Bibliographic record
Abstract
Functional region identification is of fundamental importance for protein sequences analysis for a protein family. Such knowledge not only provides a better scientific understanding but also assists drug discovery. Domain annotation is one approach but it needs to leverage existing databases. For de novo discovery, motif discovery locates and aligns locally similar sub-sequences and represents them as a position-weight matrix (PWM). However, PWM is a fixed-length model whereas protein functional region size varies. Furthermore, to obtain a PWM, a width range parameter needs to be identified through exhaustive search. Hence, it is computational intensive for large dataset. This paper presents a new method known as Pattern-Directed Aligned Pattern Clustering (PD-APCn) to discover and align residues in conserved protein functional regions. It adopts Aligned Pattern Cluster (APC) as the representation model which allows variable pattern length. It uses patterns with strong support to direct the incremental expansion of the APCs, allowing substitution and frame-shift mutations, until a robust termination condition is reached. The concept of breakpoint gap is introduced to identify uncovered conserved patterns with substitution and frame-shift mutations, where these are often rare mutants. To evaluate the performance of PD-APCn, we conducted experiments on synthetic datasets with different size and noise level. Comparing with the popular motif discovery algorithm MEME, PD-APCn has demonstrated competitive performance throughout the experiments, obtaining a higher recall and F measure with up to 400× significant computational speed up comparing to MEME.
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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 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
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".