scholarly journals Natural language processing for abstraction of cancer treatment toxicities: accuracy versus human experts

JAMIA Open ◽  
2020 ◽  
Author(s):  
Julian C Hong ◽  
Andrew T Fairchild ◽  
Jarred P Tanksley ◽  
Manisha Palta ◽  
Jessica D Tenenbaum
Keyword(s):  
Radiation Therapy ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Text Analysis ◽  
High Accuracy ◽  
Radiation Dermatitis ◽  
Clinical Text ◽  
Clinical Notes ◽  
Oncology Research

Abstract Objectives Expert abstraction of acute toxicities is critical in oncology research but is labor-intensive and variable. We assessed the accuracy of a natural language processing (NLP) pipeline to extract symptoms from clinical notes compared to physicians. Materials and Methods Two independent reviewers identified present and negated National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE) v5.0 symptoms from 100 randomly selected notes for on-treatment visits during radiation therapy with adjudication by a third reviewer. A NLP pipeline based on Apache clinical Text Analysis Knowledge Extraction System was developed and used to extract CTCAE terms. Accuracy was assessed by precision, recall, and F1. Results The NLP pipeline demonstrated high accuracy for common physician-abstracted symptoms, such as radiation dermatitis (F1 0.88), fatigue (0.85), and nausea (0.88). NLP had poor sensitivity for negated symptoms. Conclusion NLP accurately detects a subset of documented present CTCAE symptoms, though is limited for negated symptoms. It may facilitate strategies to more consistently identify toxicities during cancer therapy.

scholarly journals A deep database of medical abbreviations and acronyms for natural language processing

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Lisa Grossman Liu ◽  
Raymond H. Grossman ◽  
Elliot G. Mitchell ◽  
Chunhua Weng ◽  
Karthik Natarajan ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
American English ◽  
Substantial Improvement ◽  
Future Application ◽  
Multiple Sources ◽  
High Coverage ◽  
Clinical Text ◽  
Automated Quality Control

AbstractThe recognition, disambiguation, and expansion of medical abbreviations and acronyms is of upmost importance to prevent medically-dangerous misinterpretation in natural language processing. To support recognition, disambiguation, and expansion, we present the Medical Abbreviation and Acronym Meta-Inventory, a deep database of medical abbreviations. A systematic harmonization of eight source inventories across multiple healthcare specialties and settings identified 104,057 abbreviations with 170,426 corresponding senses. Automated cross-mapping of synonymous records using state-of-the-art machine learning reduced redundancy, which simplifies future application. Additional features include semi-automated quality control to remove errors. The Meta-Inventory demonstrated high completeness or coverage of abbreviations and senses in new clinical text, a substantial improvement over the next largest repository (6–14% increase in abbreviation coverage; 28–52% increase in sense coverage). To our knowledge, the Meta-Inventory is the most complete compilation of medical abbreviations and acronyms in American English to-date. The multiple sources and high coverage support application in varied specialties and settings. This allows for cross-institutional natural language processing, which previous inventories did not support. The Meta-Inventory is available at https://bit.ly/github-clinical-abbreviations.

scholarly journals Towards Accurate Deceptive Opinions Detection Based on Word Order-Preserving CNN

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Siyuan Zhao ◽  
Zhiwei Xu ◽  
Limin Liu ◽  
Mengjie Guo ◽  
Jing Yun
Keyword(s):  
Neural Network ◽  
Natural Language Processing ◽  
Natural Language ◽  
Convolutional Neural Network ◽  
Language Processing ◽  
Word Order ◽  
Text Analysis ◽  
Important Application ◽  
Detection Mechanism ◽  
Short Text

Convolutional neural network (CNN) has revolutionized the field of natural language processing, which is considerably efficient at semantics analysis that underlies difficult natural language processing problems in a variety of domains. The deceptive opinion detection is an important application of the existing CNN models. The detection mechanism based on CNN models has better self-adaptability and can effectively identify all kinds of deceptive opinions. Online opinions are quite short, varying in their types and content. In order to effectively identify deceptive opinions, we need to comprehensively study the characteristics of deceptive opinions and explore novel characteristics besides the textual semantics and emotional polarity that have been widely used in text analysis. In this paper, we optimize the convolutional neural network model by embedding the word order characteristics in its convolution layer and pooling layer, which makes convolutional neural network more suitable for short text classification and deceptive opinions detection. The TensorFlow-based experiments demonstrate that the proposed detection mechanism achieves more accurate deceptive opinion detection results.

An approach to neural network analysis of text information in the economic assessment of companies

2021 ◽  
Vol 20 (8) ◽  
pp. 1574-1594
Author(s):  
Aleksandr R. NEVREDINOV
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Text Analysis ◽  
Economic Assessment ◽  
Management Decision ◽  
Textual Information ◽  
Financial Condition ◽  
Analysis And Synthesis ◽  
Management Decision Making

Subject. When evaluating enterprises, maximum accuracy and comprehensiveness of analysis are important, although the use of various indicators of organization’s financial condition and external factors provide a sufficiently high accuracy of forecasting. Many researchers are increasingly focusing on the natural language processing to analyze various text sources. This subject is extremely relevant against the needs of companies to quickly and extensively analyze their activities. Objectives. The study aims at exploring the natural language processing methods and sources of textual information about companies that can be used in the analysis, and developing an approach to the analysis of textual information. Methods. The study draws on methods of analysis and synthesis, systematization, formalization, comparative analysis, theoretical and methodological provisions contained in domestic and foreign scientific works on text analysis, including for purposes of company evaluation. Results. I offer and test an approach to using non-numeric indicators for company analysis. The paper presents a unique model, which is created on the basis of existing developments that have shown their effectiveness. I also substantiate the use of this approach to analyze a company’s condition and to include the analysis results in models for overall assessment of the state of companies. Conclusions. The findings improve scientific and practical understanding of techniques for the analysis of companies, the ways of applying text analysis, using machine learning. They can be used to support management decision-making to automate the analysis of their own and other companies in the market, with which they interact.

