Bibliographic record
Abstract
Changes [feat] output the VCF with re-merged split variants used for consensus sequence construction. Fixed [fix] divide by zero in awk code in BCFTOOLS_FILTER when FDP is 0. [fix] the GT set after merging of split alleles so that it's the proper GT. bcftools norm -m +any may set an inappropriate GT for multiallelic sites where the ALT alleles are only considered even when the AF is less than major AF and the REF allele should also be represented in the consensus. What's Changed Release 2.1.1 patch bugfix BCFTOOLS_FILTER awk divide by zero on FDP=0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/7 Full Changelog: https://github.com/CFIA-NCFAD/nf-ionampliseq/compare/2.1.0...2.1.1
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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 | 0.005 | 0.025 |
| Meta-epidemiology (narrow) | 0.006 | 0.005 |
| Meta-epidemiology (broad) | 0.003 | 0.004 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.005 | 0.006 |
| Open science | 0.009 | 0.006 |
| Research integrity | 0.005 | 0.006 |
| Insufficient payload (model declined to judge) | 0.396 | 0.493 |
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".