GeoLife: Managing and Understanding Your Past Life over Maps. - Yu Zheng 004; Longhao Wang; Ruochi Zhang; Xing Xie 001; Wei-Ying Ma (MDM, 2008)

Select-the-Best-Ones: A new way to judge relative relevance. - Ruihua Song; Qingwei Guo; Ruochi Zhang; Guomao Xin; Ji-Rong Wen; Yong Yu 001; Hsiao-Wuen Hon (Inf. Process. Manag., 2011)

Stealthy control signal attacks in scalar LQG systems. - Ruochi Zhang; Parv Venkitasubramaniam (GlobalSIP, 2015)

Stealthy control signal attacks in vector LQG systems. - Ruochi Zhang; Parv Venkitasubramaniam (ACC, 2016)

A game theoretic approach to analyze false data injection and detection in LQG system. - Ruochi Zhang; Parv Venkitasubramaniam (CNS, 2017)

Exploiting sequence-based features for predicting enhancer-promoter interactions. - Yang Yang 094; Ruochi Zhang; Shashank Singh 005; Jian Ma 004 (Bioinform., 2017)

MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs). - Ruiquan Ge; Guoqin Mai; Ruochi Zhang; Xundong Wu; Qing Wu; Fengfeng Zhou (J. Integr. Bioinform., 2017)

Stealthy Control Signal Attacks in Linear Quadratic Gaussian Control Systems: Detectability Reward Tradeoff. - Ruochi Zhang; Parv Venkitasubramaniam (IEEE Trans. Inf. Forensics Secur., 2017)

Optimal Multi-Source Inference Privacy - A Generalized Lloyd-Max Algorithm. - Ruochi Zhang; Parv Venkitasubramaniam (Allerton, 2018)

Optimal Distribution Mapping for Inference Privacy. - Ruochi Zhang; Parv Venkitasubramaniam (APSIPA, 2018)

Mutual-Information-Private Online Gradient Descent Algorithm. - Ruochi Zhang; Parv Venkitasubramaniam (ICASSP, 2018)

Predicting CTCF-mediated chromatin loops using CTCF-MP. - Ruochi Zhang; Yuchuan Wang; Yang Yang 094; Yang Zhang 042; Jian Ma 004 (Bioinform., 2018)

pyHIVE, a health-related image visualization and engineering system using Python. - Ruochi Zhang; Ruixue Zhao; Xinyang Zhao; Di Wu; Weiwei Zheng; Xin Feng 004; Fengfeng Zhou (BMC Bioinform., 2018)

TriZ-a rotation-tolerant image feature and its application in endoscope-based disease diagnosis. - Ruixue Zhao; Ruochi Zhang; Tongyu Tang; Xin Feng 004; Jialiang Li 004; Yue Liu; Renxiang Zhu; Guangze Wang; Kangning Li; Wenyang Zhou; Yunfei Yang; Yuzhao Wang; et al. (Comput. Biol. Medicine, 2018)

Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. - Ruochi Zhang; Yuesong Zou; Jian Ma 004 (ICLR, 2020)

Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. - Ruochi Zhang; Jian Ma 004 (RECOMB, 2020)

False Data Injection and Detection in LQG Systems: A Game Theoretic Approach. - Ruochi Zhang; Parv Venkitasubramaniam (IEEE Trans. Control. Netw. Syst., 2020)

Optimal Local Differentially Private Quantization. - Ruochi Zhang; Parv Venkitasubramaniam (IEEE Trans. Signal Process., 2020)

XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties. - Daiguo Deng; Xiaowei Chen; Ruochi Zhang; Zengrong Lei; Xiaojian Wang; Fengfeng Zhou (J. Chem. Inf. Model., 2021)

Correction to "XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties". - Daiguo Deng; Xiaowei Chen; Ruochi Zhang; Zengrong Lei; Xiaojian Wang; Fengfeng Zhou (J. Chem. Inf. Model., 2021)

Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi. - Ruochi Zhang; Tianming Zhou; Jian Ma 004 (RECOMB, 2022)

PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids. - Ruochi Zhang; Haoran Wu; Yuting Xiu; Kewei Li; Ningning Chen; Yu Wang 225; Yan Wang 028; Xin Gao 001; Fengfeng Zhou (CoRR, 2023)

AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning. - Xiaopeng Xu; Tiantian Xu; Juexiao Zhou; Xingyu Liao; Ruochi Zhang; Yu Wang 225; Lu Zhang; Xin Gao 001 (Genom. Proteom. Bioinform., 2023)

Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis. - Meiyu Duan; Yueying Wang; Dong Zhao; Hongmei Liu; Gongyou Zhang; Kewei Li; Haotian Zhang; Lan Huang 002; Ruochi Zhang; Fengfeng Zhou (Briefings Bioinform., 2023)

OCMR: A comprehensive framework for optical chemical molecular recognition. - Yan Wang 028; Ruochi Zhang; Shengde Zhang; Liming Guo; Qiong Zhou; Bowen Zhao; Xiaotong Mo; Qian Yang; Yajuan Huang; Kewei Li; Yusi Fan; Lan Huang 002; et al. (Comput. Biol. Medicine, 2023)

HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer. - Xiaopeng Xu; Chencheng Xu; Wenjia He; Lesong Wei; Haoyang Li; Juexiao Zhou; Ruochi Zhang; Yu Wang 225; Yuanpeng Xiong; Xin Gao 001 (Bioinform., 2024)

MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning. - Ruochi Zhang; Chao Wu; Qian Yang; Chang Liu 082; Yan Wang 028; Kewei Li; Lan Huang 002; Fengfeng Zhou (Bioinform., 2024)

PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding. - Ruochi Zhang; Haoran Wu; Chang Liu 082; Huaping Li; Yuqian Wu; Kewei Li; Yifan Wang; Yifan Deng; Jiahui Chen; Fengfeng Zhou; Xin Gao 001 (CoRR, 2024)

AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides. - Kewei Li; Yuqian Wu; Yutong Guo; Yinheng Li; Yusi Fan; Ruochi Zhang; Lan Huang 002; Fengfeng Zhou (CoRR, 2024)

Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. - Yihe Deng; Ruochi Zhang; Pan Xu 002; Jian Ma 004; Quanquan Gu (Trans. Mach. Learn. Res., 2024)

FairCare: Adversarial training of a heterogeneous graph neural network with attention mechanism to learn fair representations of electronic health records. - Yan Wang 028; Ruochi Zhang; Qian Yang; Qiong Zhou; Shengde Zhang; Yusi Fan; Lan Huang 002; Kewei Li; Fengfeng Zhou (Inf. Process. Manag., 2024)

PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids. - Ruochi Zhang; Haoran Wu; Chang Liu 082; Qian Yang; Yuting Xiu; Kewei Li; Ningning Chen; Yu Wang 225; Yan Wang 028; Xin Gao 001; Fengfeng Zhou (Briefings Bioinform., 2025)

GraCEImpute: A novel graph clustering autoencoder approach for imputation of single-cell RNA-seq data. - Yueying Wang; Kewei Li; Ruochi Zhang; Yusi Fan; Lan Huang 002; Fengfeng Zhou (Comput. Biol. Medicine, 2025)

TaiChiNet: PCA-based Ying-Yang dilution of inter- and intra-BERT layers to represent anti-coronavirus peptides. - Kewei Li; Shiying Ding; Zhe Guo; Yusi Fan; Hongmei Liu; Yannan Sun; Gongyou Zhang; Ruochi Zhang; Lan Huang 002; Fengfeng Zhou (Expert Syst. Appl., 2025)

Information Entropy Invariance: Enhancing Length Extrapolation in Attention Mechanisms. - Kewei Li; Yanwen Kong; Yiping Xu; Jianlin Su; Lan Huang 002; Ruochi Zhang; Fengfeng Zhou (CoRR, 2025)

DeepSelective: Feature Gating and Representation Matching for Interpretable Clinical Prediction. - Ruochi Zhang; Qian Yang; Xiaoyang Wang; Haoran Wu; Qiong Zhou; Yu Wang 225; Kewei Li; Yueying Wang; Yusi Fan; Jiale Zhang; Lan Huang 002; Chang Liu 082; et al. (CoRR, 2025)

MolProphecy: Bridging Medicinal Chemists' Knowledge and Molecular Pre-Trained Models via a Multi-Modal Framework. - Jianping Zhao; Qiong Zhou; Tian Wang; Yusi Fan; Qian Yang; Li Jiao; Chang Liu 082; Zhehao Guo; Qi Lu; Fengfeng Zhou; Ruochi Zhang (CoRR, 2025)