SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes
Bibliographic record
Abstract
Genome Canada CanCOGeN Fund (to A.G.M., S.M.); McMaster University COVID-19 Research Fund (to A.G.M.); Canadian Institutes of Health Research (to A.G.M., S.M., K.M.); Natural Sciences and Engineering Research Council of Canada (to A.B., K.M.); McMaster Biochemistry & Biomedical Sciences Fred & Helen Knight Enrichment Award (to J.A.N.); McMaster University Dr. Jordon Page Harshman Bursary (to J.A.N.); Donald Hill Family Fellowship in Computer Science (to F.M.); McMaster University Michael G. DeGroote Institute for Infectious Disease Research Michael Kamin Hart Memorial Scholarship (to E.M.P.); University of Toronto McLaughlin Centre (to S.M., R.A.K.), University of Toronto COVID-19 Action Initiative (to S.M., R.A.K). Funding for open access charge: McMaster University COVID-19 Research Fund (to A.G.M.).
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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 | 0.004 | 0.004 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.004 |
| Insufficient payload (model declined to judge) | 0.059 | 0.053 |
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".