Interaction Networks as Scaffolds for Organizing and Interpreting Proteomes
Bibliographic record
Abstract
s1-1 Genes and proteins do not operate in isolation, but form components of highly integrated biological processes such as metabolic networks, protein complexes or signal transduction pathways. Identifying the connections between these components enables the construction of a valuable scaffold onto which additional metadata may be readily mapped.A significant challenge is the lack of large scale high quality data detailing component interactions. Here, using E. coli as a model, I will illustrate how existing lower quality datasets may be integrated to derive a highly reliable network of protein interactions. Such networks may be readily organized into discrete functional modules using graph clustering algorithms, to reveal biologically meaningful complexes and pathways. Using additional network examples, I will also show how these datasets may be used as frameworks for organizing additional metadata sets such as protein function, expression and conservation, to yield unique insights into the operation and evolution of biological processes.
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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 | 0.003 | 0.011 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.015 | 0.011 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.005 | 0.007 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.002 |
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".