Pregex: Rule-Based Detection and Extraction of Twitter Data in Pregnancy.
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ABSTRACT:
SUBMITTER: Klein AZ
PROVIDER: S-EPMC9951068 | biostudies-literature | 2023 Feb
REPOSITORIES: biostudies-literature
Publications
Pregex: Rule-Based Detection and Extraction of Twitter Data in Pregnancy.
Klein Ari Z AZ Kunatharaju Shriya S O'Connor Karen K Gonzalez-Hernandez Graciela G
Journal of medical Internet research 20230209
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Project description:BackgroundAlthough birth defects are the leading cause of infant mortality in the United States, methods for observing human pregnancies with birth defect outcomes are limited.ObjectiveThe primary objectives of this study were (i) to assess whether rare health-related events-in this case, birth defects-are reported on social media, (ii) to design and deploy a natural language processing (NLP) approach for collecting such sparse data from social media, and (iii) to utilize the collected data to discover a cohort of women whose pregnancies with birth defect outcomes could be observed on social media for epidemiological analysis.MethodsTo assess whether birth defects are mentioned on social media, we mined 432 million tweets posted by 112,647 users who were automatically identified via their public announcements of pregnancy on Twitter. To retrieve tweets that mention birth defects, we developed a rule-based, bootstrapping approach, which relies on a lexicon, lexical variants generated from the lexicon entries, regular expressions, post-processing, and manual analysis guided by distributional properties. To identify users whose pregnancies with birth defect outcomes could be observed for epidemiological analysis, inclusion criteria were (i) tweets indicating that the user's child has a birth defect, and (ii) accessibility to the user's tweets during pregnancy. We conducted a semi-automatic evaluation to estimate the recall of the tweet-collection approach, and performed a preliminary assessment of the prevalence of selected birth defects among the pregnancy cohort derived from Twitter.ResultsWe manually annotated 16,822 retrieved tweets, distinguishing tweets indicating that the user's child has a birth defect (true positives) from tweets that merely mention birth defects (false positives). Inter-annotator agreement was substantial: κ = 0.79 (Cohen's kappa). Analyzing the timelines of the 646 users whose tweets were true positives resulted in the discovery of 195 users that met the inclusion criteria. Congenital heart defects are the most common type of birth defect reported on Twitter, consistent with findings in the general population. Based on an evaluation of 4169 tweets retrieved using alternative text mining methods, the recall of the tweet-collection approach was 0.95.ConclusionsOur contributions include (i) evidence that rare health-related events are indeed reported on Twitter, (ii) a generalizable, systematic NLP approach for collecting sparse tweets, (iii) a semi-automatic method to identify undetected tweets (false negatives), and (iv) a collection of publicly available tweets by pregnant users with birth defect outcomes, which could be used for future epidemiological analysis. In future work, the annotated tweets could be used to train machine learning algorithms to automatically identify users reporting birth defect outcomes, enabling the large-scale use of social media mining as a complementary method for such epidemiological research.
| S-EPMC6295660 | biostudies-literature
Project description:Digital fraud has immensely affected ordinary consumers and the finance industry. Our dependence on internet banking has made digital fraud a substantial problem. Financial institutions across the globe are trying to improve their digital fraud detection and deterrence capabilities. Fraud detection is a reactive process, and it usually incurs a cost to save the system from an ongoing malicious activity. Fraud deterrence is the capability of a system to withstand any fraudulent attempts. Fraud deterrence is a challenging task and researchers across the globe are proposing new solutions to improve deterrence capabilities. In this work, we focus on the very important problem of fraud deterrence. Our proposed work uses an Intimation Rule Based (IRB) alert generation algorithm. These IRB alerts are classified based on severity levels. Our proposed solution uses a richer domain knowledge base and rule-based reasoning. In this work, we propose an ontology-based financial fraud detection and deterrence model.
