Lattice protein folding with variational annealing
Bibliographic record
Abstract
Abstract Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a simplified yet powerful framework for studying the complexities of protein folding, enabling the exploration of energetically optimal folds under constrained conditions. However, finding these optimal folds is a computationally challenging combinatorial optimization problem. In this work, we introduce a novel upper-bound training scheme that employs masking to identify the lowest-energy folds in two-dimensional hydrophobic-polar lattice protein folding. By leveraging dilated recurrent neural networks (RNNs) integrated with an annealing process driven by temperature-like fluctuations, our method accurately predicts optimal folds for benchmark systems of up to 60 beads. Our approach also effectively masks invalid folds from being sampled without compromising the autoregressive sampling properties of RNNs. This scheme is generalizable to three spatial dimensions and can be extended to lattice protein models with larger alphabets. Our findings emphasize the potential of advanced machine learning techniques in tackling complex protein folding problems and a broader class of constrained combinatorial optimization challenges.
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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 | 0.001 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".