Bibliographic record
Abstract
This release adds CSFV consensus sequence quality control with enhanced MultiQC reporting and fixes the low_coverage parameter default value mismatch. Added [feat] CSFV consensus sequence QC with bin/qc_csfv_fasta.py to determine quality of consensus sequence. Report is also added to MultiQC report. Changes [config] Adjusted MultiQC report general statistics table column visibility, name and order in assets/multiqc_config.yaml. [config] low_coverage param in ./nextflow.config set to 10 by default from 1 matching ./nextflow_schema.json. [docs] Updated docs/output.md What's Changed Add CSFV consensus sequence QC by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/8 Release 2.2.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/9 Full Changelog: https://github.com/CFIA-NCFAD/nf-ionampliseq/compare/2.1.1...2.2.0
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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 | 0.009 | 0.025 |
| Meta-epidemiology (narrow) | 0.004 | 0.005 |
| Meta-epidemiology (broad) | 0.003 | 0.003 |
| Bibliometrics | 0.005 | 0.004 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.007 | 0.005 |
| Open science | 0.007 | 0.005 |
| Research integrity | 0.004 | 0.006 |
| Insufficient payload (model declined to judge) | 0.360 | 0.450 |
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".