Editorial [Hot Topic: Machine Learning Models in Protein Bioinformatics (Guest Editors: Lukasz Kurgan & Yaoqi Zhou)]
Bibliographic record
Abstract
Bioinformatics is a relatively new field concerned with the computational analysis and prediction of properties of biomolecules, DNA, RNA, and proteins, in particular, on a genomic/proteomic scale. Machine learning models play increasingly important roles in development of novel methodologies, summarization, and high-throughput analysis in the bioinformatics field. Advances in the related area, including protein structure and function prediction [1, 2], structural bioinformatics [3], and peptide analysis [4] were recently summarized, and several works that overview specific sub-areas of protein bioinformatics, such as prediction of secondary structure [5, 6], helical transmembrane proteins [7], localization and targeting [8], binding sites [9, 10], and RNA-binding [11], were published in the last couple of years. This issue provides a comprehensive overview of current efforts related to the analysis of protein data, from sequences to structures to functions. It consists of two parts, the first with five reviews and the second that includes seven original methodology papers.
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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 | 0.006 | 0.018 |
| Meta-epidemiology (narrow) | 0.004 | 0.001 |
| Meta-epidemiology (broad) | 0.004 | 0.002 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.006 | 0.004 |
| Open science | 0.004 | 0.001 |
| Research integrity | 0.007 | 0.012 |
| Insufficient payload (model declined to judge) | 0.016 | 0.019 |
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".