When Does Additional Information Improve Accuracy of RNA Secondary Structure Prediction?
Bibliographic record
Abstract
The secondary structure of an RNA sequence plays an important role in determining its function, and accurate prediction of the structure is still a major goal in computational biology. Improvements in the prediction accuracy of the secondary structure can be achieved via auxiliary information. In this paper, we study features based on suboptimal formations competing with the minimum-free energy formation and investigate their role in determining the improvement of accuracy via auxiliary information, which we call directability. Here, we introduce a similarity measure among competing substructures called profiles. Then, we present an n -dimensional representation of the profiles which allows the use of topological data analysis (i.e., persistence landscapes) to obtain different metrics that represent topological features. Then, we built random forest classifiers using these novel features. We show how the similarity feature is more important for classifiers trained on sequences with similar structures while the topological features are more important for classifiers trained on sequences with dissimilar structures. We perform extensive testing on two sets of RNA sequences where we studied the sensitivity of the classification accuracy and their feature importance.
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How this classification was reachedexpand
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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, 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".