COMPUTING THE BREAKPOINT DISTANCE BETWEEN PARTIALLY ORDERED GENOMES
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Bibliographic record
Abstract
The total order of genes or markers on a chromosome is crucial for most comparative genomics studies. However, current gene mapping efforts might only suffice to provide a partial order of the genes on a chromosome. Several different genes or markers might be mapped at the same position due to the low resolution of gene mapping or missing data. Moreover, conflicting datasets might give rise to the ambiguity of gene order. In this paper, we consider the reversal distance and breakpoint distance problems for partially ordered genomes. We first prove that these problems are nondeterministic polynomial-time (NP)-hard, and then give an efficient heuristic algorithm to compute the breakpoint distance between partially ordered genomes. The algorithm is based on an efficient approximation algorithm for a natural generalization of the well-known feedback vertex set problem, and has been tested on both simulated and real biological datasets. The experimental results demonstrate that our algorithm is quite effective for estimating the breakpoint distance between partially ordered genomes and for inferring the gene (total) order.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 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) | 0.000 | 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 it