Machine learning algorithms for simultaneous supervised detection of peaks in multiple samples and cell types
Bibliographic record
Abstract
Joint peak detection is a central problem when comparing samples in epigenomic data analysis, but current algorithms for this task are unsupervised and limited to at most 2 sample types. We propose PeakSegPipeline, a new genome-wide multi-sample peak calling pipeline for epigenomic data sets. It performs peak detection using a constrained maximum likelihood segmentation model with essentially only one free parameter that needs to be tuned: the number of peaks. To select the number of peaks, we propose to learn a penalty function based on user-provided labels that indicate genomic regions with or without peaks in specific samples. In comparisons with state-of-the-art peak detection algorithms, PeakSegPipeline achieves similar or better accuracy, and a more interpretable model with overlapping peaks that occur in exactly the same positions across all samples. Our novel approach is able to learn that predicted peak sizes vary by experiment type.
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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 | 0.006 | 0.012 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.004 | 0.002 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".