scholarly journals Canary: An NLP Platform for Clinicians and Researchers

2017 ◽  
Vol 08 (02) ◽  
pp. 447-453 ◽  
Author(s):  
Shervin Malmasi ◽  
Nicolae Sandor ◽  
Naoshi Hosomura ◽  
Matt Goldberg ◽  
Stephen Skentzos ◽  
...  

SummaryInformation Extraction methods can help discover critical knowledge buried in the vast repositories of unstructured clinical data. However, these methods are underutilized in clinical research, potentially due to the absence of free software geared towards clinicians with little technical expertise. The skills required for developing/using such software constitute a major barrier for medical researchers wishing to employ these methods. To address this, we have developed Canary, a free and open-source solution designed for users without natural language processing (NLP) or software engineering experience. It was designed to be fast and work out of the box via a user-friendly graphical interface. Citation: Malmasi S, Sandor NL, Hosomura N, Goldberg M, Skentzos S, Turchin A. Canary: an NLP platform for clinicians and researchers. Appl Clin Inform 2017; 8: 447–453 https://doi.org/10.4338/ACI-2017-01-IE-0018

2021 ◽  
Vol 11 (19) ◽  
pp. 8812
Author(s):  
Ye Seul Bae ◽  
Kyung Hwan Kim ◽  
Han Kyul Kim ◽  
Sae Won Choi ◽  
Taehoon Ko ◽  
...  

Smoking is an important variable for clinical research, but there are few studies regarding automatic obtainment of smoking classification from unstructured bilingual electronic health records (EHR). We aim to develop an algorithm to classify smoking status based on unstructured EHRs using natural language processing (NLP). With acronym replacement and Python package Soynlp, we normalize 4711 bilingual clinical notes. Each EHR notes was classified into 4 categories: current smokers, past smokers, never smokers, and unknown. Subsequently, SPPMI (Shifted Positive Point Mutual Information) is used to vectorize words in the notes. By calculating cosine similarity between these word vectors, keywords denoting the same smoking status are identified. Compared to other keyword extraction methods (word co-occurrence-, PMI-, and NPMI-based methods), our proposed approach improves keyword extraction precision by as much as 20.0%. These extracted keywords are used in classifying 4 smoking statuses from our bilingual EHRs. Given an identical SVM classifier, the F1 score is improved by as much as 1.8% compared to those of the unigram and bigram Bag of Words. Our study shows the potential of SPPMI in classifying smoking status from bilingual, unstructured EHRs. Our current findings show how smoking information can be easily acquired for clinical practice and research.


2021 ◽  
Author(s):  
Nathan Ji ◽  
Yu Sun

The digital age gives us access to a multitude of both information and mediums in which we can interpret information. A majority of the time, many people find interpreting such information difficult as the medium may not be as user friendly as possible. This project has examined the inquiry of how one can identify specific information in a given text based on a question. This inquiry is intended to streamline one's ability to determine the relevance of a given text relative to his objective. The project has an overall 80% success rate given 10 articles with three questions asked per article. This success rate indicates that this project is likely applicable to those who are asking for content level questions within an article.


10.2196/16862 ◽  
2020 ◽  
Vol 8 (8) ◽  
pp. e16862
Author(s):  
Curtis Lee Petersen ◽  
Ryan Halter ◽  
David Kotz ◽  
Lorie Loeb ◽  
Summer Cook ◽  
...  

