Temporal-Spatial Analysis of the Essentiality of Hub Proteins in Protein-Protein Interaction Networks
Why this work is in the frame
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Bibliographic record
Abstract
Hubs are generally defined as nodes with a high degree centrality, and they are important for maintaining the stability of complex networks. Previous studies have shown that hub proteins tend to be essential in protein-protein interaction (PPI) networks, providing us with a new way to analyze the essentiality of proteins. Unfortunately, most of the existing studies leverage static PPI networks that are both incomplete and noisy and ignore the temporal and spatial characteristics of PPI networks. Benefiting from the development of high-throughput technologies, abundant multi-biological datasets have been accumulated and can be used for network analysis. To reexamine the relationship between the network centrality and protein essentiality in PPI networks, in this study, we integrated PPI networks with gene expression data and subcellular localization information to construct temporal-spatial dynamic PPI networks. Based on the constructed temporal-spatial dynamic PPI networks, we introduced the maximum degree centrality (MDC) method to evaluate the essentiality of hub proteins. Our results illustrate that the integration of gene expression data or subcellular localization information can significantly reduce noise effects and improve the identification accuracy of essential proteins through the temporal-spatial analysis with disparate sources of PPI networks. Moreover, we redefined hubs and classified them into two types: temporospatial hubs and static hubs. The results show that temporospatial hub proteins are more likely to be essential.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 it