Peer Review #2 of "Prioritizing bona fide bacterial small RNAs with machine learning classifiers (v0.2)"
Bibliographic record
Abstract
Bacterial small (sRNAs) are involved in the control of several cellular processes.Hundreds of putative sRNAs have been identified in many bacterial species through RNA sequencing.The existence of putative sRNAs is usually validated by Northern blot analysis.However, the large amount of novel putative sRNAs reported in the literature makes it impractical to validate each of them in the wet lab.In this work, we applied five machine learning approaches to construct twenty models to discriminate bona fide sRNAs from random genomic sequences in five bacterial species.Sequences were represented using seven features including free energy of their predicted secondary structure, their distances to the closest predicted promoter site and Rho-independent terminator, and their distance to the closest open reading frames (ORFs).To automatically calculate these features, we developed an sRNA Characterization Pipeline (sRNACharP).All seven features used in the classification task contributed positively to the performance of the predictive models.The best performing model obtained a median precision of 100% at 10% recall and of 64% at 40% recall across all five bacterial species, and it outperformed previous published approaches on two benchmark datasets in terms of precision and recall.Our results indicate that even though there is limited sRNA sequence conservation across different bacterial species, there are intrinsic features in the genomic context of sRNAs that are conserved across taxa.We show that these features are utilized by machine learning approaches to learn a species-independent model to prioritize bona fide bacterial sRNAs.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.011 | 0.079 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.006 | 0.003 |
| Science and technology studies | 0.005 | 0.001 |
| Scholarly communication | 0.011 | 0.005 |
| Open science | 0.004 | 0.007 |
| Research integrity | 0.004 | 0.003 |
| Insufficient payload (model declined to judge) | 0.438 | 0.306 |
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 source (direct Gemma or distilled Codex), 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".