scholarly journals Tracking mutational semantics of SARS-CoV-2 genomes

2021 ◽  
Author(s):  
Rohan Singh ◽  
Sunil Nagpal ◽  
Nishal Kumar Pinna ◽  
Sharmila S Mande
Keyword(s):  
Biological Sciences ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Topic Modeling ◽  
Data Science ◽  
Higher Order ◽  
Dynamic Phenomenon ◽  
Alternative Strategies ◽  
Daunting Task

Genomes have an inherent context dictated by the order in which the nucleotides and higher order genomic elements are arranged in the DNA/RNA. Learning this context is a daunting task, governed by the combinatorial complexity of interactions possible between ordered elements of genomes. Can natural language processing be employed on these orderly, complex and also evolving datatypes (genomic sequences) to reveal the latent patterns or context of genomic elements (e.g Mutations)? Here we present an approach to understand the mutational landscape of Covid-19 by treating the temporally changing (continuously mutating) SARS-CoV-2 genomes as documents. We demonstrate how the analogous interpretation of evolving genomes to temporal literature corpora provides an opportunity to use dynamic topic modeling (DTM) and temporal Word2Vec models to delineate mutation signatures corresponding to different Variants-of-Concerns and tracking the semantic drift of Mutations-of-Concern (MoC). We identified and studied characteristic mutations affiliated to Covid-infection severity and tracked their relationship with MoCs. Our ground work on utility of such temporal NLP models in genomics could supplement ongoing efforts in not only understanding the Covid pandemic but also provide alternative strategies in studying dynamic phenomenon in biological sciences through data science (especially NLP, AI/ML).

Customers' experience of purchasing event tickets: mining online reviews based on topic modeling and sentiment analysis

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Krzysztof Celuch
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Sentiment Analysis ◽  
Language Processing ◽  
Topic Modeling ◽  
Data Science ◽  
Latent Dirichlet Allocation ◽  
Online Reviews ◽  
Third Party ◽  
Content Type

PurposeIn search of creating an extraordinary experience for customers, services have gone beyond the means of a transaction between buyers and sellers. In the event industry, where purchasing tickets online is a common procedure, it remains unclear as to how to enhance the multifaceted experience. This study aims at offering a snapshot into the most valued aspects for consumers and to uncover consumers' feelings toward their experience of purchasing event tickets on third-party ticketing platforms.Design/methodology/approachThis is a cross-disciplinary study that applies knowledge from both data science and services marketing. Under the guise of natural language processing, latent Dirichlet allocation topic modeling and sentiment analysis were used to interpret the embedded meanings based on online reviews.FindingsThe findings conceptualized ten dimensions valued by eventgoers, including technical issues, value of core product and service, word-of-mouth, trustworthiness, professionalism and knowledgeability, customer support, information transparency, additional fee, prior experience and after-sales service. Among these aspects, consumers rated the value of the core product and service to be the most positive experience, whereas the additional fee was considered the least positive one.Originality/valueDrawing from the intersection of natural language processing and the status quo of the event industry, this study offers a better understanding of eventgoers' experiences in the case of purchasing online event tickets. It also provides a hands-on guide for marketers to stage memorable experiences in the era of digitalization.

An Evaluation of Patient Safety Event Report Categories Using Unsupervised Topic Modeling

2015 ◽  
Vol 54 (04) ◽  
pp. 338-345 ◽  
Author(s):  
A. Fong ◽  
R. Ratwani
Keyword(s):  
Patient Safety ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Topic Modeling ◽  
Free Text ◽  
Event Data ◽  
Event Type ◽  
Modeling Approach ◽  
Safety Event

SummaryObjective: Patient safety event data repositories have the potential to dramatically improve safety if analyzed and leveraged appropriately. These safety event reports often consist of both structured data, such as general event type categories, and unstructured data, such as free text descriptions of the event. Analyzing these data, particularly the rich free text narratives, can be challenging, especially with tens of thousands of reports. To overcome the resource intensive manual review process of the free text descriptions, we demonstrate the effectiveness of using an unsupervised natural language processing approach.Methods: An unsupervised natural language processing technique, called topic modeling, was applied to a large repository of patient safety event data to identify topics, or themes, from the free text descriptions of the data. Entropy measures were used to evaluate and compare these topics to the general event type categories that were originally assigned by the event reporter.Results: Measures of entropy demonstrated that some topics generated from the un-supervised modeling approach aligned with the clinical general event type categories that were originally selected by the individual entering the report. Importantly, several new latent topics emerged that were not originally identified. The new topics provide additional insights into the patient safety event data that would not otherwise easily be detected.Conclusion: The topic modeling approach provides a method to identify topics or themes that may not be immediately apparent and has the potential to allow for automatic reclassification of events that are ambiguously classified by the event reporter.

