Antonio H. O. Fonseca

Syed Asad Rizvi, Nazreen Pallikkavaliyaveetil, David Zhang et al.

Foundation models have achieved remarkable success across many domains, relying on pretraining over vast amounts of data. Graph-structured data often lacks the same scale as unstructured data, making the development of graph foundation models challenging. In this work, we propose Foundation-Informed Message Passing (FIMP), a Graph Neural Network (GNN) message-passing framework that leverages pretrained non-textual foundation models in graph-based tasks. We show that the self-attention layers of foundation models can effectively be repurposed on graphs to perform cross-node attention-based message-passing. Our model is evaluated on a real-world image network dataset and two biological applications (single-cell RNA sequencing data and fMRI brain activity recordings) in both finetuned and zero-shot settings. FIMP outperforms strong baselines, demonstrating that it can effectively leverage state-of-the-art foundation models in graph tasks.

Antonio H. O. Fonseca, David van Dijk

Word translation is an integral part of language translation. In machine translation, each language is considered a domain with its own word embedding. The alignment between word embeddings allows linking semantically equivalent words in multilingual contexts. Moreover, it offers a way to infer cross-lingual meaning for words without a direct translation. Current methods for word embedding alignment are either supervised, i.e. they require known word pairs, or learn a cross-domain transformation on fixed embeddings in an unsupervised way. Here we propose an end-to-end approach for word embedding alignment that does not require known word pairs. Our method, termed Word Alignment through MMD (WAM), learns embeddings that are aligned during sentence translation training using a localized Maximum Mean Discrepancy (MMD) constraint between the embeddings. We show that our method not only out-performs unsupervised methods, but also supervised methods that train on known word translations.