Increasing Women's Knowledge about HPV Using BERT Text Summarization: An Online Randomized Study.
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ABSTRACT:
SUBMITTER: Bitar H
PROVIDER: S-EPMC9265758 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundHumans must be able to cope with the huge amounts of information produced by the information technology revolution. As a result, automatic text summarization is being employed in a range of industries to assist individuals in identifying the most important information. For text summarization, two approaches are mainly considered: text summarization by the extractive and abstractive methods. The extractive summarisation approach selects chunks of sentences like source documents, while the abstractive approach can generate a summary based on mined keywords. For low-resourced languages, e.g., Urdu, extractive summarization uses various models and algorithms. However, the study of abstractive summarization in Urdu is still a challenging task. Because there are so many literary works in Urdu, producing abstractive summaries demands extensive research.MethodologyThis article proposed a deep learning model for the Urdu language by using the Urdu 1 Million news dataset and compared its performance with the two widely used methods based on machine learning, such as support vector machine (SVM) and logistic regression (LR). The results show that the suggested deep learning model performs better than the other two approaches. The summaries produced by extractive summaries are processed using the encoder-decoder paradigm to create an abstractive summary.ResultsWith the help of Urdu language specialists, the system-generated summaries were validated, showing the proposed model's improvement and accuracy.
| S-EPMC10280265 | biostudies-literature
Project description:Biomedical literature incorporates millions of figures, which are a rich and important knowledge resource for biomedical researchers. Scientists need access to the figures and the knowledge they represent in order to validate research findings and to generate new hypotheses. By themselves, these figures are nearly always incomprehensible to both humans and machines and their associated texts are therefore essential for full comprehension. The associated text of a figure, however, is scattered throughout its full-text article and contains redundant information content. In this paper, we report the continued development and evaluation of several figure summarization systems, the FigSum+ systems, that automatically identify associated texts, remove redundant information, and generate a text summary for every figure in an article. Using a set of 94 annotated figures selected from 19 different journals, we conducted an intrinsic evaluation of FigSum+. We evaluate the performance by precision, recall, F1, and ROUGE scores. The best FigSum+ system is based on an unsupervised method, achieving F1 score of 0.66 and ROUGE-1 score of 0.97. The annotated data is available at figshare.com (http://figshare.com/articles/Figure_Associated_Text_Summarization_and_Evaluation/858903).
| S-EPMC4313946 | biostudies-literature
Project description:Generalized language models that are pre-trained with a large corpus have achieved great performance on natural language tasks. While many pre-trained transformers for English are published, few models are available for Japanese text, especially in clinical medicine. In this work, we demonstrate the development of a clinical specific BERT model with a huge amount of Japanese clinical text and evaluate it on the NTCIR-13 MedWeb that has fake Twitter messages regarding medical concerns with eight labels. Approximately 120 million clinical texts stored at the University of Tokyo Hospital were used as our dataset. The BERT-base was pre-trained using the entire dataset and a vocabulary including 25,000 tokens. The pre-training was almost saturated at about 4 epochs, and the accuracies of Masked-LM and Next Sentence Prediction were 0.773 and 0.975, respectively. The developed BERT did not show significantly higher performance on the MedWeb task than the other BERT models that were pre-trained with Japanese Wikipedia text. The advantage of pre-training on clinical text may become apparent in more complex tasks on actual clinical text, and such an evaluation set needs to be developed.
| S-EPMC8577751 | biostudies-literature
Project description:BackgroundSedentary behavior (SB) has been linked to many health problems such as type 2 diabetes and heart disease. Increasing the length and frequency of breaks from sitting and increasing the time spent standing and engaged in light and moderate physical activity are ways to decrease SB. Text message-based interventions have succeeded in aiding smoking cessation and increase both physical activity and healthy eating, but they have not been shown to reduce SB.ObjectiveThe primary purpose of this pilot study was to determine the effectiveness of a text message-based intervention in increasing nonsedentary behaviors in university students. A secondary purpose was to (1) determine whether the intervention could enhance self-efficacy beliefs for decreasing SB and (2) whether these efficacious beliefs could predict actual SB.MethodsEighty-two university students were recruited via mass emails and randomized into intervention (SB-related text messages) or control (text messages unrelated to SB) groups. Participants received daily text messages scheduled by the researcher encouraging breaks from sitting, standing, light- and moderate-intensity physical activity (PA). They then reported various SBs via Web-based questionnaires at four time points (baseline, 2, 4, and 6 weeks). Self-efficacious beliefs toward taking breaks from sitting and decreasing the amount of time spent sitting were assessed at the same time points.ResultsLast observation carried forward (LOCF) method was used for incomplete data as an intent-to-treat (ITT) analysis (intervention group n=15, control group n=11). Small-to-moderate effects favoring the text intervention group were found at 6 weeks for break frequency -14.64 minutes, break length +.59 minutes, standing +24.30 min/day, light-intensity +74.34 min/day, and moderate-intensity + 9.97 min/day PA. Only light-intensity PA approached significance (P=.07). Self-efficacy beliefs also favored the text intervention group and reached significance (P=.032) for sitting less. Significant (P<.05) relations were found between the self-efficacy constructs and breaks, standing, and light or moderate PA.ConclusionsText messages have the potential to increase nonsedentary behaviors in university students. These messages can increase self-efficacy beliefs to take more breaks and reduce sitting time. Efficacious beliefs can predict actual SB and to a lesser extent light- and moderate-intensity PA.Trial registrationClinicalTrials.gov NCT02562937; https://clinicaltrials.gov/ct2/show/NCT02562937 (Archived by WebCite at http://www.webcitation.org/6jVLwXE5M).
