DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms
Bibliographic record
Abstract
Signal peptides and transit peptides are essential for directing mature proteins to their proper cellular locations, particularly through cleavage following transport. Although various prediction tools achieve strong performance in identifying and classifying targeting peptides, their accuracy in determining cleavage sites remains limited. We introduce DeepMaT, a deep learning model that integrates Mamba2 and a multihead self-attention mechanism, leveraging the global modeling capabilities of Mamba2 and the localized focus of self-attention. Experimental results show that DeepMaT significantly outperforms state-of-the-art models in cleavage site prediction, achieving an accuracy of 0.867 for thylakoid transit peptides and also performing well on other peptides. Moreover, DeepMaT can accurately learn the amino acid distribution of real samples. Ablation experiments show that the combination of Mamba and attention mechanisms can improve model efficiency, further proving the effectiveness of the combination. It also enables prediction of targeting peptides with unspecified cleavage sites, offering a valuable tool for protein database annotation. DeepMaT is freely available on GitHub at https://github.com/qianmao2001/DeepMaT.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| 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 | 0.001 |
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".