Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important domains such as biomedicine.There has been recent work on general interpretable representation learning (Onoe and Durrett, 2020), but these domain-agnostic representations do not readily transfer to the important domain of biomedicine. In this paper, we create a new entity type system and train-ing set from a large corpus of biomedical texts by mapping entities to concepts in a medical ontology, and from these to Wikipedia pages whose categories are our types. From this map-ping we deriveBiomedical Interpretable Entity Representations(BIERs), in which dimensions correspond to fine-grained entity types, and values are predicted probabilities that a given entity is of the corresponding type. We propose a novel method that exploits BIER’s final sparse and intermediate dense representations to facilitate model and entity type debugging. We show that BIERs achieve strong performance in biomedical tasks including named entity disambiguation and entity linking, and we provide error analysis to highlight the utility of their interpretability, particularly in low-supervision settings. Finally, we provide our induced 68K biomedical type system, the corresponding 37 million triples of derived data used to train BIER models and our best per-forming model.
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Interpretable Entity Representations through Large-Scale Typing
In standard methodology for natural language processing, entities in text are typically embedded in dense vector spaces with pre-trained models. The embeddings produced this way are effective when fed into downstream models, but they require end-task fine-tuning and are fundamentally difficult to interpret. In this paper, we present an approach to creating entity representations that are human readable and achieve high performance on entity-related tasks out of the box. Our representations are vectors whose values correspond to posterior probabilities over fine-grained entity types, indicating the confidence of a typing model’s decision that the entity belongs to the corresponding type. We obtain these representations using a fine-grained entity typing model, trained either on supervised ultra-fine entity typing data (Choi et al., 2018) or distantly-supervised examples from Wikipedia. On entity probing tasks involving recognizing entity identity, our embeddings used in parameter-free downstream models achieve competitive performance with ELMo- and BERT-based embeddings in trained models. We also show that it is possible to reduce the size of our type set in a learning-based way for particular domains. Finally, we show that these embeddings can be post-hoc modified through a small number of rules to incorporate domain knowledge and improve performance.
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- NSF-PAR ID:
- 10233085
- Date Published:
- Journal Name:
- Findings of the Association for Computational Linguistics: EMNLP 2020
- Page Range / eLocation ID:
- 612 to 624
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.18653/v1/2020.findings-emnlp.54
