Employing Machine Learning Techniques for Data Enrichment: Increasing the Number of Samples for Effective Gene Expression Data Analysis
Bibliographic record
Abstract
For certain domains, e.g. bioinformatics, producing more real samples is costly, error prone and time consuming. Therefore, there is a need for an intelligent automated process capable of substituting the real samples by artificial samples that carry the same characteristics as the real samples and hence could be used for running comprehensive testing of new methodologies. Motivated by this need, we describe a novel approach that integrates Probabilistic Boolean Network and genetic algorithm based techniques into a framework that uses some existing real samples as input and successfully produces new samples as output. The new samples will inspire the characteristics of the existing samples without duplicating them. This leads to diversity in the samples and hence a more rich set of samples to be used in testing. The developed framework incorporates two models (perspectives) for sample generation. We illustrate its applicability for producing new gene expression data samples, a high demanding area that has not received attention. The two perspectives employed in the process are based on models that are not closely related, the independence eliminates the bias of having the produced approach covering only certain characteristics of the domain and leading to samples skewed towards one direction. The produced results are very promising in showing the effectiveness, usefulness and applicability of the proposed multi-model framework.
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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 | 0.005 | 0.013 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".