loss (PM-FGW), that allows to directly leverage graph representations such as adjacency and feature matrices. PM-FGW exhibits all the desirable properties for SGP: it is node permutation invariant, sub-differentiable and handles graphs of different sizes by comparing their padded representations as well as their masking vectors. Moreover, we present a flexible transformer-based architecture that easily adapts to different types of input data. In the experimental section, three different tasks, a novel and challenging synthetic dataset (image2graph) and two real-world tasks, image2map and fingerprint2molecule - showcase the efficiency and versatility of the approach compared to competitors.