| S-EPMC5010648 | biostudies-literature
Project description:BackgroundAutomatic text summarization (ATS) enables users to retrieve meaningful evidence from big data of biomedical repositories to make complex clinical decisions. Deep neural and recurrent networks outperform traditional machine-learning techniques in areas of natural language processing and computer vision; however, they are yet to be explored in the ATS domain, particularly for medical text summarization.ObjectiveTraditional approaches in ATS for biomedical text suffer from fundamental issues such as an inability to capture clinical context, quality of evidence, and purpose-driven selection of passages for the summary. We aimed to circumvent these limitations through achieving precise, succinct, and coherent information extraction from credible published biomedical resources, and to construct a simplified summary containing the most informative content that can offer a review particular to clinical needs.MethodsIn our proposed approach, we introduce a novel framework, termed Biomed-Summarizer, that provides quality-aware Patient/Problem, Intervention, Comparison, and Outcome (PICO)-based intelligent and context-enabled summarization of biomedical text. Biomed-Summarizer integrates the prognosis quality recognition model with a clinical context-aware model to locate text sequences in the body of a biomedical article for use in the final summary. First, we developed a deep neural network binary classifier for quality recognition to acquire scientifically sound studies and filter out others. Second, we developed a bidirectional long-short term memory recurrent neural network as a clinical context-aware classifier, which was trained on semantically enriched features generated using a word-embedding tokenizer for identification of meaningful sentences representing PICO text sequences. Third, we calculated the similarity between query and PICO text sequences using Jaccard similarity with semantic enrichments, where the semantic enrichments are obtained using medical ontologies. Last, we generated a representative summary from the high-scoring PICO sequences aggregated by study type, publication credibility, and freshness score.ResultsEvaluation of the prognosis quality recognition model using a large dataset of biomedical literature related to intracranial aneurysm showed an accuracy of 95.41% (2562/2686) in terms of recognizing quality articles. The clinical context-aware multiclass classifier outperformed the traditional machine-learning algorithms, including support vector machine, gradient boosted tree, linear regression, K-nearest neighbor, and naïve Bayes, by achieving 93% (16127/17341) accuracy for classifying five categories: aim, population, intervention, results, and outcome. The semantic similarity algorithm achieved a significant Pearson correlation coefficient of 0.61 (0-1 scale) on a well-known BIOSSES dataset (with 100 pair sentences) after semantic enrichment, representing an improvement of 8.9% over baseline Jaccard similarity. Finally, we found a highly positive correlation among the evaluations performed by three domain experts concerning different metrics, suggesting that the automated summarization is satisfactory.ConclusionsBy employing the proposed method Biomed-Summarizer, high accuracy in ATS was achieved, enabling seamless curation of research evidence from the biomedical literature to use for clinical decision-making.
| S-EPMC7647812 | biostudies-literature
Project description:Extraction of associations of singular nucleotide polymorphism (SNP) and phenotypes from biomedical literature is a vital task in BioNLP. Recently, some methods have been developed to extract mutation-diseases affiliations. However, no accessible method of extracting associations of SNP-phenotype from content considers their degree of certainty. In this paper, several machine learning methods were developed to extract ranked SNP-phenotype associations from biomedical abstracts and then were compared to each other. In addition, shallow machine learning methods, including random forest, logistic regression, and decision tree and two kernel-based methods like subtree and local context, a rule-based and a deep CNN-LSTM-based and two BERT-based methods were developed in this study to extract associations. Furthermore, the experiments indicated that although the used linguist features could be employed to implement a superior association extraction method outperforming the kernel-based counterparts, the used deep learning and BERT-based methods exhibited the best performance. However, the used PubMedBERT-LSTM outperformed the other developed methods among the used methods. Moreover, similar experiments were conducted to estimate the degree of certainty of the extracted association, which can be used to assess the strength of the reported association. The experiments revealed that our proposed PubMedBERT-CNN-LSTM method outperformed the sophisticated methods on the task.
