A quarter of household pairs share more iSNVs than random expected by chance.
Bibliographic record
Abstract
<p><b>a.</b> We modeled the probability that 2 consensus genomes will share x mutations as Poisson-distributed with lambda equal to the number of mutations expected to accumulate in the SARS-CoV-2 genome over 5.8 days [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1009849#ppat.1009849.ref037" target="_blank">37</a>] given a substitution rate of 1.10 x 10<sup>−3</sup> substitutions per site per year [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1009849#ppat.1009849.ref001" target="_blank">1</a>]. Exploration of how these probabilities change using a range of plausible serial intervals and substitution rates is shown in <b><a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1009849#ppat.1009849.s008" target="_blank">S8 Fig</a>.</b> The vast majority of genomes that are separated by one serial interval are expected to differ by ≤2 consensus mutations. <b>b.</b> The proportion of random pairs (grey) and putative household transmission pairs (purple) is shown on the y-axis vs. the proportion of iSNVs shared. The dotted line indicates the 95th percentile among the random pairs. Household pairs that share a greater proportion of iSNVs than 95% of random pairs (i.e., are plotted to the right of the dotted line) are considered statistically significant at p = 0.05. iSNVs had to be present at a frequency of ≥3% to be considered in this analysis. <b>c.</b> We assessed the impact of household membership, clade membership, phylogenetic divergence, and geographic distance on the proportion of iSNVs shared between each pair of samples in our dataset. The mean of each estimated coefficient in the combined linear regression model including all predictors is shown on the x-axis, with lines of spread indicating the range of the estimated 95% highest posterior density interval (HPDI).</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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.527 | 0.000 |
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".