scholarly journals Forty-two Million Ways to Describe Pain: Topic Modeling of 200,000 PubMed Pain-Related Abstracts Using Natural Language Processing and Deep Learning–Based Text Generation

Pain Medicine ◽  
2020 ◽  
Vol 21 (11) ◽  
pp. 3133-3160
Author(s):  
Patrick J Tighe ◽  
Bharadwaj Sannapaneni ◽  
Roger B Fillingim ◽  
Charlie Doyle ◽  
Michael Kent ◽  
...  
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Topic Modeling ◽  
Taxonomic Structure ◽  
Generation Model ◽  
Pain Research ◽  
Embedded Model ◽  
Gated Recurrent Units

Abstract Objective Recent efforts to update the definitions and taxonomic structure of concepts related to pain have revealed opportunities to better quantify topics of existing pain research subject areas. Methods Here, we apply basic natural language processing (NLP) analyses on a corpus of >200,000 abstracts published on PubMed under the medical subject heading (MeSH) of “pain” to quantify the topics, content, and themes on pain-related research dating back to the 1940s. Results The most common stemmed terms included “pain” (601,122 occurrences), “patient” (508,064 occurrences), and “studi-” (208,839 occurrences). Contrarily, terms with the highest term frequency–inverse document frequency included “tmd” (6.21), “qol” (6.01), and “endometriosis” (5.94). Using the vector-embedded model of term definitions available via the “word2vec” technique, the most similar terms to “pain” included “discomfort,” “symptom,” and “pain-related.” For the term “acute,” the most similar terms in the word2vec vector space included “nonspecific,” “vaso-occlusive,” and “subacute”; for the term “chronic,” the most similar terms included “persistent,” “longstanding,” and “long-standing.” Topic modeling via Latent Dirichlet analysis identified peak coherence (0.49) at 40 topics. Network analysis of these topic models identified three topics that were outliers from the core cluster, two of which pertained to women’s health and obstetrics and were closely connected to one another, yet considered distant from the third outlier pertaining to age. A deep learning–based gated recurrent units abstract generation model successfully synthesized several unique abstracts with varying levels of believability, with special attention and some confusion at lower temperatures to the roles of placebo in randomized controlled trials. Conclusions Quantitative NLP models of published abstracts pertaining to pain may point to trends and gaps within pain research communities.

scholarly journals The Rise of Big Data Science: A Survey of Techniques, Methods and Approaches in the Field of Natural Language Processing and Network Theory

2018 ◽  
Vol 2 (3) ◽  
pp. 22 ◽  
Author(s):  
Jeffrey Ray ◽  
Olayinka Johnny ◽  
Marcello Trovati ◽  
Stelios Sotiriadis ◽  
Nik Bessis
Keyword(s):  
Big Data ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Network Theory ◽  
Data Science ◽  
Theoretical Foundation ◽  
Scientific Field ◽  
Research Challenges ◽  
New Research

The continuous creation of data has posed new research challenges due to its complexity, diversity and volume. Consequently, Big Data has increasingly become a fully recognised scientific field. This article provides an overview of the current research efforts in Big Data science, with particular emphasis on its applications, as well as theoretical foundation.

scholarly journals Topic Modeling for Keyword Extraction: using Natural Language Processing methods for keyword extraction in Portal Min@s

2015 ◽  
Vol 23 (3) ◽  
pp. 695 ◽  
Author(s):  
Arnaldo Candido Junior ◽  
Célia Magalhães ◽  
Helena Caseli ◽  
Régis Zangirolami
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Topic Modeling ◽  
Latent Dirichlet Allocation ◽  
Keyword Extraction ◽  
Processing Methods ◽  
Dirichlet Allocation

<p style="margin-bottom: 0cm; line-height: 100%;" align="justify"> </p><p>Este artigo tem o objetivo da avaliar a aplicação de dois métodos automáticos eficientes na extração de palavras-chave, usados pelas comunidades da Linguística de <em>Corpus </em>e do Processamento da Língua Natural para gerar palavras-chave de textos literários: o <em>WordSmith Tools </em>e o <em>Latent Dirichlet Allocation </em>(LDA). As duas ferramentas escolhidas para este trabalho têm suas especificidades e técnicas diferentes de extração, o que nos levou a uma análise orientada para a sua performance. Objetivamos entender, então, como cada método funciona e avaliar sua aplicação em textos literários. Para esse fim, usamos análise humana, com conhecimento do campo dos textos usados. O método LDA foi usado para extrair palavras-chave por meio de sua integração com o <em>Portal Min@s: Corpora de Fala e Escrita</em>, um sistema geral de processamento de <em>corpora</em>, concebido para diferentes pesquisas de Linguística de <em>Corpus</em>. Os resultados do experimento confirmam a eficácia do WordSmith Tools e do LDA na extração de palavras-chave de um <em>corpus </em>literário, além de apontar que é necessária a análise humana das listas em um estágio anterior aos experimentos para complementar a lista gerada automaticamente, cruzando os resultados do WordSmith Tools e do LDA. Também indicam que a intuição linguística do analista humano sobre as listas geradas separadamente pelos dois métodos usados neste estudo foi mais favorável ao uso da lista de palavras-chave do WordSmith Tools.</p>

