Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling
Bibliographic record
Abstract
Cross-validation based point estimates of prediction accuracy are frequently reported in microarray class prediction problems. However these point estimates can be highly variable, particularly for small sample numbers, and it would be useful to provide confidence intervals of prediction accuracy. We performed an extensive study of existing confidence interval methods and compared their performance in terms of empirical coverage and width. We developed a bootstrap case cross-validation (BCCV) resampling scheme and defined several confidence interval methods using BCCV with and without bias-correction. The widely used approach of basing confidence intervals on an independent binomial assumption of the leave-one-out cross-validation errors results in serious under-coverage of the true prediction error. Two split-sample based methods previously proposed in the literature tend to give overly conservative confidence intervals. Using BCCV resampling, the percentile confidence interval method was also found to be overly conservative without bias-correction, while the bias corrected accelerated (BCa) interval method of Efron returns substantially anti-conservative confidence intervals. We propose a simple bias reduction on the BCCV percentile interval. The method provides mildly conservative inference under all circumstances studied and outperforms the other methods in microarray applications with small to moderate sample sizes.
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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 | 0.084 | 0.382 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.006 | 0.003 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.003 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.001 | 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 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".