Bibliographic record
Abstract
We address the problem of 3D protein deformable shape classification. Proteins are macromolecules characterized by deformable and complex shapes which are related to their function making their classification an important task. Their molecular surface is represented by graphs such as triangular tessellations or meshes. In this paper, we propose a new graph embedding based approach for the classification of these 3D deformable objects. Our technique is based on graphs decomposition into a set of substructures, using triangle-stars, which are subsequently matched with the Hungarian algorithm. The proposed approach is based on an approximation of the Graph Edit Distance which is characterized by its robustness against both noise and distortion. Our algorithm defines a metric space using graph embedding techniques, where each object is represented by a set of selected 3D prototypes. We propose new approaches for prototypes selection and features reduction. The classification is performed with supervised machine learning techniques. The proposed method is evaluated against 3D protein benchmark repositories and state-of-the-art algorithms. Our experimental results consistently demonstrate the effectiveness of our approach.
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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 | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".