Mining the neuroimaging literature
Bibliographic record
Abstract
Automated analysis of the biomedical literature ( literature mining ) offers a rich source of insights. However, such analysis requires collecting a large number of articles and extracting and processing their content. This task is often prohibitively difficult and time-consuming. Here, we provide tools to easily collect, process, and annotate the biomedical literature. In particular, https://neuroquery.github.io/pubget/pubget.html is an efficient and reliable command-line tool for downloading articles in bulk from PubMed Central, extracting their contents and metadata into convenient formats, and extracting and analyzing information such as stereotactic brain coordinates. https://jeromedockes.github.io/labelbuddy/labelbuddy/current/ is a lightweight local application for annotating text, which facilitates the extraction of complex information or the creation of ground-truth labels to validate automated information extraction methods. Further, we describe repositories where researchers can share their analysis code and their manual annotations in a format that facilitates reuse. These resources can help streamline text mining and meta-science projects and make text mining of the biomedical literature more accessible, effective, and reproducible. We describe a typical workflow based on these tools and illustrate it with several example projects.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.007 | 0.041 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.058 | 0.027 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.004 | 0.004 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.012 | 0.008 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".