Bibliographic record
Abstract
This chapter develops the mathematical and algorithmic techniques utilized to address gene rearrangement problems, both in their original sense as markers of inherited traits, and in their modern interpretation as families of transcripts. This chapter focuses on the rearrangement problem between representative genomes of different species. Modern genome sequencing and annotation techniques identify the position and orientation of genes on the chromosomes. The chapter addresses the problem of enumerating the set of all optimal scenarios that transform one genome into another. The basic principle can be described in terms of balanced cycles. The chapter computes the sequences of double-cut-and-join (DCJ) operations of minimum length. One way to build balanced cycles uses the dashed edges to balance an unbalanced cycle. These dashed edges make it possible to model the fact that a DCJ operation can change the number of chromosomes, and as such, the number of telomeres in a genome, while maintaining the same gene content.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.002 | 0.008 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.003 | 0.009 |
| Scholarly communication | 0.005 | 0.011 |
| Open science | 0.001 | 0.004 |
| Research integrity | 0.002 | 0.005 |
| Insufficient payload (model declined to judge) | 0.015 | 0.004 |
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".