Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'.
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ABSTRACT:
SUBMITTER: Neveol A
PROVIDER: S-EPMC2765257 | biostudies-literature | 2009 Oct
REPOSITORIES: biostudies-literature
Publications
Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'.
Névéol Aurélie A Mork James G JG Aronson Alan R AR
Bioinformatics (Oxford, England) 20090811 20
Similar Datasets
Project description:Document classification is an important component of natural language processing, with applications that include sentiment analysis, content recommendation, and information retrieval. This article investigates the potential of Large Language Model Meta AI (LLaMA2), a cutting-edge language model, to enhance document classification in English. Our experiments show that LLaMA2 outperforms traditional classification methods, achieving higher precision and recall values on the WOS-5736 dataset. Additionally, we analyze the interpretability of LLaMA2's classification process to reveal the most pertinent features for categorization and the model's decision-making. These results emphasize the potential of advanced language models to enhance classification outcomes and provide a more profound comprehension of document structures, thereby contributing to the advancement of natural language processing methodologies.
| S-EPMC11888901 | biostudies-literature
Project description:Recently, Temporal Information Retrieval (TIR) has grabbed the major attention of the information retrieval community. TIR exploits the temporal dynamics in the information retrieval process and harnesses both textual relevance and temporal relevance to fulfill the temporal information requirements of a user Ur Rehman Khan et al., 2018. The focus time of document is an important temporal aspect which is defined as the time to which the content of the document refers Jatowt et al., 2015; Jatowt et al., 2013; Morbidoni et al., 2018, Khan et al., 2018. To the best of our knowledge, there does not exist any standard benchmark data set (publicly available) that holds the potential to comprehensively evaluate the performance of focus time assessment strategies. Considering these aspects, we have produced the Event-dataset, which is comprised of 35 queries and set of news articles for each query. Such that, C={Qs,Ds}, where C represents the dataset, Qs is query set Qs={q1,q2,q3,…….,q35} and for each qi there is a set of news articles qi={dr,dnr} . dr,dnr are sets of relevant documents and non-relevant documents respectively. Each query in the dataset represents a popular event. To annotate these articles into relevant and non-relevant, we have employed a user-study based evaluation method wherein a group of postgraduate students manually annotate the articles into the aforementioned categories. We believe that the generation of such dataset can provide an opportunity for the information retrieval researchers to use it as a benchmark to evaluate focus time assessment methods specifically and information retrieval methods generically.
| S-EPMC6554222 | biostudies-literature
Project description:Chinese hamster ovary (CHO) cells are widely used for mass production of therapeutic proteins in the pharmaceutical industry. With the growing need in optimizing the performance of producer CHO cell lines, research on CHO cell line development and bioprocess continues to increase in recent decades. Bibliographic mapping and classification of relevant research studies will be essential for identifying research gaps and trends in literature. To qualitatively and quantitatively understand the CHO literature, we have conducted topic modeling using a CHO bioprocess bibliome manually compiled in 2016, and compared the topics uncovered by the Latent Dirichlet Allocation (LDA) models with the human labels of the CHO bibliome. The results show a significant overlap between the manually selected categories and computationally generated topics, and reveal the machine-generated topic-specific characteristics. To identify relevant CHO bioprocessing papers from new scientific literature, we have developed supervized models using Logistic Regression to identify specific article topics and evaluated the results using three CHO bibliome datasets, Bioprocessing set, Glycosylation set, and Phenotype set. The use of top terms as features supports the explainability of document classification results to yield insights on new CHO bioprocessing papers.
| S-EPMC10079098 | biostudies-literature
Project description:With the exponential growth in the daily publication of scientific articles, automatic classification and categorization can assist in assigning articles to a predefined category. Article titles are concise descriptions of the articles' content with valuable information that can be useful in document classification and categorization. However, shortness, data sparseness, limited word occurrences, and the inadequate contextual information of scientific document titles hinder the direct application of conventional text mining and machine learning algorithms on these short texts, making their classification a challenging task. This study firstly explores the performance of our earlier study, TextNetTopics on the short text. Secondly, here we propose an advanced version called TextNetTopics Pro, which is a novel short-text classification framework that utilizes a promising combination of lexical features organized in topics of words and topic distribution extracted by a topic model to alleviate the data-sparseness problem when classifying short texts. We evaluate our proposed approach using nine state-of-the-art short-text topic models on two publicly available datasets of scientific article titles as short-text documents. The first dataset is related to the Biomedical field, and the other one is related to Computer Science publications. Additionally, we comparatively evaluate the predictive performance of the models generated with and without using the abstracts. Finally, we demonstrate the robustness and effectiveness of the proposed approach in handling the imbalanced data, particularly in the classification of Drug-Induced Liver Injury articles as part of the CAMDA challenge. Taking advantage of the semantic information detected by topic models proved to be a reliable way to improve the overall performance of ML classifiers.
| S-EPMC10585361 | biostudies-literature
Project description: Not available
| S-EPMC10513235 | biostudies-literature
Project description:UnlabelledGeneReporter is a web tool that reports functional information and relevant literature on a protein-coding sequence of interest. Its purpose is to support both manual genome annotation and document retrieval. PubMed references corresponding to a sequence are detected by the extraction of query words from UniProt entries of homologous sequences. Data on protein families, domains, potential cofactors, structure, function, cellular localization, metabolic contribution and corresponding DNA binding sites complement the information on a given gene product of interest.Availability and implementationGeneReporter is available at http://www.genereporter.tu-bs.de. The web site integrates databases and analysis tools as SOAP-based web services from the EBI (European Bioinformatics Institute) and NCBI (National Center for Biotechnology Information).
