Contextual word embedding models such as ELMo (, 2018) and BERT (, 2018) have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been minimally explored on specialty corpora, such as clinical text; moreover, in the clinical domain, no publicly-available pre-trained BERT models yet exist. In this work, we address this need by exploring and releasing BERT models for clinical text: one for generic clinical text and another for discharge summaries specifically. We demonstrate that using a domain-specific model yields performance improvements on three common clinical NLP tasks as compared to nonspecific embeddings. These domain-specific models are not as performant on two clinical de-identification tasks, and argue that this is a natural consequence of the differences between de-identified source text and synthetically non de-identified task text.
Traditional word-level vector representations, such as word2vec @cite_7 , GloVe @cite_20 , and fastText @cite_17 , express all possible meanings of a word as a single vector representation and cannot disambiguate the word senses based on the surrounding context. Over the last two years, ELMo @cite_19 and BERT @cite_12 present strong solutions that can provide contextualized word representations. By pre-training on a large text corpus as a language model, ELMo can create a context-sensitive embedding for each word in a given sentence, which will be fed into downstream tasks. Compared to ELMo, BERT is deeper and contains much more parameters, thus possessing greater representation power. More importantly, rather than simply providing word embeddings as features, BERT can be incorporated into a downstream task and gets fine-tuned as an integrated task-specific architecture.
@cite_7 @cite_19 @cite_12 @cite_20 @cite_17
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Vector-based word representations can help to improve a document classifier.The information of word2vec vectors and bags of words are very complementary.The combination of word2vec and BOW word representations obtains the best results.Word2vec is much more stable than bag of words models in cross-domain experiments. In this paper we show how a vector-based word representation obtained via word2vec can help to improve the results of a document classifier based on bags of words. Both models allow obtaining numeric representations from texts, but they do it very differently. The bag of words model can represent documents by means of widely dispersed vectors in which the indices are words or groups of words. word2vec generates word level representations building vectors that are much more compact, where indices implicitly contain information about the context of word occurrences. Bags of words are very effective for document classification and in our experiments no representation using only word2vec vectors is able to improve their results. However, this does not mean that the information provided by word2vec is not useful for the classification task. When this information is used in combination with the bags of words, the results are improved, showing its complementarity and its contribution to the task. We have also performed cross-domain experiments in which word2vec has shown much more stable behavior than bag of words models. Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and representations (e.g., ELMo, BERT) have further pushed the state-of-the-art in NLP, yet there are no common best practices for how to integrate these representations into clinical tasks. The purpose of this study, then, is to explore the space of possible options in utilizing these new models for clinical concept extraction, including comparing these to traditional word embedding methods (word2vec, GloVe, fastText). Both off-the-shelf, open-domain embeddings and pre-training clinical embeddings from MIMIC-III are evaluated. We explore a battery of embedding methods consisting of traditional word embeddings and contextual embeddings, and compare these on four concept extraction corpora: i2b2 2010, i2b2 2012, SemEval 2014, and SemEval 2015. We also analyze the impact of the pre-training time of a large language model like ELMo or BERT on the extraction performance. Finally, we present an intuitive way to understand the semantic information encoded by contextual embeddings. Contextual embeddings pre-trained on a large clinical corpus achieves new state-of-the-art performances across all concept extraction tasks. The best-performing model outperforms all state-of-the-art methods with respective F1-measures of 90.25, 93.18 (partial), 80.74, and 81.65. We demonstrate the potential of contextual embeddings through the state-of-the-art performance these methods achieve on clinical concept extraction. Additionally, we demonstrate contextual embeddings encode valuable semantic information not accounted for in traditional word representations. Learning distributed word representations has been a popular method for various natural language processing applications such as word analogy and similarity, document classification and sentiment analysis. However, most existing word embedding models only exploit a shallow slide window as the context to predict the target word. Because the semantic of each word is also influenced by its global context, as the distributional models usually induced the word representations from the global co-occurrence matrix, the window-based models are insufficient to capture semantic knowledge. In this paper, we propose a novel hybrid model called mixed word embedding (MWE) based on the well-known word2vec toolbox. Specifically, the proposed MWE model combines the two variants of word2vec, i.e., SKIP-GRAM and CBOW, in a seamless way via sharing a common encoding structure, which is able to capture the syntax information of words more accurately. Furthermore, it incorporates a global text vector into the CBOW variant so as to capture more semantic information. Our MWE preserves the same time complexity as the SKIP-GRAM. To evaluate our MWE model efficiently and adaptively, we study our model on linguistic and application perspectives with both English and Chinese dataset. For linguistics, we conduct empirical studies on word analogies and similarities. The learned latent representations on both document classification and sentiment analysis are considered for application point of view of this work. The experimental results show that our MWE model is very competitive in all tasks as compared with the state-of-the-art word embedding models such as CBOW, SKIP-GRAM, and GloVe. We present a novel word level vector representation based on symmetric patterns (SPs). For this aim we automatically acquire SPs (e.g., “X and Y”) from a large corpus of plain text, and generate vectors where each coordinate represents the cooccurrence in SPs of the represented word with another word of the vocabulary. Our representation has three advantages over existing alternatives: First, being based on symmetric word relationships, it is highly suitable for word similarity prediction. Particularly, on the SimLex999 word similarity dataset, our model achieves a Spearman’s score of 0.517, compared to 0.462 of the state-of-the-art word2vec model. Interestingly, our model performs exceptionally well on verbs, outperforming stateof-the-art baselines by 20.2‐41.5 . Second, pattern features can be adapted to the needs of a target NLP application. For example, we show that we can easily control whether the embeddings derived from SPs deem antonym pairs (e.g. (big,small)) as similar or dissimilar, an important distinction for tasks such as word classification and sentiment analysis. Finally, we show that a simple combination of the word similarity scores generated by our method and by word2vec results in a superior predictive power over that of each individual model, scoring as high as 0.563 in Spearman’s on SimLex999. This emphasizes the differences between the signals captured by each of the models.