Prioritizing human disease genes by multiple data integration
Bibliographic record
Abstract
Now multiple types of data are available for prioritizing human disease genes, including gene-disease associations, disease phenotype similarities, locations of genes or their corresponding proteins in biological networks, etc. Integrating multiple types of data is expected to be effective for prioritizing human disease genes. In this paper, we propose a multiple data integration method based on the theory of Markov Random Field (MRF) and the method of Bayesian analysis for prioritizing human disease genes. The proposed method is not only flexible in easily incorporating different kinds of data, but also reliable in predicting candidate disease genes. Numerical experiments are carried out by integrating known gene-disease associations, protein complexes, protein-protein interactions and gene expression profiles. Predictions are evaluated by both the leave-one-out method and the fold enrichment method. The sensitivity and the specificity can reach at roughly 80% simultaneously. The method achieves 56.02-fold enrichment on average when integrating all those biological data in our experiments.
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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 | 0.007 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".