Prediction of the Number of Helices for the Twilight Zone Proteins
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Bibliographic record
Abstract
Protein structure prediction is one of the core research areas in bioinformatics. This paper addresses the protein secondary structure prediction problem for the twilight zone proteins, which are characterized by low, about 25% homology to the sets of known sequences. The commonly used sequence alignment based algorithms fail to provide accurate prediction for sequences of such low homology, and thus alternative solutions should be sought. We propose a novel method that aims at the prediction of the number of helical structures based on the twilight zone protein sequences. The method is based on a custom designed and compact feature based sequences representation and applies a decision tree prediction algorithm. The performed experimental study shows superiority of the proposed method over three other prediction algorithms and the results provided by YASPIN algorithm, which is a state-of-the-art alignment based secondary structure prediction method designed using low homology sequences
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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