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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LATTE: Latent Type Modeling for Biomedical Entity Linking
Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate a large volume of clinical records and biomedical literature, to standardized concepts described in an ontology such as Unified Medical Language System (UMLS). We observe that with precise type information, entity disambiguation becomes a straightforward task. However, fine-grained type information is usually not available in biomedical domain. Thus, we propose LATTE, a LATent Type Entity Linking model, that improves entity linking by modeling the latent fine-grained type information about mentions and entities. Unlike previous methods that perform entity linking directly between the mentions and the entities, LATTE jointly does entity disambiguation, and latent fine-grained type learning, without direct supervision. We evaluate our model on two biomedical datasets: MedMentions, a large scale public dataset annotated with UMLS concepts, and a de-identified corpus of dictated doctor’s notes that has been annotated with ICD concepts. Extensive experimental evaluation shows our model achieves significant performance improvements over several state-of-the-art techniques.
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- NSF-PAR ID:
- 10143375
- Date Published:
- Journal Name:
- AAAI Conference on Artificial Intelligence (AAAI)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Wooldridge, Michael J ; Dy, Jennifer G ; Natarajan, Sriraam (Ed.)more » « less
Accurately typing entity mentions from text segments is a fundamental task for various natural language processing applications. Many previous approaches rely on massive human-annotated data to perform entity typing. Nevertheless, collecting such data in highly specialized science and engineering domains (e.g., software engineering and security) can be time-consuming and costly, without mentioning the domain gaps between training and inference data if the model needs to be applied to confidential datasets. In this paper, we study the task of seed-guided fine-grained entity typing in science and engineering domains, which takes the name and a few seed entities for each entity type as the only supervision and aims to classify new entity mentions into both seen and unseen types (i.e., those without seed entities). To solve this problem, we propose SEType which first enriches the weak supervision by finding more entities for each seen type from an unlabeled corpus using the contextualized representations of pre-trained language models. It then matches the enriched entities to unlabeled text to get pseudo-labeled samples and trains a textual entailment model that can make inferences for both seen and unseen types. Extensive experiments on two datasets covering four domains demonstrate the effectiveness of SEType in comparison with various baselines. Code and data are available at: https://github.com/yuzhimanhua/SEType.
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null (Ed.)Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using learned representations of entities. Previous approaches link each mention independently, ignoring the relationships within and across documents 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 knowledge base 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 entity linking by 3.0 points of accuracy, and our clustering-based inference model further improves entity linking by 2.3 points.more » « less
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We study the problem of few-shot Fine-grained Entity Typing (FET), where only a few annotated entity mentions with contexts are given for each entity type. Recently, prompt-based tuning has demonstrated superior performance to standard fine-tuning in few-shot scenarios by formulating the entity type classification task as a “fill-in-the-blank” problem. This allows effective utilization of the strong language modeling capability of Pre-trained Language Models (PLMs). Despite the success of current prompt-based tuning approaches, two major challenges remain: (1) the verbalizer in prompts is either manually designed or constructed from external knowledge bases, without considering the target corpus and label hierarchy information, and (2) current approaches mainly utilize the representation power of PLMs, but have not explored their generation power acquired through extensive general-domain pre-training. In this work, we propose a novel framework for fewshot FET consisting of two modules: (1) an entity type label interpretation module automatically learns to relate type labels to the vocabulary by jointly leveraging few-shot instances and the label hierarchy, and (2) a type-based contextualized instance generator produces new instances based on given instances to enlarge the training set for better generalization. On three benchmark datasets, our model outperforms existing methods by significant margins.more » « less
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Neural entity linking models are very powerful, but run the risk of overfitting to the domain they are trained in. For this problem, a "domain" is characterized not just by genre of text but even by factors as specific as the particular distribution of entities, as neural models tend to overfit by memorizing properties of frequent entities in a dataset. We tackle the problem of building robust entity linking models that generalize effectively and do not rely on labeled entity linking data with a specific entity distribution. Rather than predicting entities directly, our approach models fine-grained entity properties, which can help disambiguate between even closely related entities. We derive a large inventory of types (tens of thousands) from Wikipedia categories, and use hyperlinked mentions in Wikipedia to distantly label data and train an entity typing model. At test time, we classify a mention with this typing model and use soft type predictions to link the mention to the most similar candidate entity. We evaluate our entity linking system on the CoNLL-YAGO dataset and show that our approach outperforms prior domain-independent entity linking systems. We also test our approach in a harder setting derived from the WikilinksNED dataset where all the mention-entity pairs are unseen during test time. Results indicate that our approach generalizes better than a state-of-the-art neural model on the dataset.more » « less
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Accepted Manuscript1.0
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- The DOI is not currently available.
