Classifying Cytochrome c Oxidase subunit 1 by translation initiation mechanism using side effect machines
Why this work is in the frame
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Bibliographic record
Abstract
Cytochrome c oxidase subunit 1 (cox1) is unusual among mitochondrial genes in that instead of using AUG or one of the recognized alternative start codons it often appears to use an unknown means for initiating translation. However, the frequency of this unusual behavior as well as the underlying molecular mechanism are unknown. In this paper we use side effect machines to probe for signal in the sequence. Evolved side effect machines were able to correctly classify cox1 genes with ambiguous start codons 80.1% of the time. Side effect machines are finite state machines that have side effects associated with their states. In this study a simple side effect, a counter for the number of times the state was entered, is used. The problem is found to be challenging, a substantial majority of replicates found no signal, but some classifiers with statistically significant classification ability were located.
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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 | 0.000 | 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