PROTEIN FOLD RECOGNITION USING THE GRADIENT BOOST ALGORITHM
Bibliographic record
Abstract
Protein structure prediction is one of the most important and difficult problems in computational molecular biology. Protein threading represents one of the most promising techniques for this problem. One of the critical steps in protein threading, called fold recognition, is to choose the best-fit template for the query protein with the structure to be predicted. The standard method for template selection is to rank candidates according to the z-score of the sequence-template alignment. However, the z-score calculation is time-consuming, which greatly hinders structure prediction at a genome scale. In this paper, we present a machine learning approach that treats the fold recognition problem as a regression task and uses a least-squares boosting algorithm (LS_Boost) to solve it efficiently. We test our method on Lindahl's benchmark and compare it with other methods. According to our experimental results we can draw the conclusions that: (1) Machine learning techniques offer an effective way to solve the fold recognition problem. (2) Formulating protein fold recognition as a regression rather than a classification problem leads to a more effective outcome. (3) Importantly, the LS_Boost algorithm does not require the calculation of the z-score as an input, and therefore can obtain significant computational savings over standard approaches. (4) The LS_Boost algorithm obtains superior accuracy, with less computation for both training and testing, than alternative machine learning approaches such as SVMs and neural networks, which also need not calculate the z-score. Finally, by using the LS_Boost algorithm, one can identify important features in the fold recognition protocol, something that cannot be done using a straightforward SVM approach.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 0.003 |
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".