Examination of fake news from a viral perspective: an interplay of emotions, resonance, and sentiments

2022 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Krishnadas Nanath ◽  
Supriya Kaitheri ◽  
Sonia Malik ◽  
Shahid Mustafa
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Topic Modeling ◽  
Machine Learning Algorithms ◽  
Fake News ◽  
Linguistic Features ◽  
Data Set ◽  
Content Type

Purpose The purpose of this paper is to examine the factors that significantly affect the prediction of fake news from the virality theory perspective. The paper looks at a mix of emotion-driven content, sentimental resonance, topic modeling and linguistic features of news articles to predict the probability of fake news. Design/methodology/approach A data set of over 12,000 articles was chosen to develop a model for fake news detection. Machine learning algorithms and natural language processing techniques were used to handle big data with efficiency. Lexicon-based emotion analysis provided eight kinds of emotions used in the article text. The cluster of topics was extracted using topic modeling (five topics), while sentiment analysis provided the resonance between the title and the text. Linguistic features were added to the coding outcomes to develop a logistic regression predictive model for testing the significant variables. Other machine learning algorithms were also executed and compared. Findings The results revealed that positive emotions in a text lower the probability of news being fake. It was also found that sensational content like illegal activities and crime-related content were associated with fake news. The news title and the text exhibiting similar sentiments were found to be having lower chances of being fake. News titles with more words and content with fewer words were found to impact fake news detection significantly. Practical implications Several systems and social media platforms today are trying to implement fake news detection methods to filter the content. This research provides exciting parameters from a viral theory perspective that could help develop automated fake news detectors. Originality/value While several studies have explored fake news detection, this study uses a new perspective on viral theory. It also introduces new parameters like sentimental resonance that could help predict fake news. This study deals with an extensive data set and uses advanced natural language processing to automate the coding techniques in developing the prediction model.

scholarly journals Capturing the Patient’s Perspective: a Review of Advances in Natural Language Processing of Health-Related Text

2017 ◽  
Vol 26 (01) ◽  
pp. 214-227 ◽  
Author(s):  
G. Gonzalez-Hernandez ◽  
A. Sarker ◽  
K. O’Connor ◽  
G. Savova
Keyword(s):  
Social Media ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Data Science ◽  
Open Systems ◽  
Text Processing ◽  
Research Progress ◽  
Research Problems ◽  
Health Related

Summary Background: Natural Language Processing (NLP) methods are increasingly being utilized to mine knowledge from unstructured health-related texts. Recent advances in noisy text processing techniques are enabling researchers and medical domain experts to go beyond the information encapsulated in published texts (e.g., clinical trials and systematic reviews) and structured questionnaires, and obtain perspectives from other unstructured sources such as Electronic Health Records (EHRs) and social media posts. Objectives: To review the recently published literature discussing the application of NLP techniques for mining health-related information from EHRs and social media posts. Methods: Literature review included the research published over the last five years based on searches of PubMed, conference proceedings, and the ACM Digital Library, as well as on relevant publications referenced in papers. We particularly focused on the techniques employed on EHRs and social media data. Results: A set of 62 studies involving EHRs and 87 studies involving social media matched our criteria and were included in this paper. We present the purposes of these studies, outline the key NLP contributions, and discuss the general trends observed in the field, the current state of research, and important outstanding problems. Conclusions: Over the recent years, there has been a continuing transition from lexical and rule-based systems to learning-based approaches, because of the growth of annotated data sets and advances in data science. For EHRs, publicly available annotated data is still scarce and this acts as an obstacle to research progress. On the contrary, research on social media mining has seen a rapid growth, particularly because the large amount of unlabeled data available via this resource compensates for the uncertainty inherent to the data. Effective mechanisms to filter out noise and for mapping social media expressions to standard medical concepts are crucial and latent research problems. Shared tasks and other competitive challenges have been driving factors behind the implementation of open systems, and they are likely to play an imperative role in the development of future systems.

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