| S-EPMC3065684 | biostudies-literature
Project description:BackgroundThe validity and reliability of longitudinal research is highly dependent on the recruitment and retention of representative samples. Various strategies have been developed and tested for improving recruitment and follow-up rates into health-behavioural research, but few have examined the role of linguistic choices and study document readability on participation rates. This study examined the impact of one small text change, assigning an inappropriate or grade-8 reading level password for intervention access, on participation rates and attrition in an online alcohol intervention trial.MethodsParticipants were recruited into an online alcohol intervention study using Amazon's Mechanical Turk via a multi-step recruitment process which required participants to log into a study portal using a pre-assigned password. Passwords were qualitatively coded as grade-8 and/or inappropriate for use within a professional setting. Separate logistic regressions examined which demographic, clinical characteristics, and password categorizations were most strongly associated with recruitment rates and follow-up completions.ResultsInappropriate passwords were a barrier for recruitment among participants with post-secondary education as compared to those with less education (p = 0.044), while grade-8 passwords appeared to significantly facilitate the completion of 6-month follow-ups (p = 0.005).ConclusionsAltogether, these findings suggest that some linguistic choices may play an important role in recruitment, while others, such as readability, may have longer-term effects on follow-up rates and attrition. Possible explanations for the findings, as well as, sample selection biases during recruitment and follow-up are discussed. Limitations of the study are stated and recommendations for researchers are provided.Trial registrationClinicalTrials.gov NCT02977026. Registered 27 Nov 2016.
| S-EPMC6926325 | biostudies-literature
Project description:BackgroundDocument classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature.ResultsWe present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.ConclusionWe have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept.
| S-EPMC1559726 | biostudies-literature
Project description:BackgroundPatient education materials given to breast cancer survivors may not be a good fit for their information needs. Needs may change over time, be forgotten, or be misreported, for a variety of reasons. An automated content analysis of survivors' postings to online health forums can identify expressed information needs over a span of time and be repeated regularly at low cost. Identifying these unmet needs can guide improvements to existing education materials and the creation of new resources.ObjectiveThe primary goals of this project are to assess the unmet information needs of breast cancer survivors from their own perspectives and to identify gaps between information needs and current education materials.MethodsThis approach employs computational methods for content modeling and supervised text classification to data from online health forums to identify explicit and implicit requests for health-related information. Potential gaps between needs and education materials are identified using techniques from information retrieval.ResultsWe provide a new taxonomy for the classification of sentences in online health forum data. 260 postings from two online health forums were selected, yielding 4179 sentences for coding. After annotation of data and training alternative one-versus-others classifiers, a random forest-based approach achieved F1 scores from 66% (Other, dataset2) to 90% (Medical, dataset1) on the primary information types. 136 expressions of need were used to generate queries to indexed education materials. Upon examination of the best two pages retrieved for each query, 12% (17/136) of queries were found to have relevant content by all coders, and 33% (45/136) were judged to have relevant content by at least one.ConclusionsText from online health forums can be analyzed effectively using automated methods. Our analysis confirms that breast cancer survivors have many information needs that are not covered by the written documents they typically receive, as our results suggest that at most a third of breast cancer survivors' questions would be addressed by the materials currently provided to them.
| S-EPMC5974460 | biostudies-literature
Project description:BackgroundBehavioral interventions such as psychotherapy are leading, evidence-based practices for a variety of problems (e.g., substance abuse), but the evaluation of provider fidelity to behavioral interventions is limited by the need for human judgment. The current study evaluated the accuracy of statistical text classification in replicating human-based judgments of provider fidelity in one specific psychotherapy--motivational interviewing (MI).MethodParticipants (n = 148) came from five previously conducted randomized trials and were either primary care patients at a safety-net hospital or university students. To be eligible for the original studies, participants met criteria for either problematic drug or alcohol use. All participants received a type of brief motivational interview, an evidence-based intervention for alcohol and substance use disorders. The Motivational Interviewing Skills Code is a standard measure of MI provider fidelity based on human ratings that was used to evaluate all therapy sessions. A text classification approach called a labeled topic model was used to learn associations between human-based fidelity ratings and MI session transcripts. It was then used to generate codes for new sessions. The primary comparison was the accuracy of model-based codes with human-based codes.ResultsReceiver operating characteristic (ROC) analyses of model-based codes showed reasonably strong sensitivity and specificity with those from human raters (range of area under ROC curve (AUC) scores: 0.62 - 0.81; average AUC: 0.72). Agreement with human raters was evaluated based on talk turns as well as code tallies for an entire session. Generated codes had higher reliability with human codes for session tallies and also varied strongly by individual code.ConclusionTo scale up the evaluation of behavioral interventions, technological solutions will be required. The current study demonstrated preliminary, encouraging findings regarding the utility of statistical text classification in bridging this methodological gap.
| S-EPMC4026152 | biostudies-literature