Bibliographic record
Abstract
ecies 1 s 2 ( e applied on 3 a 4 f 5 p 6 p te 7 s 8 m 9 s 10 q ecies tree 11 m 12 c 13 s 14 I introduce the software JML that tests for the presence of hybridization in multi-sp equence datasets by posterior predictive checking following Joly, McLenachan and Lockhart 2009, American Naturalist 174:e54-e70). Although their method could potentially b ny dataset, the lack of appropriate software made its application difficult. The software JML thus ills a need for an easy application of the method, but also includes improvements such as the ossibility to incorporate uncertainty in the species tree topology. The JML software uses a osterior distribution of species trees, population sizes and branch lengths to simulate replica equence datasets using the coalescent with no migration. A test quantity, defined as the inimum pairwise sequence distance between sequences of two species, is then evaluated on the imulated datasets and compared to the one estimated from the original data. Because the test uantity is a good predictor of hybridization events, departure from the bifurcating sp odel could be interpreted as evidence of hybridization. Software performance in terms of omputing time is evaluated for several parameters. I also show an application example of the oftware for detecting hybridization among native diploid North American roses.
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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 | 0.013 | 0.063 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.007 | 0.003 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.004 |
| Open science | 0.004 | 0.003 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.015 | 0.005 |
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".