Biomedical entity linking (BioEL) is the process of connecting entities referenced in documents to entries in biomedical databases such as the Unified Medical Language System (UMLS) or Medical Subject Headings (MeSH). The study objective was to comprehensively evaluate nine recent state-of-the-art biomedical entity linking models under a unified framework. We compare these models along axes of (1) accuracy, (2) speed, (3) ease of use, (4) generalization, and (5) adaptability to new ontologies and datasets. We additionally quantify the impact of various preprocessing choices such as abbreviation detection. Systematic evaluation reveals several notable gaps in current methods. In particular, current methods struggle to correctly link genes and proteins and often have difficulty effectively incorporating context into linking decisions. To expedite future development and baseline testing, we release our unified evaluation framework and all included models on GitHub at https://github.com/davidkartchner/biomedical-entity-linking

Knowledge Graph Completion (KGC) predicts missing facts in an incomplete Knowledge Graph (KG). Multilingual KGs associate entities and relations with surface forms written in different languages. An entity or relation may be associated with distinct IDs in different KGs, necessitating entity alignment (EA) and relation alignment (RA). Many effective algorithms have been proposed for completion and alignment as separate tasks. Here we show that these tasks are synergistic and best solved together. Our multitask approach starts with a state-of-the-art KG embedding scheme, but adds a novel relation representation based on sets of embeddings of (subject, object) entity pairs. This representation leads to a new relation alignment loss term based on a maximal bipartite matching between two sets of embedding vectors. This loss is combined with traditional KGC loss and optionally, losses based on text embeddings of entity (and relation) names. In experiments over KGs in seven languages, we find that our system achieves large improvements in KGC compared to a strong completion model that combines known facts in all languages. It also outperforms strong EA and RA baselines, underscoring the value of joint alignment and completion.