ArticleAMIA ... Annual Symposium proceedings. AMIA Symposium2024
Publication Type Tagging using Transformer Models and Multi-Label Classification.
Article in AMIA ... Annual Symposium proceedings. AMIA Symposium, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed.
- Thematic Mapping and Evolution of Social Media Mining in Health Research: Hybrid Bibliometric Synthesis.Journal of medical Internet research · 2026Review
- Creating an indexing scheme for case series articles.BMC medical research methodology · 2026Article
- A Similarity Metric, Rubric and Unified Hierarchy for Biomedical Publication Types and Study Designs.medRxiv : the preprint server for health sciences · 2026Article
- A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs.Database : the journal of biological databases and curation · 2026Article
- Goals and strategies for the indexing of publication types and study designs.Database : the journal of biological databases and curation · 2026Article
- Creating an Indexing Scheme for Case Series Articles.medRxiv : the preprint server for health sciences · 2025Article
- StudyTypeTeller-Large language models to automatically classify research study types for systematic reviews.Research synthesis methods · 2025Article
- Enhancing automated indexing of publication types and study designs in biomedical literature using full-text features.medRxiv : the preprint server for health sciences · 2025Article
- Issues regarding the Indexing of Adaptive Clinical Trial Articles.medRxiv : the preprint server for health sciences · 2025Article
- Article
Corrections and comments
- Update of
Authors and funding
3 authors.
Funding
Abstract
Indexing articles by their publication type and study design is essential for efficient search and filtering of the biomedical literature, but is understudied compared to indexing by MeSH topical terms. In this study, we leveraged the human-curated publication types and study designs in PubMed to generate a dataset of more than 1.2M articles (titles and abstracts) and used state-of-the-art Transformer-based models for automatic tagging of publication types and study designs. Specifically, we trained PubMedBERT-based models using a multi-label classification approach, and explored undersampling, feature verbalization, and contrastive learning to improve model performance. Our results show that PubMedBERT provides a strong baseline for publication type and study design indexing; undersampling, feature verbalization, and unsupervised constrastive loss have a positive impact on performance, whereas supervised contrastive learning degrades the performance. We obtained the best overall performance with 80% undersampling and feature verbalization (0.632 macro-F1, 0.969 macro-AUC). The model outperformed previous models (MultiTagger) across all metrics and the performance difference was statistically significant (
Indexed as
Identifiers
40417522PMC12099436What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.