Bibliographic record
Abstract
<ns3:p>As the year 2020 came to a close, several new strains have been reported of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 mutates and evolves in its human hosts. To get an appreciation for the rapid evolution of the coronavirus, we built interactive scalable vector graphics maps that show daily nucleotide variations in genomes from the six most populated continents compared to that of the initial, ground-zero SARS-CoV-2 isolate sequenced at the beginning of the pandemic.</ns3:p> <ns3:p> <ns3:bold>Availability:</ns3:bold> The tool used to perform the reported mutation analysis results, ntEdit, is available from <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://github.com/bcgsc/ntedit">GitHub</ns3:ext-link> . Genome mutation reports are available for download from <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://www.bcgsc.ca/downloads/btl/SARS-CoV-2/mutations/">BCGSC</ns3:ext-link> . Mutation time maps are available from <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://bcgsc.github.io/SARS2/">https://bcgsc.github.io/SARS2/</ns3:ext-link> . </ns3:p>
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.001 | 0.004 |
| Insufficient payload (model declined to judge) | 0.000 | 0.002 |
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 teacher head, 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".