Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing

Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing

23 May 2025

Papers citing "Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing"

18 / 18 papers shown

Title
Tokenization Constraints in LLMs: A Study of Symbolic and Arithmetic Reasoning Limits Xiang Zhang Juntai Cao Jiaqi Wei Yiwei Xu Chenyu You LRM 44 2 0 20 May 2025
AlignRAG: Leveraging Critique Learning for Evidence-Sensitive Retrieval-Augmented Reasoning Jiaqi Wei Hao Zhou Xiang Zhang Di Zhang Zijie Qiu Wei Wei Jinzhe Li Wanli Ouyang Siqi Sun 58 0 0 21 Apr 2025
Counting Ability of Large Language Models and Impact of Tokenization Xiang Zhang Juntai Cao Chenyu You LRM 101 6 0 25 Oct 2024
NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics Jingbo Zhou Shaorong Chen Jun Xia Sizhe Liu Tianze Ling Wenjie Du Yue Liu Jianwei Yin Stan Z. Li 42 3 0 16 Jun 2024
$AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information$ AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information Jun Xia Shaorong Chen Jingbo Zhou Tianze Ling Wenjie Du Sizhe Liu Stan Z. Li 29 3 0 09 Mar 2024
ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing Zhi Jin Sheng Xu Xiang Zhang Tianze Ling Nanqing Dong Wanli Ouyang Zhiqiang Gao Cheng Chang Siqi Sun 35 13 0 18 Dec 2023
LLM-Blender: Ensembling Large Language Models with Pairwise Ranking and Generative Fusion Dongfu Jiang Xiang Ren Bill Yuchen Lin ELM 63 310 0 05 Jun 2023
TTIDA: Controllable Generative Data Augmentation via Text-to-Text and Text-to-Image Models Yuwei Yin Jean Kaddour Xiang Zhang Yixin Nie Zhenguang Liu Lingpeng Kong Qi Liu DiffM 65 10 0 18 Apr 2023
RankT5: Fine-Tuning T5 for Text Ranking with Ranking Losses Honglei Zhuang Zhen Qin R. Jagerman Kai Hui Ji Ma Jing Lu Jianmo Ni Xuanhui Wang Michael Bendersky AIMat 46 140 0 12 Oct 2022
A Character-Level Length-Control Algorithm for Non-Autoregressive Sentence Summarization Puyuan Liu Xiang Zhang Lili Mou 45 10 0 28 May 2022
Training language models to follow instructions with human feedback Long Ouyang Jeff Wu Xu Jiang Diogo Almeida Carroll L. Wainwright ... Amanda Askell Peter Welinder Paul Christiano Jan Leike Ryan J. Lowe OSLM ALM 769 12,835 0 04 Mar 2022
RocketQAv2: A Joint Training Method for Dense Passage Retrieval and Passage Re-ranking Ruiyang Ren Yingqi Qu Jing Liu Wayne Xin Zhao Qiaoqiao She Hua Wu Haifeng Wang Ji-Rong Wen 249 255 0 14 Oct 2021
Rethinking Attention with Performers K. Choromanski Valerii Likhosherstov David Dohan Xingyou Song Andreea Gane ... Afroz Mohiuddin Lukasz Kaiser David Belanger Lucy J. Colwell Adrian Weller 169 1,570 0 30 Sep 2020
Axial-DeepLab: Stand-Alone Axial-Attention for Panoptic Segmentation Huiyu Wang Yukun Zhu Bradley Green Hartwig Adam Alan Yuille Liang-Chieh Chen 3DPC 114 670 0 17 Mar 2020
Document Ranking with a Pretrained Sequence-to-Sequence Model Rodrigo Nogueira Zhiying Jiang Jimmy J. Lin 67 578 0 14 Mar 2020
Axial Attention in Multidimensional Transformers Jonathan Ho Nal Kalchbrenner Dirk Weissenborn Tim Salimans 98 528 0 20 Dec 2019
Multi-Stage Document Ranking with BERT Rodrigo Nogueira Wei Yang Kyunghyun Cho Jimmy J. Lin 70 393 0 31 Oct 2019
CCNet: Criss-Cross Attention for Semantic Segmentation Zilong Huang Xinggang Wang Yunchao Wei Lichao Huang Humphrey Shi Wenyu Liu Chang Huang VOS 200 2,540 0 28 Nov 2018