External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
Recently contextual text representation models like ELMo , BERT @cite_10 and OpenAI GPT @cite_8 @cite_28 have pushed the state-of-the-art results of various NLP tasks. Language modeling on a giant corpus learns powerful representations, which provides huge benefits to supervised tasks, especially where labeled data is scarce. These models use sequential or attention networks to generate word representations in context. In the biomedical domain, there is also BioBERT @cite_25 , a BERT model trained on PubMed abstracts and PubMed Central full-text articles, offering competitive results to state-of-the-art models on medical text processing tasks.
@cite_28 @cite_10 @cite_25 @cite_8
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We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models, BERT is designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers. As a result, the pre-trained BERT model can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of tasks, such as question answering and language inference, without substantial task-specific architecture modifications. BERT is conceptually simple and empirically powerful. It obtains new state-of-the-art results on eleven natural language processing tasks, including pushing the GLUE score to 80.5 (7.7 point absolute improvement), MultiNLI accuracy to 86.7 (4.6 absolute improvement), SQuAD v1.1 question answering Test F1 to 93.2 (1.5 point absolute improvement) and SQuAD v2.0 Test F1 to 83.1 (5.1 point absolute improvement). Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in machine learning, extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, as deep learning models require a large amount of training data, applying deep learning to biomedical text mining is often unsuccessful due to the lack of training data in biomedical fields. Recent researches on training contextualized language representation models on text corpora shed light on the possibility of leveraging a large number of unannotated biomedical text corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain specific language representation model pre-trained on large-scale biomedical corpora. Based on the BERT architecture, BioBERT effectively transfers the knowledge from a large amount of biomedical texts to biomedical text mining models with minimal task-specific architecture modifications. While BERT shows competitive performances with previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.51 absolute improvement), biomedical relation extraction (3.49 absolute improvement), and biomedical question answering (9.61 absolute improvement). We make the pre-trained weights of BioBERT freely available at this https URL, and the source code for fine-tuning BioBERT available at this https URL. Word embeddings learned on unlabeled data are a popular tool in semantics, but may not capture the desired semantics. We propose a new learning objective that incorporates both a neural language model objective (, 2013) and prior knowledge from semantic resources to learn improved lexical semantic embeddings. We demonstrate that our embeddings improve over those learned solely on raw text in three settings: language modeling, measuring semantic similarity, and predicting human judgements.