| S-EPMC8356649 | biostudies-literature
Project description:BackgroundThe use of classification algorithms is becoming increasingly important for the field of computational biology. However, not only the quality of the classification, but also its biological interpretation is important. This interpretation may be eased if interacting elements can be identified and visualized, something that requires appropriate tools and methods.ResultsWe developed a new approach to detecting interactions in complex systems based on classification. Using rule-based classifiers, we previously proposed a rule network visualization strategy that may be applied as a heuristic for finding interactions. We now complement this work with Ciruvis, a web-based tool for the construction of rule networks from classifiers made of IF-THEN rules. Simulated and biological data served as an illustration of how the tool may be used to visualize and interpret classifiers. Furthermore, we used the rule networks to identify feature interactions, compared them to alternative methods, and computationally validated the findings.ConclusionsRule networks enable a fast method for model visualization and provide an exploratory heuristic to interaction detection. The tool is made freely available on the web and may thus be used to aid and improve rule-based classification.
| S-EPMC4030460 | biostudies-literature
Project description:Despite the prevalence in the United States of miscarriage [1], stillbirth [2], and infant mortality associated with preterm birth and low birthweight [3], their causes remain largely unknown [4], [5], [6]. To advance the use of social media data as a complementary resource for epidemiology of adverse pregnancy outcomes, we present a data set of 6487 tweets that mention miscarriage, stillbirth, preterm birth or premature labor, low birthweight, neonatal intensive care, or fetal/infant loss in general. These tweets are a subset of 22,912 tweets retrieved by applying hand-written regular expressions to a database containing more than 400 million public tweets posted by more than 100,000 women who have announced their pregnancy on Twitter [7]. Two professional annotators labeled the 6487 tweets in a binary fashion, distinguishing those potentially reporting that the user has personally experienced the outcome ("outcome" tweets) from those that merely mention the outcome ("non-outcome" tweets). Inter-annotator agreement was κ = 0.90 (Cohen's kappa). The tweets annotated as "outcome" include 1318 women reporting miscarriage, 94 stillbirth, 591 preterm birth or premature labor, 171 low birthweight, 453 neonatal intensive care, and 356 fetal/infant loss in general. These "outcome" tweets can be used to explore patient experiences and perceptions of adverse pregnancy outcomes, and can direct researchers to the users' broader timelines-tweets posted by a user over time-for observational studies. Our past work demonstrates the analysis of timelines for selecting a study population [8] and conducting a case-control study [9] of users reporting that their child has a birth defect. For larger-scale studies, the full annotated corpus can be used to train supervised machine learning algorithms to automatically identify additional users reporting adverse pregnancy outcomes on Twitter. We used the annotated corpus to train feature-engineered and deep learning-based classifiers presented in "A natural language processing pipeline to advance the use of Twitter data for digital epidemiology of adverse pregnancy outcomes" [10].
| S-EPMC7481818 | biostudies-literature
Project description: Not available
| S-EPMC11041470 | biostudies-literature
Project description:ObjectiveIn the i2b2 Medication Extraction Challenge, medication names together with details of their administration were to be extracted from medical discharge summaries.DesignThe task of the challenge was decomposed into three pipelined components: named entity identification, context-aware filtering and relation extraction. For named entity identification, first a rule-based (RB) method that was used in our overall fifth place-ranked solution at the challenge was investigated. Second, a conditional random fields (CRF) approach is presented for named entity identification (NEI) developed after the completion of the challenge. The CRF models are trained on the 17 ground truth documents, the output of the rule-based NEI component on all documents, a larger but potentially inaccurate training dataset. For both NEI approaches their effect on relation extraction performance was investigated. The filtering and relation extraction components are both rule-based.MeasurementsIn addition to the official entry level evaluation of the challenge, entity level analysis is also provided.ResultsOn the test data an entry level F(1)-score of 80% was achieved for exact matching and 81% for inexact matching with the RB-NEI component. The CRF produces a significantly weaker result, but CRF outperforms the rule-based model with 81% exact and 82% inexact F(1)-score (p<0.02).ConclusionThis study shows that a simple rule-based method is on a par with more complicated machine learners; CRF models can benefit from the addition of the potentially inaccurate training data, when only very few training documents are available. Such training data could be generated using the outputs of rule-based methods.
