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.
Several works have explored the utility of contextual models in the clinical and biomedical domains. BioBERT @cite_13 trains a BERT model over a corpus of biomedical research articles sourced from PubMed https: www.ncbi.nlm.nih.gov pubmed article abstracts and PubMed Central https: www.ncbi.nlm.nih.gov pmc article full texts. They find the specificity offered by biomedical texts translated to improved performance on several biomedical NLP tasks, and fully release their pre-trained BERT model.
@cite_13
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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. 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. Objective Build probabilistic topic model representations of hospital admissions processes and compare the ability of such models to predict clinical order patterns as compared to preconstructed order sets. @PARASPLIT Materials and Methods The authors evaluated the first 24 hours of structured electronic health record data for > 10 K inpatients. Drawing an analogy between structured items (e.g., clinical orders) to words in a text document, the authors performed latent Dirichlet allocation probabilistic topic modeling. These topic models use initial clinical information to predict clinical orders for a separate validation set of > 4 K patients. The authors evaluated these topic model-based predictions vs existing human-authored order sets by area under the receiver operating characteristic curve, precision, and recall for subsequent clinical orders. @PARASPLIT Results Existing order sets predict clinical orders used within 24 hours with area under the receiver operating characteristic curve 0.81, precision 16 , and recall 35 . This can be improved to 0.90, 24 , and 47 ( P < 10−20) by using probabilistic topic models to summarize clinical data into up to 32 topics. Many of these latent topics yield natural clinical interpretations (e.g., “critical care,” “pneumonia,” “neurologic evaluation”). @PARASPLIT Discussion Existing order sets tend to provide nonspecific, process-oriented aid, with usability limitations impairing more precise, patient-focused support. Algorithmic summarization has the potential to breach this usability barrier by automatically inferring patient context, but with potential tradeoffs in interpretability. @PARASPLIT Conclusion Probabilistic topic modeling provides an automated approach to detect thematic trends in patient care and generate decision support content. A potential use case finds related clinical orders for decision support. With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, XLNet outperforms BERT on 20 tasks, often by a large margin, and achieves state-of-the-art results on 18 tasks including question answering, natural language inference, sentiment analysis, and document ranking. In this paper, we present a Multi-Task Deep Neural Network (MT-DNN) for learning representations across multiple natural language understanding (NLU) tasks. MT-DNN not only leverages large amounts of cross-task data, but also benefits from a regularization effect that leads to more general representations in order to adapt to new tasks and domains. MT-DNN extends the model proposed in (2015) by incorporating a pre-trained bidirectional transformer language model, known as BERT (, 2018). MT-DNN obtains new state-of-the-art results on ten NLU tasks, including SNLI, SciTail, and eight out of nine GLUE tasks, pushing the GLUE benchmark to 82.7 (2.2 absolute improvement). We also demonstrate using the SNLI and SciTail datasets that the representations learned by MT-DNN allow domain adaptation with substantially fewer in-domain labels than the pre-trained BERT representations. The code and pre-trained models are publicly available at this https URL. Recently, neural models pretrained on a language modeling task, such as ELMo (, 2017), OpenAI GPT (, 2018), and BERT (, 2018), have achieved impressive results on various natural language processing tasks such as question-answering and natural language inference. In this paper, we describe a simple re-implementation of BERT for query-based passage re-ranking. Our system is the state of the art on the TREC-CAR dataset and the top entry in the leaderboard of the MS MARCO passage retrieval task, outperforming the previous state of the art by 27 (relative) in MRR@10. The code to reproduce our results is available at this https URL A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http: biotea.github.io. Pre-trained text encoders have rapidly advanced the state of the art on many NLP tasks. We focus on one such model, BERT, and aim to quantify where linguistic information is captured within the network. We find that the model represents the steps of the traditional NLP pipeline in an interpretable and localizable way, and that the regions responsible for each step appear in the expected sequence: POS tagging, parsing, NER, semantic roles, then coreference. Qualitative analysis reveals that the model can and often does adjust this pipeline dynamically, revising lower-level decisions on the basis of disambiguating information from higher-level representations. This issue of JAMIA focuses on natural language processing (NLP) techniques for clinical-text information extraction. Several articles are offshoots of the yearly ‘Informatics for Integrating Biology and the Bedside’ (i2b2) (http: www.i2b2.org) NLP shared-task challenge, introduced by ( see page 552 )1 and co-sponsored by the Veteran's Administration for the last 2 years. This shared task follows long-running challenge evaluations in other fields, such as the Message Understanding Conference (MUC) for information extraction,2 TREC3 for text information retrieval, and CASP4 for