GNNs with ontology-derived semantic loss create hierarchy-aware box embeddings of a yeast knowledge graph that raise double-knockout growth prediction R² to 0.377 and generalize to triple knockouts while identifying a validated trait association.
and Billington, Richard and Caspi, Ron and Fulcher, Carol A
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Graph Neural Network based Hierarchy-Aware Embeddings of Knowledge Graphs: Applications to Yeast Phenotype Prediction
GNNs with ontology-derived semantic loss create hierarchy-aware box embeddings of a yeast knowledge graph that raise double-knockout growth prediction R² to 0.377 and generalize to triple knockouts while identifying a validated trait association.