Escape from Parsimony of a Double-Cut-and-Join Genome Evolution Process
Bibliographic record
Abstract
We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. Not only do our models allow different types of operations generated by DCJs (including reversals, translocations, transpositions, fissions, and fusions) to take different weights during the course of evolution, but they also let these weights fluctuate over time. We compare the number of operations along the evolutionary trajectory with the DCJ distance of the genome from its ancestor at each step, and determine at what point they diverge: the process escapes from parsimony. Adapting the method developed by Berestycki and Durrett, we approximate the number of cycles in the breakpoint graph of a random genome at time t and its ancestral genome by the number of tree components in a random graph (not necessarily an Erdös–Rényi one) constructed from the model of evolution. In both models, the process on a genome of size n is bound to its parsimonious estimate up to t≈n∕2 steps.
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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 | 0.003 | 0.014 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".