BioPrediction-PPI: Simplifying the Prediction of Protein-Protein actions through Artificial Intelligence
Bibliographic record
Abstract
Abstract Proteins are essential in biological processes, primarily through their interactions with other molecules, including proteins. These interactions are crucial for cellular functions and maintaining life. Predicting Protein-Protein Interactions (PPIs) is very important, although challenging, for understanding cellular functions and diseases. This paper presents BioPrediction-PPI, a new end-to-end Machine Learning (ML) framework for PPI prediction, automating the entire process from feature extraction to interpretability, with no manual intervention required. BioPrediction-PPI stands as one of the few end-to-end models that do not rely on deep learning, enabling the automated use of trained models on new data. It offers interpretability graphs for creating auditable models and has been evaluated through comparative experiments with 30 previous studies, using 15 datasets. Additionally, the interpretability graphs offer valuable insights for model evaluation and experimental design, facilitating informed decision-making. BioPrediction-PPI demonstrates competitive performance across multiple datasets, even without the use of deep learning, and is a transparent, white-box model that can be easily used by biologists and practitioners without a background in computer science. The proposed framework has the potential to accelerate research in biology and related fields by making AI-driven tools more accessible.
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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 | 0.002 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.002 | 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".