Log In Sign Up

Clustering-based Inference for Zero-Shot Biomedical Entity Linking

by   Rico Angell, et al.

Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates a zero-shot entity linking model which is able to link mentions of unseen entities using learned representations of entities. Existing zero-shot entity linking models however link each mention independently, ignoring the inter/intra-document relationships between the entity mentions. These relations can be very useful for linking mentions in biomedical text where linking decisions are often difficult due mentions having a generic or a highly specialized form. In this paper, we introduce a model in which linking decisions can be made not merely by linking to a KB entity but also by grouping multiple mentions together via clustering and jointly making linking predictions. In experiments on the largest publicly available biomedical dataset, we improve the best independent prediction for zero-shot entity linking by 2.5 points of accuracy, and our joint inference model further improves entity linking by 1.8 points.


page 1

page 2

page 3

page 4


Entity Linking and Discovery via Arborescence-based Supervised Clustering

Previous work has shown promising results in performing entity linking b...

Zero-shot Entity Linking with Dense Entity Retrieval

We consider the zero-shot entity-linking challenge where each entity is ...

ReFinED: An Efficient Zero-shot-capable Approach to End-to-End Entity Linking

We introduce ReFinED, an efficient end-to-end entity linking model which...

Knowledge-Rich Self-Supervised Entity Linking

Entity linking faces significant challenges, such as prolific variations...

Linking Entities to Unseen Knowledge Bases with Arbitrary Schemas

In entity linking, mentions of named entities in raw text are disambigua...

Strong Heuristics for Named Entity Linking

Named entity linking (NEL) in news is a challenging endeavour due to the...

Find the Funding: Entity Linking with Incomplete Funding Knowledge Bases

Automatic extraction of funding information from academic articles adds ...