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.
@cite_1 , released in late February 2019, train a clinical note corpus BERT language model and uses complex task-specific models to yield improvements over both traditional embeddings and ELMo embeddings on the i2b2 2010 and 2012 tasks @cite_9 @cite_14 and the SemEval 2014 task 7 @cite_11 and 2015 task 14 @cite_18 tasks, establishing new state-of-the-art results on all four corpora. However, this work neither releases their embeddings for the larger community nor examines the performance opportunities offered by fine-tuning BioBERT with clinical text or by training note-type specific embedding models, as we do.
@cite_18 @cite_14 @cite_9 @cite_1 @cite_11
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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. Automatic extraction of clinical concepts is an essential step for turning the unstructured data within a clinical note into structured and actionable information. In this work, we propose a clinical concept extraction model for automatic annotation of clinical problems, treatments, and tests in clinical notes utilizing domain-specific contextual word embedding. A contextual word embedding model is first trained on a corpus with a mixture of clinical reports and relevant Wikipedia pages in the clinical domain. Next, a bidirectional LSTM-CRF model is trained for clinical concept extraction using the contextual word embedding model. We tested our proposed model on the I2B2 2010 challenge dataset. Our proposed model achieved the best performance among reported baseline models and outperformed the state-of-the-art models by 3.4 in terms of F1-score. 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. This paper describes the SemEval-2014, Task 7 on the Analysis of Clinical Text and presents the evaluation results. It focused on two subtasks: (i) identification (Task A) and (ii) normalization (Task B) of diseases and disorders in clinical reports as annotated in the Shared Annotated Resources (ShARe) 1 corpus. This task was a follow-up to the ShARe CLEF eHealth 2013 shared task, subtasks 1a and 1b, 2 but using a larger test set. A total of 21 teams competed in Task A, and 18 of those also participated in Task B. For Task A, the best system had a strict F1-score of 81.3, with a precision of 84.3 and recall of 78.6. For Task B, the same group had the best strict accuracy of 74.1. The organizers have made the text corpora, annotations, and evaluation tools available for future research and development at the shared task website. 3 Citation relationship between scientific publications has been successfully used for scholarly bibliometrics, information retrieval and data mining tasks, and citation-based recommendation algorithms are well documented. While previous studies investigated citation relations from various viewpoints, most of them share the same assumption that, if paper1 cites paper2 (or author1 cites author2), they are connected, regardless of citation importance, sentiment, reason, topic, or motivation. However, this assumption is oversimplified. In this study, we employ an innovative "context-rich heterogeneous network" approach, which paves a new way for citation recommendation task. In the network, we characterize 1) the importance of citation relationships between citing and cited papers, and 2) the topical citation motivation. Unlike earlier studies, the citation information, in this paper, is characterized by citation textual contexts extracted from the full-text citing paper. We also propose algorithm to cope with the situation when large portion of full-text missing information exists in the bibliographic repository. Evaluation results show that, context-rich heterogeneous network can significantly enhance the citation recommendation performance. Pretraining sentence encoders with language modeling and related unsupervised tasks has recently been shown to be very effective for language understanding tasks. By supplementing language model-style pretraining with further training on data-rich supervised tasks, such as natural language inference, we obtain additional performance improvements on the GLUE benchmark. Applying supplementary training on BERT (, 2018), we attain a GLUE score of 81.8---the state of the art (as of 02 24 2019) and a 1.4 point improvement over BERT. We also observe reduced variance across random restarts in this setting. Our approach yields similar improvements when applied to ELMo (, 2018a) and (2018)'s model. In addition, the benefits of supplementary training are particularly pronounced in data-constrained regimes, as we show in experiments with artificially limited training data. Rapid growth in electronic health records (EHRs) use has led to an unprecedented expansion of available clinical data in electronic formats. However, much of the important healthcare information is locked in the narrative documents. Therefore Natural Language Processing (NLP) technologies, e.g., Named Entity Recognition that identifies boundaries and types of entities, have been extensively studied to unlock important clinical information in free text. In this study, we investigated a novel deep learning method to recognize clinical entities in Chinese clinical documents using the minimal feature engineering approach. We developed a deep neural network (DNN) to generate word embeddings from a large unlabeled corpus through unsupervised learning and another DNN for the NER task. The experiment results showed that the DNN with word embeddings trained from the large unlabeled corpus outperformed the state-of-the-art CRF’s model in the minimal feature engineering setting, achieving the highest F1-score of 0.9280. Further analysis showed that word embeddings derived through unsupervised learning from large unlabeled corpus remarkably improved the DNN with randomized embedding, denoting the usefulness of unsupervised feature learning. 