Constraint programming approaches for the discretizable molecular distance geometry problem
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Bibliographic record
Abstract
Abstract The Distance Geometry Problem (DGP) seeks to find positions for a set of points in geometric space when some distances between pairs of these points are known. The so‐called discretization assumptions allow us to discretize the search space of DGP instances. In this paper, we focus on a key subclass of DGP, namely the Discretizable Molecular DGP, and study its associated graph vertex ordering problem, the Contiguous Trilateration Ordering Problem (CTOP), which helps solve DGP. We propose the first constraint programming formulations for CTOP, as well as a set of checks for proving infeasibility, domain reduction techniques, symmetry breaking constraints, and valid inequalities. Our computational results on random and pseudo‐protein instances indicate that our formulations outperform the state‐of‐the‐art integer programming formulations.
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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 | 0.000 | 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