Mining Human Prostate Cancer Datasets: The “camcAPP” Shiny App
Bibliographic record
Abstract
Obtaining access to robust, well-annotated human genomic datasets is an important step in demonstrating the relevance of experimental findings and, often, in generating the hypotheses that led to those experiments being conducted in the first place. We recently published data from the CamCaP Study Group which comprised two cohorts of men with prostate cancer who had undergone prostatectomy in Cambridge, UK and Stockholm, Sweden (Ross-Adams et al., 2015). We considered how we might best share our output with those who wish to interrogate the data with their own ideas, gene lists and clinical questions.
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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 | 0.003 | 0.013 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.005 | 0.005 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.004 | 0.006 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.067 | 0.033 |
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".