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统计口径与数据新鲜度

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版本更新 · v3arXiv:2609.15545

The Token Before the Value Is the Key

Ke Cheng, Xin Xu, Zhichao Chen, Yixiao Chen, Lei Xin, Jianbo Zhao, Fanhu Zeng, Yue Liu 等 10 位作者

原文摘要

Induction circuits retrieve a value by matching a query to information carried from the token before that value. How this address forms, incorporates context, and supports sequential retrieval remains less clear. We use hybrid language models as a tractable testbed and identify the historical source key as a common causal interface between local preparation and global retrieval. Probes and restoration interventions connect this interface across controlled models, pretrained recurrent and sliding-window hybrids, and released language models. We organize the analysis by address context radius and sequential retrieval depth. First, shared local parameters couple predecessor Carrying to recurrent state processing; separating these demands or biasing initialization promotes address formation. Second, adapting input representations extends an established literal circuit to category matching, making semantically compatible records active competitors. Earlier context resolves this competition through the source key, with a sharp visibility boundary in a controlled single-read model and compositional relays across local layers. Third, fixed relations support memorization shortcuts, whereas sequential generalization requires learning an output-to-query bridge between retrievals. Controlled state-tracking and compositional in-context tasks demonstrate this requirement across stacked stages, looped recurrence, and intermediate-token generation. Together, these results connect circuit formation, contextual disambiguation, and sequential use through a shared retrieval interface. Code is available at https://github.com/ckpassenger/bind-match-copy.

cs.LG

新论文 · v1arXiv:2611.05260

NovoCRF:基于前缀质量格的全归一化从头肽段测序

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

Rui Qiao, Lei Xin, Baozhen Shan

AI 速读 基于摘要

NovoCRF 将从头肽段测序建模为状态为前缀质量的 CRF,在所有质量可行肽段上做精确全局归一化训练,并报告了召回率与吞吐量优势。

cs.LG

查看原文摘要

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.