scholarly journals Disease Named Entity Recognition (D-NER) Evaluation

2021 ◽  
Author(s):  
Xie-Yuan Xie
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Clinical Case ◽  
Case Reports ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Biomedical Domain ◽  
Named Entity ◽  
Medical Domain

Abstract Named Entity Recognition (NER) is a key task in Natural Language Processing (NLP). In medical domain, NER is very important phase in all end-to-end systems. In this paper, we investigate the performance of NER for disease (D-NER). TaggerOne was evaluated on 52 cardiovascular-related clinical case reports against hand annotation for diseases. Different training sets have been used to evaluate the performance of TaggerOne as a famous tool for NER in biomedical domain.

scholarly journals Obtaining Knowledge in Pathology Reports Through a Natural Language Processing Approach With Classification, Named-Entity Recognition, and Relation-Extraction Heuristics

2019 ◽  
pp. 1-8 ◽  
Author(s):  
Tomasz Oliwa ◽  
Steven B. Maron ◽  
Leah M. Chase ◽  
Samantha Lomnicki ◽  
Daniel V.T. Catenacci ◽  
...  
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Classification Model ◽  
Supervised Machine Learning ◽  
Named Entity ◽  
Pathology Reports

PURPOSE Robust institutional tumor banks depend on continuous sample curation or else subsequent biopsy or resection specimens are overlooked after initial enrollment. Curation automation is hindered by semistructured free-text clinical pathology notes, which complicate data abstraction. Our motivation is to develop a natural language processing method that dynamically identifies existing pathology specimen elements necessary for locating specimens for future use in a manner that can be re-implemented by other institutions. PATIENTS AND METHODS Pathology reports from patients with gastroesophageal cancer enrolled in The University of Chicago GI oncology tumor bank were used to train and validate a novel composite natural language processing-based pipeline with a supervised machine learning classification step to separate notes into internal (primary review) and external (consultation) reports; a named-entity recognition step to obtain label (accession number), location, date, and sublabels (block identifiers); and a results proofreading step. RESULTS We analyzed 188 pathology reports, including 82 internal reports and 106 external consult reports, and successfully extracted named entities grouped as sample information (label, date, location). Our approach identified up to 24 additional unique samples in external consult notes that could have been overlooked. Our classification model obtained 100% accuracy on the basis of 10-fold cross-validation. Precision, recall, and F1 for class-specific named-entity recognition models show strong performance. CONCLUSION Through a combination of natural language processing and machine learning, we devised a re-implementable and automated approach that can accurately extract specimen attributes from semistructured pathology notes to dynamically populate a tumor registry.

Probing Patient Messages Enhanced by Natural Language Processing: A Top-Down Message Corpus Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
George Mastorakos ◽  
Aditya Khurana ◽  
Ming Huang ◽  
Sunyang Fu ◽  
Ahmad P. Tafti ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Corpus Analysis ◽  
Entity Recognition ◽  
Message Content ◽  
Named Entity ◽  
Medical Concepts ◽  
Insight Into

Background. Patients increasingly use asynchronous communication platforms to converse with care teams. Natural language processing (NLP) to classify content and automate triage of these messages has great potential to enhance clinical efficiency. We characterize the contents of a corpus of portal messages generated by patients using NLP methods. We aim to demonstrate descriptive analyses of patient text that can contribute to the development of future sophisticated NLP applications. Methods. We collected approximately 3,000 portal messages from the cardiology, dermatology, and gastroenterology departments at Mayo Clinic. After labeling these messages as either Active Symptom, Logistical, Prescription, or Update, we used NER (named entity recognition) to identify medical concepts based on the UMLS library. We hierarchically analyzed the distribution of these messages in terms of departments, message types, medical concepts, and keywords therewithin. Results. Active Symptom and Logistical content types comprised approximately 67% of the message cohort. The “Findings” medical concept had the largest number of keywords across all groupings of content types and departments. “Anatomical Sites” and “Disorders” keywords were more prevalent in Active Symptom messages, while “Drugs” keywords were most prevalent in Prescription messages. Logistical messages tended to have the lower proportions of “Anatomical Sites,”, “Disorders,”, “Drugs,”, and “Findings” keywords when compared to other message content types. Conclusions. This descriptive corpus analysis sheds light on the content and foci of portal messages. The insight into the content and differences among message themes can inform the development of more robust NLP models.

Advances in Computational Linguistics and Text Processing Frameworks

2020 ◽  
pp. 217-244
Author(s):  
Ayush Srivastav ◽  
Hera Khan ◽  
Amit Kumar Mishra
Keyword(s):  
Neural Networks ◽  
Natural Language Processing ◽  
Natural Language ◽  
Computational Linguistics ◽  
Language Processing ◽  
Text Processing ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity ◽  
Part Of Speech

The chapter provides an eloquent account of the major methodologies and advances in the field of Natural Language Processing. The most popular models that have been used over time for the task of Natural Language Processing have been discussed along with their applications in their specific tasks. The chapter begins with the fundamental concepts of regex and tokenization. It provides an insight to text preprocessing and its methodologies such as Stemming and Lemmatization, Stop Word Removal, followed by Part-of-Speech tagging and Named Entity Recognition. Further, this chapter elaborates the concept of Word Embedding, its various types, and some common frameworks such as word2vec, GloVe, and fastText. A brief description of classification algorithms used in Natural Language Processing is provided next, followed by Neural Networks and its advanced forms such as Recursive Neural Networks and Seq2seq models that are used in Computational Linguistics. A brief description of chatbots and Memory Networks concludes the chapter.

