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The landscape of biomedical research.

Rita González-Márquez^1,2, Luca Schmidt^1,2, Benjamin M Schmidt³

¹Hertie Institute for AI in Brain Health, University of Tübingen, Germany.

Patterns (New York, N.Y.)

|July 15, 2024

Summary

Researchers created a 2D map of 21 million biomedical articles using PubMedBERT and t-SNE. This map visualizes scientific trends, including COVID-19 research and machine learning adoption, offering new insights into the life sciences literature.

Keywords:

PubMed embeddings gender bias language models machine learning metascience publications retractions visualization

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Area of Science:

Biomedical Informatics
Bibliometrics
Computational Biology

Background:

The exponential growth of biomedical publications poses challenges for tracking scientific progress and understanding field evolution.
Existing methods for analyzing large-scale scientific literature are often limited in scope and scalability.

Purpose of the Study:

To develop a comprehensive two-dimensional (2D) map of the entire biomedical literature corpus.
To enable the visualization and analysis of trends, emerging fields, and specific phenomena within scientific publications.

Main Methods:

Utilized abstracts from 21 million English articles in the PubMed database.
Employed the PubMedBERT large language model for abstract embedding.
Applied t-distributed Stochastic Neighbor Embedding (t-SNE) optimized for large datasets to generate the 2D map.

Main Results:

Successfully created a 2D map representing the vast biomedical literature.
Analyzed the emergence of COVID-19 research, the evolution of neuroscience, and the adoption of machine learning.
Investigated gender imbalance in academic authorship and the prevalence of retracted paper mill articles.

Conclusions:

The 2D map provides a novel tool for navigating and understanding the complex landscape of biomedical research.
The interactive website facilitates exploration and discovery of insights within the scientific literature.
This approach can aid researchers in identifying trends, understanding disciplinary shifts, and addressing issues like authorship and research integrity.