Clinical Concept Extraction with Contextual Word Embedding

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.Comment: Machine Learning for Health (ML4H) Workshop at NeurIPS 2018 arXiv:1811.0721

Transfer Learning for Scientific Data Chain Extraction in Small Chemical Corpus with BERT-CRF Model

Computational chemistry develops fast in recent years due to the rapid growth and breakthroughs in AI. Thanks for the progress in natural language processing, researchers can extract more fine-grained knowledge in publications to stimulate the development in computational chemistry. While the works and corpora in chemical entity extraction have been restricted in the biomedicine or life science field instead of the chemistry field, we build a new corpus in chemical bond field annotated for 7 types of entities: compound, solvent, method, bond, reaction, pKa and pKa value. This paper presents a novel BERT-CRF model to build scientific chemical data chains by extracting 7 chemical entities and relations from publications. And we propose a joint model to extract the entities and relations simultaneously. Experimental results on our Chemical Special Corpus demonstrate that we achieve state-of-art and competitive NER performance

Advancing NLP with Cognitive Language Processing Signals

When we read, our brain processes language and generates cognitive processing data such as gaze patterns and brain activity. These signals can be recorded while reading. Cognitive language processing data such as eye-tracking features have shown improvements on single NLP tasks. We analyze whether using such human features can show consistent improvement across tasks and data sources. We present an extensive investigation of the benefits and limitations of using cognitive processing data for NLP. Specifically, we use gaze and EEG features to augment models of named entity recognition, relation classification, and sentiment analysis. These methods significantly outperform the baselines and show the potential and current limitations of employing human language processing data for NLP

Second-Order Word Embeddings from Nearest Neighbor Topological Features

We introduce second-order vector representations of words, induced from nearest neighborhood topological features in pre-trained contextual word embeddings. We then analyze the effects of using second-order embeddings as input features in two deep natural language processing models, for named entity recognition and recognizing textual entailment, as well as a linear model for paraphrase recognition. Surprisingly, we find that nearest neighbor information alone is sufficient to capture most of the performance benefits derived from using pre-trained word embeddings. Furthermore, second-order embeddings are able to handle highly heterogeneous data better than first-order representations, though at the cost of some specificity. Additionally, augmenting contextual embeddings with second-order information further improves model performance in some cases. Due to variance in the random initializations of word embeddings, utilizing nearest neighbor features from multiple first-order embedding samples can also contribute to downstream performance gains. Finally, we identify intriguing characteristics of second-order embedding spaces for further research, including much higher density and different semantic interpretations of cosine similarity.Comment: Submitted to NIPS 2017. (8 pages + 4 reference

Fine Grained Classification of Personal Data Entities

Entity Type Classification can be defined as the task of assigning category labels to entity mentions in documents. While neural networks have recently improved the classification of general entity mentions, pattern matching and other systems continue to be used for classifying personal data entities (e.g. classifying an organization as a media company or a government institution for GDPR, and HIPAA compliance). We propose a neural model to expand the class of personal data entities that can be classified at a fine grained level, using the output of existing pattern matching systems as additional contextual features. We introduce new resources, a personal data entities hierarchy with 134 types, and two datasets from the Wikipedia pages of elected representatives and Enron emails. We hope these resource will aid research in the area of personal data discovery, and to that effect, we provide baseline results on these datasets, and compare our method with state of the art models on OntoNotes dataset

Seq2Biseq: Bidirectional Output-wise Recurrent Neural Networks for Sequence Modelling

During the last couple of years, Recurrent Neural Networks (RNN) have reached state-of-the-art performances on most of the sequence modelling problems. In particular, the "sequence to sequence" model and the neural CRF have proved to be very effective in this domain. In this article, we propose a new RNN architecture for sequence labelling, leveraging gated recurrent layers to take arbitrarily long contexts into account, and using two decoders operating forward and backward. We compare several variants of the proposed solution and their performances to the state-of-the-art. Most of our results are better than the state-of-the-art or very close to it and thanks to the use of recent technologies, our architecture can scale on corpora larger than those used in this work.Comment: Slightly improved version of the paper accepted to the CICling 2019 conferenc

Neural Metric Learning for Fast End-to-End Relation Extraction

Relation extraction (RE) is an indispensable information extraction task in several disciplines. RE models typically assume that named entity recognition (NER) is already performed in a previous step by another independent model. Several recent efforts, under the theme of end-to-end RE, seek to exploit inter-task correlations by modeling both NER and RE tasks jointly. Earlier work in this area commonly reduces the task to a table-filling problem wherein an additional expensive decoding step involving beam search is applied to obtain globally consistent cell labels. In efforts that do not employ table-filling, global optimization in the form of CRFs with Viterbi decoding for the NER component is still necessary for competitive performance. We introduce a novel neural architecture utilizing the table structure, based on repeated applications of 2D convolutions for pooling local dependency and metric-based features, that improves on the state-of-the-art without the need for global optimization. We validate our model on the ADE and CoNLL04 datasets for end-to-end RE and demonstrate $\approx 1\%$ gain (in F-score) over prior best results with training and testing times that are seven to ten times faster --- the latter highly advantageous for time-sensitive end user applications

An Attentive Sequence Model for Adverse Drug Event Extraction from Biomedical Text

Adverse reaction caused by drugs is a potentially dangerous problem which may lead to mortality and morbidity in patients. Adverse Drug Event (ADE) extraction is a significant problem in biomedical research. We model ADE extraction as a Question-Answering problem and take inspiration from Machine Reading Comprehension (MRC) literature, to design our model. Our objective in designing such a model, is to exploit the local linguistic context in clinical text and enable intra-sequence interaction, in order to jointly learn to classify drug and disease entities, and to extract adverse reactions caused by a given drug. Our model makes use of a self-attention mechanism to facilitate intra-sequence interaction in a text sequence. This enables us to visualize and understand how the network makes use of the local and wider context for classification.Comment: 7 pages, 5 figures, 4 table

Grounded Recurrent Neural Networks

In this work, we present the Grounded Recurrent Neural Network (GRNN), a recurrent neural network architecture for multi-label prediction which explicitly ties labels to specific dimensions of the recurrent hidden state (we call this process "grounding"). The approach is particularly well-suited for extracting large numbers of concepts from text. We apply the new model to address an important problem in healthcare of understanding what medical concepts are discussed in clinical text. Using a publicly available dataset derived from Intensive Care Units, we learn to label a patient's diagnoses and procedures from their discharge summary. Our evaluation shows a clear advantage to using our proposed architecture over a variety of strong baselines

SciBERT: A Pretrained Language Model for Scientific Text

Obtaining large-scale annotated data for NLP tasks in the scientific domain is challenging and expensive. We release SciBERT, a pretrained language model based on BERT (Devlin et al., 2018) to address the lack of high-quality, large-scale labeled scientific data. SciBERT leverages unsupervised pretraining on a large multi-domain corpus of scientific publications to improve performance on downstream scientific NLP tasks. We evaluate on a suite of tasks including sequence tagging, sentence classification and dependency parsing, with datasets from a variety of scientific domains. We demonstrate statistically significant improvements over BERT and achieve new state-of-the-art results on several of these tasks. The code and pretrained models are available at https://github.com/allenai/scibert/.Comment: https://github.com/allenai/sciber