BIDSonym - a BIDSapp for the pseudo-anonymization of neuroimaging datasets
Bibliographic record
Abstract
This release includes a variety of bug fixes and JOSS review process Concerning bug fixes an argument swap in the copy_no_deid function was corrected, plotting functions were adapted (wrt T2w defacing and main plotting function and mridefacer problems solved. Regarding the JOSS review process, multiple sections of the documentation were extended and several typos were fixed. A new section displaying a usage example was added to help interested users and allow software testing. As this uses an open non-deidentified dataset, the example data was removed. Additionally, the Singularity image was dropped due to recent developments around Singularity hub and adapted to suggest obtaining a Singularity image through a direct download from Dockerhub.
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 | 0.015 | 0.076 |
| Meta-epidemiology (narrow) | 0.002 | 0.003 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.005 | 0.004 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.007 | 0.006 |
| Open science | 0.003 | 0.010 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.369 | 0.332 |
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".