Transfer Learning for Sequence Tagging with Hierarchical Recurrent Networks

Recent papers have shown that neural networks obtain state-of-the-art performance on several different sequence tagging tasks. One appealing property of such systems is their generality, as excellent performance can be achieved with a unified architecture and without task-specific feature engineering. However, it is unclear if such systems can be used for tasks without large amounts of training data. In this paper we explore the problem of transfer learning for neural sequence taggers, where a source task with plentiful annotations (e.g., POS tagging on Penn Treebank) is used to improve performance on a target task with fewer available annotations (e.g., POS tagging for microblogs). We examine the effects of transfer learning for deep hierarchical recurrent networks across domains, applications, and languages, and show that significant improvement can often be obtained. These improvements lead to improvements over the current state-of-the-art on several well-studied tasks.Comment: Accepted as a conference paper at ICLR 2017. This is an extended version of the original paper (https://arxiv.org/abs/1603.06270). The original paper proposes a new architecture, while this version focuses on transfer learning for a general model clas

SwellShark: A Generative Model for Biomedical Named Entity Recognition without Labeled Data

We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak supervision. We then use a generative model to unify and denoise this supervision and construct large-scale, probabilistically labeled datasets for training high-accuracy NER taggers. In three biomedical NER tasks, SwellShark achieves competitive scores with state-of-the-art supervised benchmarks using no hand-labeled training data. In a drug name extraction task using patient medical records, one domain expert using SwellShark achieved within 5.1% of a crowdsourced annotation approach -- which originally utilized 20 teams over the course of several weeks -- in 24 hours

An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining

Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language processing tasks such as text similarity, relation extraction, named entity recognition, and text inference. Our empirical results demonstrate that the MTL fine-tuned models outperform state-of-the-art transformer models (e.g., BERT and its variants) by 2.0% and 1.3% in biomedical and clinical domains, respectively. Pairwise MTL further demonstrates more details about which tasks can improve or decrease others. This is particularly helpful in the context that researchers are in the hassle of choosing a suitable model for new problems. The code and models are publicly available at https://github.com/ncbi-nlp/bluebertComment: Accepted by BioNLP 202

Effective Use of Bidirectional Language Modeling for Transfer Learning in Biomedical Named Entity Recognition

Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their parameters can be learned end-to-end without the need for hand-engineered features. However, these approaches rely on high-quality labeled data, which is expensive to obtain. To address this issue, we investigate how to use unlabeled text data to improve the performance of NER models. Specifically, we train a bidirectional language model (BiLM) on unlabeled data and transfer its weights to "pretrain" an NER model with the same architecture as the BiLM, which results in a better parameter initialization of the NER model. We evaluate our approach on four benchmark datasets for biomedical NER and show that it leads to a substantial improvement in the F1 scores compared with the state-of-the-art approaches. We also show that BiLM weight transfer leads to a faster model training and the pretrained model requires fewer training examples to achieve a particular F1 score.Comment: Machine Learning for Healthcare (MLHC) 2018, Comments: 12 pages, updated authors affiliation

A Study of Recent Contributions on Information Extraction

This paper reports on modern approaches in Information Extraction (IE) and its two main sub-tasks of Named Entity Recognition (NER) and Relation Extraction (RE). Basic concepts and the most recent approaches in this area are reviewed, which mainly include Machine Learning (ML) based approaches and the more recent trend to Deep Learning (DL) based methods

Learning Named Entity Tagger using Domain-Specific Dictionary

Recent advances in deep neural models allow us to build reliable named entity recognition (NER) systems without handcrafting features. However, such methods require large amounts of manually-labeled training data. There have been efforts on replacing human annotations with distant supervision (in conjunction with external dictionaries), but the generated noisy labels pose significant challenges on learning effective neural models. Here we propose two neural models to suit noisy distant supervision from the dictionary. First, under the traditional sequence labeling framework, we propose a revised fuzzy CRF layer to handle tokens with multiple possible labels. After identifying the nature of noisy labels in distant supervision, we go beyond the traditional framework and propose a novel, more effective neural model AutoNER with a new Tie or Break scheme. In addition, we discuss how to refine distant supervision for better NER performance. Extensive experiments on three benchmark datasets demonstrate that AutoNER achieves the best performance when only using dictionaries with no additional human effort, and delivers competitive results with state-of-the-art supervised benchmarks

Unlocking the Power of Deep PICO Extraction: Step-wise Medical NER Identification

The PICO framework (Population, Intervention, Comparison, and Outcome) is usually used to formulate evidence in the medical domain. The major task of PICO extraction is to extract sentences from medical literature and classify them into each class. However, in most circumstances, there will be more than one evidences in an extracted sentence even it has been categorized to a certain class. In order to address this problem, we propose a step-wise disease Named Entity Recognition (DNER) extraction and PICO identification method. With our method, sentences in paper title and abstract are first classified into different classes of PICO, and medical entities are then identified and classified into P and O. Different kinds of deep learning frameworks are used and experimental results show that our method will achieve high performance and fine-grained extraction results comparing with conventional PICO extraction works.Comment: 9 pages, 3 figure

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

MASK: A flexible framework to facilitate de-identification of clinical texts

Medical health records and clinical summaries contain a vast amount of important information in textual form that can help advancing research on treatments, drugs and public health. However, the majority of these information is not shared because they contain private information about patients, their families, or medical staff treating them. Regulations such as HIPPA in the US, PHIPPA in Canada and GDPR regulate the protection, processing and distribution of this information. In case this information is de-identified and personal information are replaced or redacted, they could be distributed to the research community. In this paper, we present MASK, a software package that is designed to perform the de-identification task. The software is able to perform named entity recognition using some of the state-of-the-art techniques and then mask or redact recognized entities. The user is able to select named entity recognition algorithm (currently implemented are two versions of CRF-based techniques and BiLSTM-based neural network with pre-trained GLoVe and ELMo embedding) and masking algorithm (e.g. shift dates, replace names/locations, totally redact entity)

Named Entity Recognition for Electronic Health Records: A Comparison of Rule-based and Machine Learning Approaches

This work investigates multiple approaches to Named Entity Recognition (NER) for text in Electronic Health Record (EHR) data. In particular, we look into the application of (i) rule-based, (ii) deep learning and (iii) transfer learning systems for the task of NER on brain imaging reports with a focus on records from patients with stroke. We explore the strengths and weaknesses of each approach, develop rules and train on a common dataset, and evaluate each system's performance on common test sets of Scottish radiology reports from two sources (brain imaging reports in ESS -- Edinburgh Stroke Study data collected by NHS Lothian as well as radiology reports created in NHS Tayside). Our comparison shows that a hand-crafted system is the most accurate way to automatically label EHR, but machine learning approaches can provide a feasible alternative where resources for a manual system are not readily available.Comment: 8 pages, presented at HealTAC 2019, Cardiff, 24-25/04/201