4 accepted papers
Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks like de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bid…
Peptide sequencing—the process of identifying amino acid sequences from mass spectrometry data—is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate token…
Retrieval-augmented generation (RAG) has become a widely adopted paradigm for enabling knowledge-grounded large language models (LLMs). However, standard RAG pipelines often fail to ensure that model reasoning remains consistent with the evidence retrieved, leading to factual inconsistencies or unsu…
De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the…