LM-Based Word Embeddings Improve Biomedical Named Entity Recognition: A Detailed Analysis

Recent studies have shown that contextualized word embeddings outperform other types of embeddings on a variety of tasks. However, there is little research done to evaluate their effectiveness in the biomedical domain under multi-task settings. We derive the contextualized word embeddings from the Flair framework and apply them to the task of biomedical NER on 5 benchmark datasets, yielding major improvements over the baseline and achieving competitive results over the current best systems. We analyze the sources of these improvements, reporting model performances over different combinations of word embeddings, and fine-tuning and casing modes

Simultaneously Linking Entities and Extracting Relations from Biomedical Text Without Mention-level Supervision

Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks are nearly always viewed as separate components within a pipeline, each requiring a distinct model and training data. While relation extraction can often be trained with readily available weak or distant supervision, entity linkers typically require expensive mention-level supervision -- which is not available in many domains. Instead, we propose a model which is trained to simultaneously produce entity linking and relation decisions while requiring no mention-level annotations. This approach avoids cascading errors that arise from pipelined methods and more accurately predicts entity relationships from text. We show that our model outperforms a state-of-the art entity linking and relation extraction pipeline on two biomedical datasets and can drastically improve the overall recall of the system.Comment: Accepted in AAAI 202

A hybrid representation based simile component extraction

Simile, a special type of metaphor, can help people to express their ideas more clearly. Simile component extraction is to extract tenors and vehicles from sentences. This task has a realistic significance since it is useful for building cognitive knowledge base. With the development of deep neural networks, researchers begin to apply neural models to component extraction. Simile components should be in cross-domain. According to our observations, words in cross-domain always have different concepts. Thus, concept is important when identifying whether two words are simile components or not. However, existing models do not integrate concept into their models. It is difficult for these models to identify the concept of a word. What’s more, corpus about simile component extraction is limited. There are a number of rare words or unseen words, and the representations of these words are always not proper enough. Exiting models can hardly extract simile components accurately when there are low-frequency words in sentences. To solve these problems, we propose a hybrid representation-based component extraction (HRCE) model. Each word in HRCE is represented in three different levels: word level, concept level and character level. Concept representations (representations in concept level) can help HRCE to identify the words in cross-domain more accurately. Moreover, with the help of character representations (representations in character levels), HRCE can represent the meaning of a word more properly since words are consisted of characters and these characters can partly represent the meaning of words. We conduct experiments to compare the performance between HRCE and existing models. The experiment results show that HRCE significantly outperforms current models