GenericBioMatch: A novel generic pattern match algorithm for biological sequences
Why this work is in the frame
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Bibliographic record
Abstract
GenericBioMatch is a novel algorithm for exact match in biological sequences. It allows the sequence motif pattern to contain one or more wild card letters (eg. Y, R, W in DNA sequences) and one or more gaps of any number of bases. GenericBioMatch is a relatively fast algorithm as compared to probabilistic algorithms, and has very little computational overhead. It is able to perform exact match of protein motifs as well as DNA motifs. This algorithm can serve as a quick validation tool for implementation of other algorithms, and can also serve as a supporting tool for probabilistic algorithms in order to reduce computational overhead. This algorithm has been implemented in the BioMiner software (http://iit-iti.nrc-cnrc.gc.ca/biomine e.trx), a suite of Java tools for integrated data mining in genomics. It has been tested successfully with DNA sequences from human, yeast, and Arabidopsis.
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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 | 0.001 | 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