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1. 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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2. 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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3. 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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4. Generative Entity-to-Entity Stance Detection with Knowledge Graph Augmentation

   https://doi.org/10.18653/v1/2022.emnlp-main.676  

   Zhang, Xinliang Frederick; Beauchamp, Nick; Wang, Lu (November 2022, Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing)

   Stance detection is typically framed as predicting the sentiment in a given text towards a target entity. However, this setup overlooks the importance of the source entity, i.e., who is expressing the opinion. In this paper, we emphasize the imperative need for studying interactions among entities when inferring stances. We first introduce a new task, entity-to-entity (E2E) stance detection, which primes models to identify entities in their canonical names and discern stances jointly. To support this study, we curate a new dataset with 10,641 annotations labeled at the sentence level from news articles of different ideological leanings. We present a novel generative framework to allow the generation of canonical names for entities as well as stances among them. We further enhance the model with a graph encoder to summarize entity activities and external knowledge surrounding the entities. Experiments show that our model outperforms strong comparisons by large margins. Further analyses demonstrate the usefulness of E2E stance detection for understanding media quotation and stance landscape as well as inferring entity ideology. 

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5. Biomedical Interpretable Entity Representations

   Garcia-Olano, Diego; Onoe, Yasumasa; Baldini, Ioana; Ghosh, Joydeep; Wallace, Byron C.; Varshney, Kush (April 2021, Proceedings of the Association for Computational Linguistics (ACL))

   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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