Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing
Much of biomedical and healthcare data is encoded in discrete, symbolic form such as text and medical codes. There is a wealth of expert-curated biomedical domain knowledge stored in knowledge bases and ontologies, but the lack of reliable methods for learning knowledge representation has limited their usefulness in machine learning applications. While text-based representation learning has significantly improved in recent years through advances in natural language processing, attempts to learn biomedical concept embeddings so far have been lacking. A recent family of models called knowledge graph embeddings have shown promising results on general domain knowledge graphs, and we explore their capabilities in the biomedical domain. We train several state-of-the-art knowledge graph embedding models on the SNOMED-CT knowledge graph, provide a benchmark with comparison to existing methods and in-depth discussion on best practices, and make a case for the importance of leveraging the multi-relational nature of knowledge graphs for learning biomedical knowledge representation. The embeddings, code, and materials will be made available to the community.
TuckER: Tensor Factorization for Knowledge Graph Completion
Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP)
Knowledge graphs are structured representations of real world facts. However, they typically contain only a small subset of all possible facts. Link prediction is a task of inferring missing facts based on existing ones. We propose TuckER, a relatively straightforward but powerful linear model based on Tucker decomposition of the binary tensor representation of knowledge graph triples. TuckER outperforms previous state-of-the-art models across standard link prediction datasets, acting as a strong baseline for more elaborate models. We show that TuckER is a fully expressive model, derive sufficient bounds on its embedding dimensionalities and demonstrate that several previously introduced linear models can be viewed as special cases of TuckER.