📃 Publications

NovoBench: Benchmarking Deep Learning-based De Novo Sequencing Methods in Proteomics

Jingbo Zhou†, Shaorong Chen†, Jun Xia†, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li

VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention

Jingbo Zhou†, Jun Xia†, Chang Yu†, Siyuan Li, Yunfan Liu, Wenjun Wang, Yufei Huang, Changxi Chi, Mutian Hong, Zhuoli Ouyang, Shu Wang, Zhongqi Wang, Xingyu Wu, Stan Z. Li

Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module

Jingbo Zhou†, Yixuan Du†, Ruqiong Zhang†, Jun Xia, Zhizhi Yu, Zelin Zang, Di Jin, Carl Yang, Rui Zhang, Stan Z. Li

AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information

Jun Xia†, Shaorong Chen†, Jingbo Zhou†, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li

Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo

Jun Xia†, Sizhe Liu†, Jingbo Zhou†, Shaorong Chen, hongxin xiang, Zicheng Liu, Yue Liu, Stan Z. Li
🔥 NeurIPS 2024 AIDrugX Spotlight

ReNovo: Retrieval-Based De Novo Mass Spectrometry Peptide Sequencing

Shaorong Chen†, Jun Xia†, Jingbo Zhou†, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z. Li

Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control

Shaorong Chen, Jingbo Zhou, Jun Xia

A comprehensive and systematic review for deep learning-based de novo peptide sequencing

Jun Xia†, Jingbo Zhou†, Shaorong Chen†, Tianze Ling†, Stan Z. Li

MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging

Siyuan Li, Zicheng Liu, Kai Yu, Chang Yu, Jingbo Zhou, Anna Wang, Qirong Yang, yucheng guo, Xiaoming Zhang, Stan Z. Li

CDBridge: A Cross-omics Post-training Bridge Strategy for Context-aware Biological Modeling

Chang Yu, Siyuan Li, Zicheng Liu, Jingbo Zhou, Xianglong Guo, Kai Yu,Yuqing Zhou, Ken Li, Zelin Zang, Zhen Lei, Stan Z. Li

PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation

Jiabei Cheng, Changxi Chi, Jingbo Zhou, Hongyi Xin, Jun Xia

Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation

Changxi Chi, Jun Xia, Yufei Huang, Zhuoli Ouyang, Cheng Tan, Yunfan Liu, Jingbo Zhou, Chang Yu, Liangyu Yuan, Siyuan Li, Zelin Zang, Stan Z. Li

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

Changxi Chi, Xia Jun, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li

NodeReg: Mitigating the Imbalance and Distribution Shift Effects in Semi-Supervised Node Classification via Norm Consistency

Shenzhi Yang, Jun Xia, Jingbo Zhou, Xingkai Yao, Xiaofang Zhang

SteinsGate: Adding Causality to Diffusions for Long Video Generation via Path Integral

Yufei Huang, Liangyu Yuan, Changxi Chi, Yunfan Liu, Cheng Tan, Siyuan Li, Jingbo Zhou, Haitao Lin, Chang Yu, Stan Z. Li

VitaMol: Lightweight Molecular Modality Expansion in Discrete Space for Multi-Task Transfer Learning

Yunfan Liu, Zhifeng Gao, Lirong Wu, Jingbo Zhou, Tongyue Xu, Cheng Tan, Yufei Huang, Changxi Chi, Chang Yu, Stan Z. Li

scTranslation: A Comprehensive Benchmark for Single-Cell Multi-Omics Modality Translation

Jiabei Cheng†, Jingbo Zhou†, Jun Xia, Changkai Li, Zhen Lei, Chang Yu, Stan Z. Li

MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry

Dongxin Lyu, Jingbo Zhou, Hongxin Xiang, Yuqiang Li, Jun Xia

scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

Xichen Yan, Zelin Zang, Changxi Chi, Jingbo Zhou, Chang Yu, Jinlin Wu, Shenghui Cheng, Fuji Yang, Jiebo Luo, Zhen Lei, Stan Z. Li

Geometric Flow Grounding: A Unified Manifold Decoupling Framework for Dynamics Discovery and Verification

Chang Yu, Yuxuan Luo, Yixuan Du, Yuqing Zhou, Siyuan Li, Jingbo Zhou, Jiawei Jiang, Zhen Lei, Stan Z. Li

HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference

Zelin Zang, WenZhe Li, Yongjie Xu, Chang Yu, Changxi Chi, Jingbo Zhou, Zhen Lei, Stan Z. Li