Background Sarcopenia, defined as the age-associated loss of muscle mass and strength, can be effectively mitigated through resistance-based physical activity. With compliance at approximately 40% for home-based exercise prescriptions, implementing a remote sensing system would help patients and clinicians to better understand treatment progress and increase compliance. The inclusion of end users in the development of mobile apps for remote-sensing systems can ensure that they are both user friendly and facilitate compliance. With advancements in natural language processing (NLP), there is potential for these methods to be used with data collected through the user-centered design process. Objective This study aims to develop a mobile app for a novel device through a user-centered design process with both older adults and clinicians while exploring whether data collected through this process can be used in NLP and sentiment analysis Methods Through a user-centered design process, we conducted semistructured interviews during the development of a geriatric-friendly Bluetooth-connected resistance exercise band app. We interviewed patients and clinicians at weeks 0, 5, and 10 of the app development. Each semistructured interview consisted of heuristic evaluations, cognitive walkthroughs, and observations. We used the Bing sentiment library for a sentiment analysis of interview transcripts and then applied NLP-based latent Dirichlet allocation (LDA) topic modeling to identify differences and similarities in patient and clinician participant interviews. Sentiment was defined as the sum of positive and negative words (each word with a +1 or −1 value). To assess utility, we used quantitative assessment questionnaires—System Usability Scale (SUS) and Usefulness, Satisfaction, and Ease of use (USE). Finally, we used multivariate linear models—adjusting for age, sex, subject group (clinician vs patient), and development—to explore the association between sentiment analysis and SUS and USE outcomes. Results The mean age of the 22 participants was 68 (SD 14) years, and 17 (77%) were female. The overall mean SUS and USE scores were 66.4 (SD 13.6) and 41.3 (SD 15.2), respectively. Both patients and clinicians provided valuable insights into the needs of older adults when designing and building an app. The mean positive-negative sentiment per sentence was 0.19 (SD 0.21) and 0.47 (SD 0.21) for patient and clinician interviews, respectively. We found a positive association with positive sentiment in an interview and SUS score (ß=1.38; 95% CI 0.37 to 2.39; P=.01). There was no significant association between sentiment and the USE score. The LDA analysis found no overlap between patients and clinicians in the 8 identified topics. Conclusions Involving patients and clinicians allowed us to design and build an app that is user friendly for older adults while supporting compliance. This is the first analysis using NLP and usability questionnaires in the quantification of user-centered design of technology for older adults.


AI Magazine ◽  
2011 ◽  
Vol 32 (2) ◽  
pp. 42 ◽  
Author(s):  
Anton Leuski ◽  
David Traum

NPCEditor is a system for building a natural language processing component for virtual humans capable of engaging a user in spoken dialog on a limited domain. It uses statistical language classification technology for mapping from a user’s text input to system responses. NPCEditor provides a user-friendly editor for creating effective virtual humans quickly. It has been deployed as a part of various virtual human systems in several applications.


Author(s):  
Arron Lacey ◽  
Jane Lyons ◽  
Ashley Akbari ◽  
Samantha L Turner ◽  
Angharad M Walters ◽  
...  

ABSTRACT ObjectivesElectronic healthcare records (EHR) are the main data sources that facilitate epidemiology research. Routinely collected data such as primary and secondary care are now easily linked to produce novel and high impact research. There are, however, rich data locked in the free text of clinical letters that are not otherwise translated into EHRs. It is highly desirable to be able to extract this information to strengthen the body of information in existing EHRs. The Swansea Collaborative in Analysis of NLP Research (SCANR) group at Swansea University has been established to evaluate the usage of Natural Language Processing platforms for obtaining new clinical data. To use Clix Enrich to extract SNOMED concepts from a variety of clinical free texts and produce EHRs from the extraction process. Approach SNOMED concepts contain common items of interest such as diagnosis, medication and symptoms, as well as contextual concepts such as historical reference and negation. Clix Enrich uses the SNOMED dictionary to encode clinical free text (pre-co-ordinated) and find contextually correct SNOMED concepts (post co-ordinated). We used Clix Enrich to extract meaningful clinical terms from MS and Epilepsy consultant letters, as well as presenting complaint fields from a Welsh Emergency Department (ED). ResultsWe tailored Clix Enrich to extract a wide variety of clinical terms from each source (fourty texts per source) and validated the extraction accuracy with clinical experts in each domain. Clix Enrich was able to accurately extract the correct diagnosis for MS, Epilepsy and ED attendance (100%, 95% and 80%), dosage and frequency of anti-epileptic medication and MS modifying therapy (90%, 100%) and EDDS score (94%). We note a probable source of discrepancy in extraction accuracy between letter sources in the frequency of abbreviated terms, particularly within the presenting complaint field of the ED sample. ConclusionClix Enrich can be used to accurately extract SNOMED concepts from clinical letters. The resulting datasets are readily available to link to existing EHRs, and can be linked to EHRs that adopt the SNOMED coding structure, or backward compatible hierarchies. Clix Enrich comes with out-of-the-box extraction methods but the optimum way to extract the correct information would be to build in custom queries, thus requiring clinical expertise to validate extraction.