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). Previous research indicates that during the past 20 years, the highest-quality work has been published in an increasingly diverse and larger group of journals. In this article, we examine whether this diversification has also affected the handful of elite journals that are traditionally considered to be the best. We examine citation patterns during the past 40 years of seven long-standing traditionally elite journals and six journals that have been increasing in importance during the past 20 years. To be among the top 5 or 1 cited papers, papers now need about twice as many citations as they did 40 years ago. Since the late 1980s and early 1990s, elite journals have been publishing a decreasing proportion of these top-cited papers. This also applies to the two journals that are typically considered as the top venues and often used as bibliometric indicators of "excellence": Science and Nature. On the other hand, several new and established journals are publishing an increasing proportion of the most-cited papers. These changes bring new challenges and opportunities for all parties. Journals can enact policies to increase or maintain their relative position in the journal hierarchy. Researchers now have the option to publish in more diverse venues knowing that their work can still reach the same audiences. Finally, evaluators and administrators need to know that although there will always be a certain prestige associated with publishing in "elite" journals, journal hierarchies are in constant flux. In a document network such as a citation network of scientific documents, web-logs, etc., the content produced by authors exhibits their interest in certain topics. In addition some authors influence other authors' interests. In this work, we propose to model the influence of cited authors along with the interests of citing authors. Moreover, we hypothesize that apart from the citations present in documents, the context surrounding the citation mention provides extra topical information about the cited authors. However, associating terms in the context to the cited authors remains an open problem. We propose novel document generation schemes that incorporate the context while simultaneously modeling the interests of citing authors and influence of the cited authors. Our experiments show significant improvements over baseline models for various evaluation criteria such as link prediction between document and cited author, and quantitatively explaining unseen text. Compositional embedding models build a representation (or embedding) for a linguistic structure based on its component word embeddings. We propose a Feature-rich Compositional Embedding Model (FCM) for relation extraction that is expressive, generalizes to new domains, and is easy-to-implement. The key idea is to combine both (unlexicalized) handcrafted features with learned word embeddings. The model is able to directly tackle the difficulties met by traditional compositional embeddings models, such as handling arbitrary types of sentence annotations and utilizing global information for composition. We test the proposed model on two relation extraction tasks, and demonstrate that our model outperforms both previous compositional models and traditional feature rich models on the ACE 2005 relation extraction task, and the SemEval 2010 relation classification task. The combination of our model and a loglinear classifier with hand-crafted features gives state-of-the-art results. We made our implementation available for general use 1 . Scholars are increasingly citing electronic “web references” which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To “webcite” a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its “instructions for authors” accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) “prospectively” before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted “citing articles” (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. @PARASPLIT [J Med Internet Res 2005;7(5):e60] While efforts have been made on bridging the semantic gap in image understanding, the in situ understanding of social media images is arguably more important but has had less progress. In this work, we enrich the representation of images in image tweets by considering their social context. We argue that in the microblog context, traditional image features, e.g., low-level SIFT or high-level detected objects, are far from adequate in interpreting the necessary semantics latent in image tweets. To bridge this gap, we move from the images' pixels to their context and propose a context-aware image bf tweet modelling (CITING) framework to mine and fuse contextual text to model such social media images' semantics. We start with tweet's intrinsic contexts, namely, 1) text within the image itself and 2) its accompanying text; and then we turn to the extrinsic contexts: 3) the external web page linked to by the tweet's embedded URL, and 4) the Web as a whole. These contexts can be leveraged to benefit many fundamental applications. To demonstrate the effectiveness our framework, we focus on the task of personalized image tweet recommendation, developing a feature-aware matrix factorization framework that encodes the contexts as a part of user interest modelling. Extensive experiments on a large Twitter dataset show that our proposed method significantly improves performance. Finally, to spur future studies, we have released both the code of our recommendation model and our image tweet dataset. Neural Machine Translation (NMT) has obtained state-of-the