Bibliographic record
Abstract
An effective publication-quality visualization tells a concise story from data. Methods and tools that facilitate making such visualizations are valuable to the scientific community. In this paper, we introduce pineplot, an R package for generating insightful visualizations called pine plots. Pine plots are applicable to a wide variety of datasets and create a holistic picture of the relationship between variables across different experimental conditions. A pine plot provides a means to visualize a group of symmetric matrices, each represented by triangular heat maps. Pine plots can be used to visualize large datasets for exploratory data analysis while controlling for different potentially confounding factors. The utility of the package is demonstrated by visualizing gene expression values of tissue-specific genes from RNA-seq data and the clinical factors in a liver disease and a heart disease dataset. The implementation of pineplot offers a straightforward procedure for generating pine plots; full control of the aesthetic elements of generated plots; and the possibility of augmenting generated plots with extra layers of graphical elements to further extend their usability.
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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 | 0.004 | 0.018 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.004 | 0.005 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.005 | 0.004 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.150 | 0.058 |
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".