Pattern Discovery in Protein Networks Reveals High-Confidence Predictions of Novel Interactions
Bibliographic record
Abstract
Pattern discovery in protein interaction networks can reveal crucial biological knowledge on the inner workings of cellular machinery. Although far from complete, extracting meaningful patterns from proteomic networks is a nontrivial task due to their size-complexity. This paper proposes a computational framework to efficiently discover topologically-similar patterns from large proteomic networks using Particle Swarm Optimization (PSO). PSO is a robust and low-cost optimization technique that demonstrated to work effectively on the complex, mostly sparse proteomic networks. The resulting topologicallysimilar patterns of close proximity are utilized to systematically predict new high-confidence protein-protein interactions (PPIs). The proposed PSO-based PPI prediction method (3PI) managed to predict high-confidence PPIs, validated by more than one computational/experimental source, through a proposed PPI knowledge transfer process between topologically-similar interaction patterns of close proximity. In three case studies, over 50% of the predicted interactions for EFGR, ERBB2, ERBB3, GRB2 and UBC are overlapped with publically available interaction databases, ~80% of the predictions are found among the Top 1% results of another PPI prediction method and their genes are significantly co-expressed across different tissues. Moreover, the only single prediction example that did not overlap with any of our validation sources was recently experimentally supported by two PubMed publications.
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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 | 0.001 | 0.006 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| 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".