Towards a theoretical understanding of false positives in DNA motif finding
Bibliographic record
Abstract
Detection of false-positive motifs is one of the main causes of low performance in motif finding methods. It is generally assumed that false-positives are mostly due to algorithmic weakness of motif-finders. Here, however, we derive the theoretical dependence of false positives on dataset size and find that false positives can arise as a result of large dataset size, irrespective of the algorithm used. Interestingly, the false-positive strength depends more on the number of sequences in the dataset than it does on the sequence length. As expected, false-positives can be reduced by decreasing the sequence length or by adding more sequences to the dataset. The dependence on number of sequences, however, diminishes and reaches a plateau after which adding more sequences to the dataset does not reduce the false-positive rate significantly. Based on the theoretical results presented here, we provide a number of intuitive rules of thumb that may be used to enhance motif-finding results in practice.
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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 | 0.065 | 0.380 |
| Meta-epidemiology (narrow) | 0.003 | 0.003 |
| Meta-epidemiology (broad) | 0.004 | 0.003 |
| Bibliometrics | 0.007 | 0.004 |
| Science and technology studies | 0.002 | 0.015 |
| Scholarly communication | 0.010 | 0.019 |
| Open science | 0.009 | 0.008 |
| Research integrity | 0.008 | 0.013 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
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".