| S-EPMC10099837 | biostudies-literature
Project description:Due to the massive growth of scientific publications, literature mining is becoming increasingly popular for researchers to thoroughly explore scientific text and extract such data to create new databases or augment existing databases. Efforts in literature-mining software design and implementation have improved text-mining productivity, but most of the toolkits that mine text are based on traditional machine-learning-algorithms which hinder the performance of downstream text-mining tasks. Natural-language processing (NLP) and text-mining technologies have seen a rapid development since the release of transformer models, such as bidirectional encoder representations from transformers (BERT). Upgrading rule-based or machine-learning-based literature-mining toolkits by embedding transformer models into the software is therefore likely to improve their text-mining performance. To this end, we release a Python-based literature-mining toolkit for the field of battery materials, BatteryDataExtractor, which involves the embedding of BatteryBERT models in its automated data-extraction pipeline. This pipeline employs BERT models for token-classification tasks, such as abbreviation detection, part-of-speech tagging, and chemical-named-entity recognition, as well as new double-turn question-answering data-extraction models for auto-generating repositories of inter-related material and property data as well as general information. We demonstrate that BatteryDataExtractor exhibits state-of-the-art performance on the evaluation data sets for both token classification and automated data extraction. To aid the use of BatteryDataExtractor, its code is provided as open-source software, with associated documentation to serve as a user guide.
| S-EPMC9627715 | biostudies-literature
Project description:Uptake of human papillomavirus (HPV) vaccinations by 17- to 18-year-old girls in England is below (<35%) target (80%). This trial assesses (a) the impact of financial incentives on uptake and completion of an HPV vaccination program, and (b) whether impacts are moderated by participants' deprivation level. It also assesses the impact of incentives on decision quality to get vaccinated, as measured by attitudes toward the vaccination and knowledge of its consequences.One thousand 16- to 18-year-old girls were invited to participate in an HPV vaccination program: 500 previously uninvited, and 500 unresponsive to previous invitations. Girls randomly received either a standard invitation letter or a letter including the offer of vouchers worth £ 45 (€ 56; $73) for undergoing 3 vaccinations. Girls attending their first vaccination appointment completed a questionnaire assessing decision quality to be vaccinated. Outcomes were uptake of the first and third vaccinations and decision quality.The intervention increased uptake of the first (first-time invitees: 28.4% vs. 19.6%, odds ratio [OR] = 1.63, 95% confidence interval [CI; 1.08, 2.47]; previous nonattenders: 23.6% vs. 10.4%, OR = 2.65, 95% CI [1.61, 4.38]) and third (first-time invitees: 22.4% vs. 12%, OR = 2.15, 95% CI [1.32, 3.50]; previous nonattenders: 12.4% vs. 3%, OR = 4.28, 95% CI [1.92, 9.55]) vaccinations. Impacts were not moderated by deprivation level. Decision quality was unaffected by the intervention.Although the intervention increased completion of HPV vaccinations, uptake remained lower than the national target, which, in addition to cost effectiveness and acceptability issues, necessitates consideration of other ways of achieving it.
| S-EPMC4312136 | biostudies-other
Project description:Pre-trained language models such as Bidirectional Encoder Representations from Transformers (BERT) have been applied to a wide range of natural language processing (NLP) tasks and obtained significantly positive results. A growing body of research has investigated the reason why BERT is so efficient and what language knowledge BERT is able to learn. However, most of these works focused almost exclusively on English. Few studies have explored the language information, particularly syntactic information, that BERT has learned in Chinese, which is written as sequences of characters. In this study, we adopted some probing methods for identifying syntactic knowledge stored in the attention heads and hidden states of Chinese BERT. The results suggest that some individual heads and combination of heads do well in encoding corresponding and overall syntactic relations, respectively. The hidden representation of each layer also contained syntactic information to different degrees. We also analyzed the fine-tuned models of Chinese BERT for different tasks, covering all levels. Our results suggest that these fine-turned models reflect changes in conserving language structure. These findings help explain why Chinese BERT can show such large improvements across many language-processing tasks.
| S-EPMC10403162 | biostudies-literature
Project description:ObjectiveBiomedical text summarization helps biomedical information seekers avoid information overload by reducing the length of a document while preserving the contents' essence. Our systematic review investigates the most recent biomedical text summarization researches on biomedical literature and electronic health records by analyzing their techniques, areas of application, and evaluation methods. We identify gaps and propose potential directions for future research.Materials and methodsThis review followed the PRISMA methodology and replicated the approaches adopted by the previous systematic review published on the same topic. We searched 4 databases (PubMed, ACM Digital Library, Scopus, and Web of Science) from January 1, 2013 to April 8, 2021. Two reviewers independently screened title, abstract, and full-text for all retrieved articles. The conflicts were resolved by the third reviewer. The data extraction of the included articles was in 5 dimensions: input, purpose, output, method, and evaluation.ResultsFifty-eight out of 7235 retrieved articles met the inclusion criteria. Thirty-nine systems used single-document biomedical research literature as their input, 17 systems were explicitly designed for clinical support, 47 systems generated extractive summaries, and 53 systems adopted hybrid methods combining computational linguistics, machine learning, and statistical approaches. As for the assessment, 51 studies conducted an intrinsic evaluation using predefined metrics.Discussion and conclusionThis study found that current biomedical text summarization systems have achieved good performance using hybrid methods. Studies on electronic health records summarization have been increasing compared to a previous survey. However, the majority of the works still focus on summarizing literature.
| S-EPMC8449627 | biostudies-literature