SeqDA-HLA: Language Model and Dual Attention-Based Network to Predict Peptide-HLA Class I Binding
Bibliographic record
Abstract
Accurate prediction of peptide-HLA class I binding is crucial for immunotherapy and vaccine development, but existing methods often struggle to capture the intricate biological relationships between peptides and diverse HLA alleles. Here, we introduce SeqDA-HLA, a pan-specific prediction model that combines language model-based embeddings (ELMo) with a dual attention mechanism-self-aligned cross-attention and self-attention-to capture rich contextual features and pairwise interactions. Evaluations against 14 state-of-the-art methods on multiple benchmark datasets demonstrate that SeqDA-HLA consistently outperforms competing approaches, achieving an AUC value up to 0.9856 and accuracy as high as 0.9408. Notably, SeqDA-HLA maintains robust performance across peptide lengths (8-14) and HLA alleles, showcasing its generalizability. Beyond predictive accuracy, SeqDA-HLA offers interpretability by highlighting essential anchor residues and revealing key binding motifs, thereby aligning with experimentally validated biological insights. As a further demonstration of practical impact, we fine-tune SeqDA-HLA on an Influenza virus dataset, successfully predicting binding changes induced by single amino acid mutations. Overall, SeqDA-HLA serves as a powerful and interpretable tool for peptide-HLA binding prediction, with potential applications in epitope-based vaccine design and precision immunotherapy.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".