art performance for several language pairs, while only using parallel data for training. Target-side monolingual data plays an important role in boosting fluency for phrase-based statistical machine translation, and we investigate the use of monolingual data for NMT. In contrast to previous work, which combines NMT models with separately trained language models, we note that encoder-decoder NMT architectures already have the capacity to learn the same information as a language model, and we explore strategies to train with monolingual data without changing the neural network architecture. By pairing monolingual training data with an automatic back-translation, we can treat it as additional parallel training data, and we obtain substantial improvements on the WMT 15 task English German (+2.8-3.7 BLEU), and for the low-resourced IWSLT 14 task Turkish->English (+2.1-3.4 BLEU), obtaining new state-of-the-art results. We also show that fine-tuning on in-domain monolingual and parallel data gives substantial improvements for the IWSLT 15 task English->German. Distributed word representations (word embeddings) have recently contributed to competitive performance in language modeling and several NLP tasks. In this work, we train word embeddings for more than 100 languages using their corresponding Wikipedias. We quantitatively demonstrate the utility of our word embeddings by using them as the sole features for training a part of speech tagger for a subset of these languages. We find their performance to be competitive with near state-of-art methods in English, Danish and Swedish. Moreover, we investigate the semantic features captured by these embeddings through the proximity of word groupings. We will release these embeddings publicly to help researchers in the development and enhancement of multilingual applications. Compositional embedding models build a representation (or embedding) for a linguistic structure based on its component word embeddings. We propose a Feature-rich Compositional Embedding Model (FCM) for relation extraction that is expressive, generalizes to new domains, and is easy-to-implement. The key idea is to combine both (unlexicalized) hand-crafted features with learned word embeddings. The model is able to directly tackle the difficulties met by traditional compositional embeddings models, such as handling arbitrary types of sentence annotations and utilizing global information for composition. We test the proposed model on two relation extraction tasks, and demonstrate that our model outperforms both previous compositional models and traditional feature rich models on the ACE 2005 relation extraction task, and the SemEval 2010 relation classification task. The combination of our model and a log-linear classifier with hand-crafted features gives state-of-the-art results. De-identification is the process of removing 18 protected health information (PHI) from clinical notes in order for the text to be considered not individually identifiable. Recent advances in natural language processing (NLP) has allowed for the use of deep learning techniques for the task of de-identification. In this paper, we present a deep learning architecture that builds on the latest NLP advances by incorporating deep contextualized word embeddings and variational drop out Bi-LSTMs. We test this architecture on two gold standard datasets and show that the architecture achieves state-of-the-art performance on both data sets while also converging faster than other systems without the use of dictionaries or other knowledge sources. Modern deep transfer learning approaches have mainly focused on learning generic feature vectors from one task that are transferable to other tasks, such as word embeddings in language and pretrained convolutional features in vision. However, these approaches usually transfer unary features and largely ignore more structured graphical representations. This work explores the possibility of learning generic latent relational graphs that capture dependencies between pairs of data units (e.g., words or pixels) from large-scale unlabeled data and transferring the graphs to downstream tasks. Our proposed transfer learning framework improves performance on various tasks including question answering, natural language inference, sentiment analysis, and image classification. We also show that the learned graphs are generic enough to be transferred to different embeddings on which the graphs have not been trained (including GloVe embeddings, ELMo embeddings, and task-specific RNN hidden unit), or embedding-free units such as image pixels. Modeling polyphonic music is a particularly challenging task because of the intricate interplay between melody and harmony. A good model should satisfy three requirements: statistical accuracy (capturing faithfully the statistics of correlations at various ranges, horizontally and vertically), flexibility (coping with arbitrary user constraints), and generalization capacity (inventing new material, while staying in the style of the training corpus). Models proposed so far fail on at least one of these requirements. We propose a statistical model of polyphonic music, based on the maximum entropy principle. This model is able to learn and reproduce pairwise statistics between neighboring note events in a given corpus. The model is also able to invent new chords and to harmonize unknown melodies. We evaluate the invention capacity of the model by assessing the amount of cited, re-discovered, and invented chords on a corpus of Bach chorales. We discuss how the model enables the user to specify and enforce user-defined constraints, which makes it useful for style-based, interactive music generation. A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results.