scholarly journals DeNERT-KG: Named Entity and Relation Extraction Model Using DQN, Knowledge Graph, and BERT

2020 ◽  
Vol 10 (18) ◽  
pp. 6429
Author(s):  
SungMin Yang ◽  
SoYeop Yoo ◽  
OkRan Jeong
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Language Model ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Knowledge Graph ◽  
Named Entity ◽  
Artificial Intelligence Technology

Along with studies on artificial intelligence technology, research is also being carried out actively in the field of natural language processing to understand and process people’s language, in other words, natural language. For computers to learn on their own, the skill of understanding natural language is very important. There are a wide variety of tasks involved in the field of natural language processing, but we would like to focus on the named entity registration and relation extraction task, which is considered to be the most important in understanding sentences. We propose DeNERT-KG, a model that can extract subject, object, and relationships, to grasp the meaning inherent in a sentence. Based on the BERT language model and Deep Q-Network, the named entity recognition (NER) model for extracting subject and object is established, and a knowledge graph is applied for relation extraction. Using the DeNERT-KG model, it is possible to extract the subject, type of subject, object, type of object, and relationship from a sentence, and verify this model through experiments.

scholarly journals Large Language Models for Latvian Named Entity Recognition

2020 ◽  
Author(s):  
Rinalds Vīksna ◽  
Inguna Skadiņa
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Language Models ◽  
Named Entity ◽  
Language Data

Transformer-based language models pre-trained on large corpora have demonstrated good results on multiple natural language processing tasks for widely used languages including named entity recognition (NER). In this paper, we investigate the role of the BERT models in the NER task for Latvian. We introduce the BERT model pre-trained on the Latvian language data. We demonstrate that the Latvian BERT model, pre-trained on large Latvian corpora, achieves better results (81.91 F1-measure on average vs 78.37 on M-BERT for a dataset with nine named entity types, and 79.72 vs 78.83 on another dataset with seven types) than multilingual BERT and outperforms previously developed Latvian NER systems.

scholarly journals Deep learning in clinical natural language processing: a methodical review

2019 ◽  
Vol 27 (3) ◽  
pp. 457-470 ◽  
Author(s):  
Stephen Wu ◽  
Kirk Roberts ◽  
Surabhi Datta ◽  
Jingcheng Du ◽  
Zongcheng Ji ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Computational Linguistics ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity

Abstract Objective This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research. Materials and Methods We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers. Results DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) and word2vec embeddings (74.1%) were the most popular methods; the information extraction tasks of text classification, named entity recognition, and relation extraction were dominant (89.2%). However, there was a “long tail” of other methods and specific tasks. Most contributions were methodological variants or applications, but 20.8% were new methods of some kind. The earliest adopters were in the NLP community, but the medical informatics community was the most prolific. Discussion Our analysis shows growing acceptance of deep learning as a baseline for NLP research, and of DL-based NLP in the medical community. A number of common associations were substantiated (eg, the preference of recurrent neural networks for sequence-labeling named entity recognition), while others were surprisingly nuanced (eg, the scarcity of French language clinical NLP with deep learning). Conclusion Deep learning has not yet fully penetrated clinical NLP and is growing rapidly. This review highlighted both the popular and unique trends in this active field.

scholarly journals Integrated Model for Morphological Analysis and Named Entity Recognition Based on Label Attention Networks in Korean

2020 ◽  
Vol 10 (11) ◽  
pp. 3740
Author(s):  
Hongjin Kim ◽  
Harksoo Kim
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Error Propagation ◽  
Morphological Analysis ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Attention Networks ◽  
Named Entity ◽  
Proposed Model

In well-spaced Korean sentences, morphological analysis is the first step in natural language processing, in which a Korean sentence is segmented into a sequence of morphemes and the parts of speech of the segmented morphemes are determined. Named entity recognition is a natural language processing task carried out to obtain morpheme sequences with specific meanings, such as person, location, and organization names. Although morphological analysis and named entity recognition are closely associated with each other, they have been independently studied and have exhibited the inevitable error propagation problem. Hence, we propose an integrated model based on label attention networks that simultaneously performs morphological analysis and named entity recognition. The proposed model comprises two layers of neural network models that are closely associated with each other. The lower layer performs a morphological analysis, whereas the upper layer performs a named entity recognition. In our experiments using a public gold-labeled dataset, the proposed model outperformed previous state-of-the-art models used for morphological analysis and named entity recognition. Furthermore, the results indicated that the integrated architecture could alleviate the error propagation problem.

scholarly journals Quantifying Uncertainties in Natural Language Processing Tasks

2019 ◽  
Vol 33 ◽  
pp. 7322-7329 ◽  
Author(s):  
Yijun Xiao ◽  
William Yang Wang
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Intelligent Systems ◽  
Named Entity Recognition ◽  
Network Models ◽  
Entity Recognition ◽  
Neural Network Models ◽  
Named Entity ◽  
Modeling Uncertainties

Reliable uncertainty quantification is a first step towards building explainable, transparent, and accountable artificial intelligent systems. Recent progress in Bayesian deep learning has made such quantification realizable. In this paper, we propose novel methods to study the benefits of characterizing model and data uncertainties for natural language processing (NLP) tasks. With empirical experiments on sentiment analysis, named entity recognition, and language modeling using convolutional and recurrent neural network models, we show that explicitly modeling uncertainties is not only necessary to measure output confidence levels, but also useful at enhancing model performances in various NLP tasks.

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