Estimating Boltzmann Averages for Protein Structural Quantities Using Sequential Monte Carlo
Why this work is in the frame
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Bibliographic record
Abstract
Sequential Monte Carlo (SMC) methods are widely used to draw samples from intractable target distributions. Weight degeneracy can hinder the use of SMC when the target distribution is highly constrained. As a motivating application, we consider the problem of sampling protein structures from the Boltzmann distribution. This paper proposes a general SMC method that propagates multiple descendants for each particle, followed by resampling to maintain the desired number of particles. A simulation study demonstrates the efficacy of the method for tackling the protein sampling problem, compared to existing SMC methods. As a real data example, we estimate the number of atomic contacts for a key segment of the SARS-CoV-2 viral spike protein.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 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) | 0.001 | 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