Summarizing a Posterior Distribution of Trees Using Agreement Subtrees
Bibliographic record
Abstract
Bayesian inference of phylogeny is unique among phylogenetic reconstruction methods in that it produces a posterior distribution of trees rather than a point estimate of the best tree. The most common way to summarize this distribution is to report the majority-rule consensus tree annotated with the marginal posterior probabilities of each partition. Reporting a single tree discards information contained in the full underlying distribution and reduces the Bayesian analysis to simply another method for finding a point estimate of the tree. Even when a point estimate of the phylogeny is desired, the majority-rule consensus tree is only one possible method, and there may be others that are more appropriate for the given data set and application. We present a method for summarizing the distribution of trees that is based on identifying agreement subtrees that are frequently present in the posterior distribution. This method provides fully resolved binary trees for subsets of taxa with high marginal posterior probability on the entire tree and includes additional information about the spread of the distribution.
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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 | 0.008 | 0.042 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.005 | 0.003 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.004 | 0.004 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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".