| S-EPMC2995683 | biostudies-literature
Project description:BackgroundScholars have used data from in-person interviews, administrative systems, and surveys for sexual violence research. Using Twitter as a data source for examining the nature of sexual violence is a relatively new and underexplored area of study.ObjectiveWe aimed to perform a scoping review of the current literature on using Twitter data for researching sexual violence, elaborate on the validity of the methods, and discuss the implications and limitations of existing studies.MethodsWe performed a literature search in the following 6 databases: APA PsycInfo (Ovid), Scopus, PubMed, International Bibliography of Social Sciences (ProQuest), Criminal Justice Abstracts (EBSCO), and Communications Abstracts (EBSCO), in April 2022. The initial search identified 3759 articles that were imported into Covidence. Seven independent reviewers screened these articles following 2 steps: (1) title and abstract screening, and (2) full-text screening. The inclusion criteria were as follows: (1) empirical research, (2) focus on sexual violence, (3) analysis of Twitter data (ie, tweets or Twitter metadata), and (4) text in English. Finally, we selected 121 articles that met the inclusion criteria and coded these articles.ResultsWe coded and presented the 121 articles using Twitter-based data for sexual violence research. About 70% (89/121, 73.6%) of the articles were published in peer-reviewed journals after 2018. The reviewed articles collectively analyzed about 79.6 million tweets. The primary approaches to using Twitter as a data source were content text analysis (112/121, 92.5%) and sentiment analysis (31/121, 25.6%). Hashtags (103/121, 85.1%) were the most prominent metadata feature, followed by tweet time and date, retweets, replies, URLs, and geotags. More than a third of the articles (51/121, 42.1%) used the application programming interface to collect Twitter data. Data analyses included qualitative thematic analysis, machine learning (eg, sentiment analysis, supervised machine learning, unsupervised machine learning, and social network analysis), and quantitative analysis. Only 10.7% (13/121) of the studies discussed ethical considerations.ConclusionsWe described the current state of using Twitter data for sexual violence research, developed a new taxonomy describing Twitter as a data source, and evaluated the methodologies. Research recommendations include the following: development of methods for data collection and analysis, in-depth discussions about ethical norms, exploration of specific aspects of sexual violence on Twitter, examination of tweets in multiple languages, and decontextualization of Twitter data. This review demonstrates the potential of using Twitter data in sexual violence research.
| S-EPMC10227696 | biostudies-literature
Project description:ObjectiveThe metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases.Materials and methodsWe developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus.ResultsWe found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively.DiscussionOur system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction.ConclusionOur system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles.
| S-EPMC4997033 | biostudies-literature
Project description:This paper presents a bibliographic analysis of Nature articles based on altmetrics. We assess the concern degree of social users on the Nature articles through the coverage analysis of Twitter and Facebook by publication year and discipline. The social media impact of a Nature article is examined by evaluating the mention rates on Twitter and on Facebook. Moreover, the correlation between tweets and citations is analyzed by publication year, discipline and Twitter user type to explore factors affecting the correlation. The results show that Twitter users have a higher concern degree on Nature articles than Facebook users, and Nature articles have higher and faster-growing impact on Twitter than on Facebook. The results also show that tweets and citations are somewhat related, and they mostly measure different types of impact. In addition, the correlation between tweets and citations highly depends on publication year, discipline and Twitter user type.
| S-EPMC5132397 | biostudies-literature
Project description:Incidental learning plays a crucial role in the initial phases of language acquisition. However the knowledge derived from implicit learning, which is based on prediction-based mechanisms, may become explicit. The role that attention plays in the formation of implicit and explicit knowledge of the learned material is unclear. In the present study, we investigated the role that attention plays in the acquisition of non-adjacent rule learning from speech. In addition, we also tested whether the amount of attention during learning changes the representation of the learned material after a 24h delay containing sleep. For that, we developed an experiment run on two consecutive days consisting on the exposure to an artificial language that contained non-adjacent dependencies (rules) between words whereas different conditions were established to manipulate the amount of attention given to the rules (target and non-target conditions). Furthermore, we used both indirect and direct measures of learning that are more sensitive to implicit and explicit knowledge, respectively. Whereas the indirect measures indicated that learning of the rules occurred regardless of attention, more explicit judgments after learning showed differences in the type of learning reached under the two attention conditions. 24 hours later, indirect measures showed no further improvements during additional language exposure and explicit judgments indicated that only the information more robustly learned in the previous day, was consolidated.
| S-EPMC4869066 | biostudies-literature