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)

An Instance Transfer based Approach Using Enhanced Recurrent Neural Network for Domain Named Entity Recognition

Recently, neural networks have shown promising results for named entity recognition (NER), which needs a number of labeled data to for model training. When meeting a new domain (target domain) for NER, there is no or a few labeled data, which makes domain NER much more difficult. As NER has been researched for a long time, some similar domain already has well labelled data (source domain). Therefore, in this paper, we focus on domain NER by studying how to utilize the labelled data from such similar source domain for the new target domain. We design a kernel function based instance transfer strategy by getting similar labelled sentences from a source domain. Moreover, we propose an enhanced recurrent neural network (ERNN) by adding an additional layer that combines the source domain labelled data into traditional RNN structure. Comprehensive experiments are conducted on two datasets. The comparison results among HMM, CRF and RNN show that RNN performs bette than others. When there is no labelled data in domain target, compared to directly using the source domain labelled data without selecting transferred instances, our enhanced RNN approach gets improvement from 0.8052 to 0.9328 in terms of F1 measure

Syllable-based Neural Named Entity Recognition for Myanmar Language

Named Entity Recognition (NER) for Myanmar Language is essential to Myanmar natural language processing research work. In this work, NER for Myanmar language is treated as a sequence tagging problem and the effectiveness of deep neural networks on NER for Myanmar language has been investigated. Experiments are performed by applying deep neural network architectures on syllable level Myanmar contexts. Very first manually annotated NER corpus for Myanmar language is also constructed and proposed. In developing our in-house NER corpus, sentences from online news website and also sentences supported from ALT-Parallel-Corpus are also used. This ALT corpus is one part of the Asian Language Treebank (ALT) project under ASEAN IVO. This paper contributes the first evaluation of neural network models on NER task for Myanmar language. The experimental results show that those neural sequence models can produce promising results compared to the baseline CRF model. Among those neural architectures, bidirectional LSTM network added CRF layer above gives the highest F-score value. This work also aims to discover the effectiveness of neural network approaches to Myanmar textual processing as well as to promote further researches on this understudied language.Comment: Myanmar NE

Investigating how well contextual features are captured by bi-directional recurrent neural network models

Learning algorithms for natural language processing (NLP) tasks traditionally rely on manually defined relevant contextual features. On the other hand, neural network models using an only distributional representation of words have been successfully applied for several NLP tasks. Such models learn features automatically and avoid explicit feature engineering. Across several domains, neural models become a natural choice specifically when limited characteristics of data are known. However, this flexibility comes at the cost of interpretability. In this paper, we define three different methods to investigate ability of bi-directional recurrent neural networks (RNNs) in capturing contextual features. In particular, we analyze RNNs for sequence tagging tasks. We perform a comprehensive analysis on general as well as biomedical domain datasets. Our experiments focus on important contextual words as features, which can easily be extended to analyze various other feature types. We also investigate positional effects of context words and show how the developed methods can be used for error analysis.Comment: Camera ready version of ICON-201

A Biomedical Information Extraction Primer for NLP Researchers

Biomedical Information Extraction is an exciting field at the crossroads of Natural Language Processing, Biology and Medicine. It encompasses a variety of different tasks that require application of state-of-the-art NLP techniques, such as NER and Relation Extraction. This paper provides an overview of the problems in the field and discusses some of the techniques used for solving them

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

Extraction and Analysis of Clinically Important Follow-up Recommendations in a Large Radiology Dataset

Communication of follow-up recommendations when abnormalities are identified on imaging studies is prone to error. In this paper, we present a natural language processing approach based on deep learning to automatically identify clinically important recommendations in radiology reports. Our approach first identifies the recommendation sentences and then extracts reason, test, and time frame of the identified recommendations. To train our extraction models, we created a corpus of 567 radiology reports annotated for recommendation information. Our extraction models achieved 0.92 f-score for recommendation sentence, 0.65 f-score for reason, 0.73 f-score for test, and 0.84 f-score for time frame. We applied the extraction models to a set of over 3.3 million radiology reports and analyzed the adherence of follow-up recommendations.Comment: Under Review at American Medical Informatics Association Fall Symposium'201

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

A Joint Named-Entity Recognizer for Heterogeneous Tag-sets Using a Tag Hierarchy

We study a variant of domain adaptation for named-entity recognition where multiple, heterogeneously tagged training sets are available. Furthermore, the test tag-set is not identical to any individual training tag-set. Yet, the relations between all tags are provided in a tag hierarchy, covering the test tags as a combination of training tags. This setting occurs when various datasets are created using different annotation schemes. This is also the case of extending a tag-set with a new tag by annotating only the new tag in a new dataset. We propose to use the given tag hierarchy to jointly learn a neural network that shares its tagging layer among all tag-sets. We compare this model to combining independent models and to a model based on the multitasking approach. Our experiments show the benefit of the tag-hierarchy model, especially when facing non-trivial consolidation of tag-sets.Comment: Accepted at ACL 201

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