protein structure prediction. Shared tasks in the clinical domain are recent and include annual i2b2 Challenges that began in 2006, a challenge for multi-label classification of radiology reports sponsored by Cincinnati Children's Hospital in 2007,5 a 2011 Cincinnati Children's Hospital challenge on suicide notes,6 and the 2011 TREC information retrieval shared task involving retrieval of clinical cases from narrative records.7 @PARASPLIT Although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications for clinical text has been slow and lags behind progress in the general NLP domain. There are several barriers to NLP development in the clinical domain, and shared tasks like the i2b2 VA Challenge address some of these barriers. Nevertheless, many barriers remain and unless the community takes a more active role in developing novel approaches for addressing the barriers, advancement and innovation will continue to be slow. @PARASPLIT Historically, there have been substantial barriers to NLP development in the clinical domain. These barriers are not unique to the clinical domain: they also occur in the fields of software engineering and general NLP. @PARASPLIT ### Lack of access to shared data @PARASPLIT Because of concerns regarding patient privacy and worry about revealing unfavorable institutional practices, hospitals and clinics have been extremely reluctant to allow access to clinical data for researchers from outside … @PARASPLIT Correspondence to Dr Wendy W Chapman, Department of Biomedical Informatics, University of California San Diego, 9500 Gilman Dr, Bldg 2 #0728, La Jolla, California, USA; wwchapman at ucsd.edu The volume of biomedical literature has experienced explosive growth in recent years. This is reflected in the corresponding increase in the size of MEDLINE^(R), the largest bibliographic database of biomedical citations. Indexers at the US National Library of Medicine (NLM) need efficient tools to help them accommodate the ensuing workload. After reviewing issues in the automatic assignment of Medical Subject Headings (MeSH^(R) terms) to biomedical text, we focus more specifically on the new subheading attachment feature for NLM's Medical Text Indexer (MTI). Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading subheading pair recommendations were assessed independently and combined. The best combination achieves 48 precision and 30 recall. After validation by NLM indexers, a suitable combination of the methods presented in this paper was integrated into MTI as a subheading attachment feature producing MeSH indexing recommendations compliant with current state-of-the-art indexing practice. 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). Language model pretraining has led to significant performance gains but careful comparison between different approaches is challenging. Training is computationally expensive, often done on private datasets of different sizes, and, as we will show, hyperparameter choices have significant impact on the final results. We present a replication study of BERT pretraining (, 2019) that carefully measures the impact of many key hyperparameters and training data size. We find that BERT was significantly undertrained, and can match or exceed the performance of every model published after it. Our best model achieves state-of-the-art results on GLUE, RACE and SQuAD. These results highlight the importance of previously overlooked design choices, and raise questions about the source of recently reported improvements. We release our models and code. Attentional, RNN-based encoder-decoder models for abstractive summarization have achieved good performance on short input and output sequences. For longer documents and summaries however these models often include repetitive and incoherent phrases. We introduce a neural network model with a novel intra-attention that attends over the input and continuously generated output separately, and a new training method that combines standard supervised word prediction and reinforcement learning (RL). Models trained only with supervised learning often exhibit "exposure bias" - they assume ground truth is provided at each step during training. However, when standard word prediction is combined with the global sequence prediction training of RL the resulting summaries become more readable. We evaluate this model on the CNN Daily Mail and New York Times datasets. Our model obtains a 41.16 ROUGE-1 score on the CNN Daily Mail dataset, an improvement over previous state-of-the-art models. Human evaluation also shows that our model produces higher quality summaries. 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. Motivation: The abundance of biomedical literature has attracted significant interest in novel methods to automatically extract biomedical relations from the literature. Until recently, most research was focused on extracting binary relations such as protein–protein interactions and drug–disease relations. However, these binary relations cannot fully represent the original biomedical data. Therefore, there is a need for methods that can extract fine-grained and complex relations known as biomedical events. Results: In this article we propose a novel method to extract biomedical events from text. Our method consists of two phases. In the first phase, training data are mapped into structured representations. Based on that, templates are used to extract rules automatically. In the second phase, extraction methods are developed to process the obtained rules. When evaluated against the Genia event extraction abstract and full-text test datasets (Task 1), we obtain results with F-scores of 52.34 and 53.34, respectively, which are comparable to the state-of-the-art systems. Furthermore, our system achieves superior