Nonlinear Projection for the Display of High Dimensional Distance Data
Bibliographic record
Abstract
Display and visualization of high dimensional data are typically performed with a well-chosen linear projection of the data or by displaying many linear projections to form an animation. This study presents an evolutionary algorithm for producing nonlinear projections of high dimensional data with cues, in the drawing of the projection, as to the types of distortions introduced. Such projections can provide drawings closer to the true high dimensional distances of the displayed data than any single linear drawing. This permits a researcher to view a good analog to a scatter plot for high dimensional data. The system is demonstrated on a synthetic four dimensional fitness landscape and on distance data derived from RNA folds. Because fitness landscapes often have more dimensions than can be easily visualized it is difficult to gain an intuitive understanding of a fitness landscape. The nonlinear projection algorithm is applied to an abstraction of the fitness landscape called a fitness web. Fitness webs can be used to display the relative quality of optima, the frequency with which they were found by different evolutionary runs, or other factors of interest. In addition to displaying the relative position of optima in a fitness landscape, a graph of the fitness function along the edges a fitness web displays important slices of the fitness landscape. Called fitness morphs these plots can provide intuition about the fitness landscapes as well as direction for subsequent evolutionary searches. The second demonstration of the nonlinear projection algorithm is to data generated from an ad hoc metric on RNA folds. The algorithm yields drawings that permit a researcher to correctly distinguish two different types of folds for iron response elements.
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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 | 0.002 | 0.007 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.035 | 0.008 |
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".