---
title: "NovoCRF: Globally Normalized De Novo Peptide Sequencing on a Prefix-Mass Lattice"
source: "arXiv AI/CL/LG（论文）"
source_tier: "t2"
url: "https://arxiv.org/abs/2611.05260v1"
permalink: "https://feed.astralor.com/items/itm_b2ad99a75ce33a24b922c793"
published: "2026-11-03T17:48:42.000Z"
score: 60
channel: "finance"
tags: ["推理效率","RAG","NovoCRF","Globally Normalized","Novo Peptide Sequencing","Prefix-Mass Lattice","CRF"]
---

# NovoCRF: Globally Normalized De Novo Peptide Sequencing on a Prefix-Mass Lattice

## 速览

De novo peptide sequencing has moved from dynamic programming over hand-designed or generative scores to large transformers that learn the task end to end. We present NovoCRF, a conditional random field (CRF) whose stat…

## 关键点

- De novo peptide sequencing has moved from dynamic programming over hand-designed or generative scores to large transformers that learn the task end to end.
- We present NovoCRF, a conditional random field (CRF) whose states are prefix masses, so that its paths are exactly the peptides within +/-0.06 Da of the precursor mass.
- A small network scores each edge from physics-derived ion-match features and is trained with its scores globally normalized over all mass-feasible peptides.

## 全文

De novo peptide sequencing has moved from dynamic programming over hand-designed or generative scores to large transformers that learn the task end to end. We present NovoCRF, a conditional random field (CRF) whose states are prefix masses, so that its paths are exactly the peptides within +/-0.06 Da of the precursor mass. A small network scores each edge from physics-derived ion-match features and is trained with its scores globally normalized over all mass-feasible peptides. To our knowledge, NovoCRF is the first de novo method trained with exact normalization over all mass-feasible peptides. Our software has three modules, each with exactly one job: a precursor mass finder recovers the accurate precursor mass from MS1, the CRF finds the peptides that fit the precursor mass by exact k-best decoding, and two BiGRU rerankers add sequence context and internal-fragment evidence. The model has 310k parameters and trains in about 17 GPU-hours. On seven held-out data-dependent acquisition datasets published in 2026 (126,262 labeled spectra), NovoCRF's mean peptide recall is 42.4%, against 39.1% for Casanovo v5 with five beams, and its amino-acid recall 64.0% against 53.1%, at 1,746 spectra/s on 18 CPU threads, 55x Casanovo's throughput on a GPU. Split by fragment evidence, NovoCRF leads on labels with up to three peptide bonds without a b or y ion, and Casanovo only beyond. NovoCRF can also search modifications it was never trained on at their exact mass: it finds 32.1% of the hydroxyproline peptides of a lion bone sample.

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