performance in terms of computational efficiency. Availability: Our source code is available for academic use at http: dl.dropbox.com u 10256952 BioEvent.zip Contact: [email protected] Background We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from term frequencies, modeled as Poisson distributions. Unlike previous probabilistic retrieval models, we do not attempt to estimate relevance–but rather our focus is "relatedness", the probability that a user would want to examine a particular document given known interest in another. We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH ® in MEDLINE ®. Abstract Objective Acquiring and representing biomedical knowledge is an increasingly important component of contemporary bioinformatics. A critical step of the process is to identify and retrieve relevant documents among the vast volume of modern biomedical literature efficiently. In the real world, many information retrieval tasks are difficult because of high data dimensionality and the lack of annotated examples to train a retrieval algorithm. Under such a scenario, the performance of information retrieval algorithms is often unsatisfactory, therefore improvements are needed. Design We studied two approaches that enhance the text categorization performance on sparse and high data dimensionality: (1) semantic-preserving dimension reduction by representing text with semantic-enriched features; and (2) augmenting training data with semi-supervised learning. A probabilistic topic model was applied to extract major semantic topics from a corpus of text of interest. The representation of documents was projected from the high-dimensional vocabulary space onto a semantic topic space with reduced dimensionality. A semi-supervised learning algorithm based on graph theory was applied to identify potential positive training cases, which were further used to augment training data. The effects of data transformation and augmentation on text categorization by support vector machine (SVM) were evaluated. Results and Conclusion Semantic-enriched data transformation and the pseudo-positive-cases augmented training data enhance the efficiency and performance of text categorization by SVM. We describe a neural network model that jointly learns distributed representations of texts and knowledge base (KB) entities. Given a text in the KB, we train our proposed model to predict entities that are relevant to the text. Our model is designed to be generic with the ability to address various NLP tasks with ease. We train the model using a large corpus of texts and their entity annotations extracted from Wikipedia. We evaluated the model on three important NLP tasks (i.e., sentence textual similarity, entity linking, and factoid question answering) involving both unsupervised and supervised settings. As a result, we achieved state-of-the-art results on all three of these tasks. Our code and trained models are publicly available for further academic research. Neural IR models, such as DRMM and PACRR, have achieved strong results by successfully capturing relevance matching signals. We argue that the context of these matching signals is also important. Intuitively, when extracting, modeling, and combining matching signals, one would like to consider the surrounding text (local context) as well as other signals from the same document that can contribute to the overall relevance score. In this work, we highlight three potential shortcomings caused by not considering context information and propose three neural ingredients to address them: a disambiguation component, cascade k-max pooling, and a shuffling combination layer. Incorporating these components into the PACRR model yields Co-PACRR, a novel context-aware neural IR model. Extensive comparisons with established models on Trec Web Track data confirm that the proposed model can achieve superior search results. In addition, an ablation analysis is conducted to gain insights into the impact of and interactions between different components. We release our code to enable future comparisons. Motivation: In recent years, several biomedical event extraction (EE) systems have been developed. However, the nature of the annotated training corpora, as well as the training process itself, can limit the performance levels of the trained EE systems. In particular, most event-annotated corpora do not deal adequately with coreference. This impacts on the trained systems' ability to recognize biomedical entities, thus affecting their performance in extracting events accurately. Additionally, the fact that most EE systems are trained on a single annotated corpus further restricts their coverage. Results: We have enhanced our existing EE system, EventMine, in two ways. First, we developed a new coreference resolution (CR) system and integrated it with EventMine. The standalone performance of our CR system in resolving anaphoric references to proteins is considerably higher than the best ranked system in the COREF subtask of the BioNLP'11 Shared Task. Secondly, the improved EventMine incorporates domain adaptation (DA) methods, which extend EE coverage by allowing several different annotated corpora to be used during training. Combined with a novel set of methods to increase the generality and efficiency of EventMine, the integration of both CR and DA have resulted in significant improvements in EE, ranging between 0.5 and 3.4 F-Score. The enhanced EventMine outperforms the highest ranked systems from the BioNLP'09 shared task, and from the GENIA and Infectious Diseases subtasks of the BioNLP'11 shared task. Availability: The improved version of EventMine, incorporating the CR system and DA methods, is available at: http: www.nactem.ac.uk EventMine . Contact: makoto.miwa@manchester.ac.uk