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1. Interpretable Entity Representations through Large-Scale Typing

   https://doi.org/10.18653/v1/2020.findings-emnlp.54  

   Onoe, Yasumasa ; Durrett, Greg ( January 2020 , Findings of the Association for Computational Linguistics: EMNLP 2020)

   null (Ed.)

   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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2. Plant Science Knowledge Graph Corpus: a gold standard entity and relation corpus for the molecular plant sciences

   https://doi.org/10.1093/insilicoplants/diad021  

   Lotreck, Serena ; Segura Abá, Kenia ; Lehti-Shiu, Melissa D. ; Seeger, Abigail ; Brown, Brianna N. I. ; Ranaweera, Thilanka ; Schumacher, Ally ; Ghassemi, Mohammad ; Shiu, Shin-Han ; Marshall-Colon, ed., Amy ( November 2023 , in silico Plants)

   Natural language processing (NLP) techniques can enhance our ability to interpret plant science literature. Many state-of-the-art algorithms for NLP tasks require high-quality labelled data in the target domain, in which entities like genes and proteins, as well as the relationships between entities, are labelled according to a set of annotation guidelines. While there exist such datasets for other domains, these resources need development in the plant sciences. Here, we present the Plant ScIenCe KnowLedgE Graph (PICKLE) corpus, a collection of 250 plant science abstracts annotated with entities and relations, along with its annotation guidelines. The annotation guidelines were refined by iterative rounds of overlapping annotations, in which inter-annotator agreement was leveraged to improve the guidelines. To demonstrate PICKLE’s utility, we evaluated the performance of pretrained models from other domains and trained a new, PICKLE-based model for entity and relation extraction (RE). The PICKLE-trained models exhibit the second-highest in-domain entity performance of all models evaluated, as well as a RE performance that is on par with other models. Additionally, we found that computer science-domain models outperformed models trained on a biomedical corpus (GENIA) in entity extraction, which was unexpected given the intuition that biomedical literature is more similar to PICKLE than computer science. Upon further exploration, we established that the inclusion of new types on which the models were not trained substantially impacts performance. The PICKLE corpus is, therefore, an important contribution to training resources for entity and RE in the plant sciences.

    

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3. LATTE: Latent Type Modeling for Biomedical Entity Linking

   Zhu, Ming ; Celikkaya, Busra ; Bhatia, Parminder ; Reddy, Chandan K. ( January 2020 , AAAI Conference on Artificial Intelligence (AAAI))

   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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4. Fine-Grained Entity Typing for Domain Independent Entity Linking

   Onoe, Yasumasa ; Durrett, Greg ( January 2020 , Proceedings of the AAAI Conference on Artificial Intelligence)

   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. 

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5. Fine-Grained Entity Typing for Domain Independent Entity Linking

   Onoe, Yasumasa ; Durrett, Greg ( January 2020 , Proceedings of the AAAI Conference on Artificial Intelligence)

   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 (Hoffart et al. 2011) 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 (Eshel et al. 2017) 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. 

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