RefineNovo, a non-autoregressive peptide sequencing model with CTC-based curriculum masking and iterative refinement, reports state-of-the-art amino acid precision and peptide recall on the 9-species benchmarks.
Context-Aware Cross-Attention for Non-Autoregressive Translation
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abstract
Non-autoregressive translation (NAT) significantly accelerates the inference process by predicting the entire target sequence. However, due to the lack of target dependency modelling in the decoder, the conditional generation process heavily depends on the cross-attention. In this paper, we reveal a localness perception problem in NAT cross-attention, for which it is difficult to adequately capture source context. To alleviate this problem, we propose to enhance signals of neighbour source tokens into conventional cross-attention. Experimental results on several representative datasets show that our approach can consistently improve translation quality over strong NAT baselines. Extensive analyses demonstrate that the enhanced cross-attention achieves better exploitation of source contexts by leveraging both local and global information.
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q-bio.BM 1years
2025 1verdicts
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Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing
RefineNovo, a non-autoregressive peptide sequencing model with CTC-based curriculum masking and iterative refinement, reports state-of-the-art amino acid precision and peptide recall on the 9-species benchmarks.