Additional file 5 of Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding
Bibliographic record
Abstract
Additional file 5: Figure S3. Automatic oligo-banding pattern analysis of the rcp(3;6). The “Analyze” tool of the Oligo-Banding plugin [39] analyzes the fluorophore signals of each traced chromosome and generates an output containing ROI manager tracing ID (ROI column), detected fluorophore banding patterns (Signature column), associated chromosome based on pattern identity (Ref column), the number of differences between the detected pattern and the expected one (Err column) and the reference banding pattern of the associated chromosome (Sequence column) (a). The tool also generates plots for each traced chromosome in order to visualize and confirm detected patterns. For instance, the der(3) and der(6) plots of the rcp(3;6) boar are shown in b and c. Based on outputted results table and signal plots, real chromosomal abnormalities and signal detection errors can be distinguished. d After chromosomal abnormality confirmation, images can be generated using basic ImageJ tools. More details on the plugin are available on the associated GitHub page [39].
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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 | 0.001 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.821 | 0.182 |
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".