Systematic review of current natural language processing methods and applications in cardiology

Heart ◽  
2021 ◽  
pp. heartjnl-2021-319769
Author(s):  
Meghan Reading Turchioe ◽  
Alexander Volodarskiy ◽  
Jyotishman Pathak ◽  
Drew N Wright ◽  
James Enlou Tcheng ◽  
...  
Keyword(s):  
Systematic Review ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Clinical Care ◽  
Real World Data ◽  
Clinical Text ◽  
Clinical Notes ◽  
Artery Disease ◽  
Automated Methods

Natural language processing (NLP) is a set of automated methods to organise and evaluate the information contained in unstructured clinical notes, which are a rich source of real-world data from clinical care that may be used to improve outcomes and understanding of disease in cardiology. The purpose of this systematic review is to provide an understanding of NLP, review how it has been used to date within cardiology and illustrate the opportunities that this approach provides for both research and clinical care. We systematically searched six scholarly databases (ACM Digital Library, Arxiv, Embase, IEEE Explore, PubMed and Scopus) for studies published in 2015–2020 describing the development or application of NLP methods for clinical text focused on cardiac disease. Studies not published in English, lacking a description of NLP methods, non-cardiac focused and duplicates were excluded. Two independent reviewers extracted general study information, clinical details and NLP details and appraised quality using a checklist of quality indicators for NLP studies. We identified 37 studies developing and applying NLP in heart failure, imaging, coronary artery disease, electrophysiology, general cardiology and valvular heart disease. Most studies used NLP to identify patients with a specific diagnosis and extract disease severity using rule-based NLP methods. Some used NLP algorithms to predict clinical outcomes. A major limitation is the inability to aggregate findings across studies due to vastly different NLP methods, evaluation and reporting. This review reveals numerous opportunities for future NLP work in cardiology with more diverse patient samples, cardiac diseases, datasets, methods and applications.

scholarly journals Toward a clinical text encoder: pretraining for clinical natural language processing with applications to substance misuse

2019 ◽  
Vol 26 (11) ◽  
pp. 1272-1278 ◽  
Author(s):  
Dmitriy Dligach ◽  
Majid Afshar ◽  
Timothy Miller
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Substance Misuse ◽  
Research Direction ◽  
Clinical Text ◽  
Universal Properties ◽  
Classification Tasks ◽  
Performance Gains ◽  
Clinical Natural Language Processing

Abstract Objective Our objective is to develop algorithms for encoding clinical text into representations that can be used for a variety of phenotyping tasks. Materials and Methods Obtaining large datasets to take advantage of highly expressive deep learning methods is difficult in clinical natural language processing (NLP). We address this difficulty by pretraining a clinical text encoder on billing code data, which is typically available in abundance. We explore several neural encoder architectures and deploy the text representations obtained from these encoders in the context of clinical text classification tasks. While our ultimate goal is learning a universal clinical text encoder, we also experiment with training a phenotype-specific encoder. A universal encoder would be more practical, but a phenotype-specific encoder could perform better for a specific task. Results We successfully train several clinical text encoders, establish a new state-of-the-art on comorbidity data, and observe good performance gains on substance misuse data. Discussion We find that pretraining using billing codes is a promising research direction. The representations generated by this type of pretraining have universal properties, as they are highly beneficial for many phenotyping tasks. Phenotype-specific pretraining is a viable route for trading the generality of the pretrained encoder for better performance on a specific phenotyping task. Conclusions We successfully applied our approach to many phenotyping tasks. We conclude by discussing potential limitations of our approach.

Leveraging Python to Process Cross-Cultural Temperament Interviews: A Novel Platform for Text Analysis

2020 ◽  
Vol 51 (2) ◽  
pp. 168-181 ◽  
Author(s):  
Joshua J. Underwood ◽  
Cornelia Kirchhoff ◽  
Haven Warwick ◽  
Maria A. Gartstein
Keyword(s):  
Early Childhood ◽  
Natural Language Processing ◽  
Individual Differences ◽  
Natural Language ◽  
Language Processing ◽  
Data Reduction ◽  
Text Analysis ◽  
Cross Cultural ◽  
Two Samples ◽  
Do So

During childhood, parents represent the most commonly used source of their child’s temperament information and, typically, do so by responding to questionnaires. Despite their wide-ranging applications, interviews present notorious data reduction challenges, as quantification of narratives has proven to be a labor-intensive process. However, for the purposes of this study, the labor-intensive nature may have conferred distinct advantages. The present study represents a demonstration project aimed at leveraging emerging technologies for this purpose. Specifically, we used Python natural language processing capabilities to analyze semistructured temperament interviews conducted with U.S. and German mothers of toddlers, expecting to identify differences between these two samples in the frequency of words used to describe individual differences, along with some similarities. Two different word lists were used: (a) a set of German personality words and (b) temperament-related words extracted from the Early Childhood Behavior Questionnaire (ECBQ). Analyses using the German trait word demonstrated that mothers from Germany described their toddlers as significantly more “cheerful” and “careful” compared with U.S. caregivers. According to U.S. mothers, their children were more “independent,” “emotional,” and “timid.” For the ECBQ analysis, German mothers described their children as “calm” and “careful” more often than U.S. mothers. U.S. mothers, however, referred to their children as “upset,” “happy,” and “frustrated” more frequently than German caregivers. The Python code developed herein illustrates this software as a viable research tool for cross-cultural investigations.

Sign in / Sign up

Export Citation Format

Share Document