2019 ◽  
Author(s):  
Curtis Lee Petersen ◽  
Ryan Halter ◽  
David Kotz ◽  
Lorie Loeb ◽  
Summer Cook ◽  
...  

BACKGROUND Sarcopenia, defined as the age-associated loss of muscle mass and strength, can be effectively mitigated through resistance-based physical activity. With compliance at approximately 40% for home-based exercise prescriptions, implementing a remote sensing system would help patients and clinicians to better understand treatment progress and increase compliance. The inclusion of end users in the development of mobile apps for remote-sensing systems can ensure that they are both user friendly and facilitate compliance. With advancements in natural language processing (NLP), there is potential for these methods to be used with data collected through the user-centered design process. OBJECTIVE This study aims to develop a mobile app for a novel device through a user-centered design process with both older adults and clinicians while exploring whether data collected through this process can be used in NLP and sentiment analysis METHODS Through a user-centered design process, we conducted semistructured interviews during the development of a geriatric-friendly Bluetooth-connected resistance exercise band app. We interviewed patients and clinicians at weeks 0, 5, and 10 of the app development. Each semistructured interview consisted of heuristic evaluations, cognitive walkthroughs, and observations. We used the Bing sentiment library for a sentiment analysis of interview transcripts and then applied NLP-based latent Dirichlet allocation (LDA) topic modeling to identify differences and similarities in patient and clinician participant interviews. Sentiment was defined as the sum of positive and negative words (each word with a +1 or −1 value). To assess utility, we used quantitative assessment questionnaires—System Usability Scale (SUS) and Usefulness, Satisfaction, and Ease of use (USE). Finally, we used multivariate linear models—adjusting for age, sex, subject group (clinician vs patient), and development—to explore the association between sentiment analysis and SUS and USE outcomes. RESULTS The mean age of the 22 participants was 68 (SD 14) years, and 17 (77%) were female. The overall mean SUS and USE scores were 66.4 (SD 13.6) and 41.3 (SD 15.2), respectively. Both patients and clinicians provided valuable insights into the needs of older adults when designing and building an app. The mean positive-negative sentiment per sentence was 0.19 (SD 0.21) and 0.47 (SD 0.21) for patient and clinician interviews, respectively. We found a positive association with positive sentiment in an interview and SUS score (ß=1.38; 95% CI 0.37 to 2.39; <i>P</i>=.01). There was no significant association between sentiment and the USE score. The LDA analysis found no overlap between patients and clinicians in the 8 identified topics. CONCLUSIONS Involving patients and clinicians allowed us to design and build an app that is user friendly for older adults while supporting compliance. This is the first analysis using NLP and usability questionnaires in the quantification of user-centered design of technology for older adults.


2015 ◽  
Author(s):  
Abdur Rahman M.A. Basher ◽  
Alexander S. Purdy ◽  
Inanc Birol

The breadth and scope of the biomedical literature hinders a timely and thorough comprehension of its content. PubMed, the leading repository for biomedical literature, currently holds over 26 million records, and is growing at a rate of over 1.2 million records per year, with about 300 records added daily that mention `cancer' in the title or abstract. Natural language processing (NLP) can assist in accessing and interpreting this massive volume of literature, including its quality. NLP approaches to the automatic extraction of biomedical entities and relationships may assist the development of explanatory models that can comprehensively scan and summarize biomedical articles for end users. Users can also formulate structured queries against these entities, and their interactions, to mine the latest developments in related areas of interest. In this article, we explore the latest advances in automated event extraction methods in the biomedical domain, focusing primarily on tools participated in the Biomedical NLP (BioNLP) Shared Task (ST) competitions. We review the leading BioNLP methods, summarize their results, and their innovative contributions in this field.


2021 ◽  
Vol 24 (2) ◽  
pp. 1740-1747
Author(s):  
Anton Leuski ◽  
David Traum

NPCEditor is a system for building a natural language processing component for virtual humans capable of engaging a user in spoken dialog on a limited domain. It uses a statistical language classification technology for mapping from user's text input to system responses. NPCEditor provides a user-friendly editor for creating effective virtual humans quickly. It has been deployed as a part of various virtual human systems in several applications.


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