Guo, Hongyu

44 publications

ICLR 2025 AssembleFlow: Rigid Flow Matching with Inertial Frames for Molecular Assembly Hongyu Guo, Yoshua Bengio, Shengchao Liu

ICLR 2025 Structure Language Models for Protein Conformation Generation Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu, Chence Shi, Hongyu Guo, Yoshua Bengio, Jian Tang

ICLRW 2025 Towards Protein Sequence & Structure Co-Design with Multi-Modal Language Models Stephen Zhewen Lu, Jiarui Lu, Hongyu Guo, Jian Tang

NeurIPSW 2024 A Geometric Foundation Model for Crystalline Material Discovery Shengchao Liu, Liang Yan, Weitao Du, Zhuoxinran Li, Zhiling Zheng, Omar M. Yaghi, Christian Borgs, Hongyu Guo, Anima Anandkumar, Jennifer T Chayes

ICLRW 2024 A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics Shengchao Liu, Weitao Du, Yanjing Li, Zhuoxinran Li, Vignesh C Bhethanabotla, Nakul Rampal, Omar M. Yaghi, Christian Borgs, Anima Anandkumar, Hongyu Guo, Jennifer T Chayes

ICMLW 2024 An Equivariant Flow Matching Framework for Learning Molecular Crystallization Shengchao Liu, Liang Yan, Hongyu Guo, Anima Anandkumar

TMLR 2024 Calibration Attacks: A Comprehensive Study of Adversarial Attacks on Model Confidence Stephen Obadinma, Xiaodan Zhu, Hongyu Guo

ICLR 2024 Conversational Drug Editing Using Retrieval and Domain Feedback Shengchao Liu, Jiongxiao Wang, Yijin Yang, Chengpeng Wang, Ling Liu, Hongyu Guo, Chaowei Xiao

NeurIPSW 2024 Geometry-Text Multi-Modal Foundation Model for Reactivity-Oriented Molecule Editing Haorui Li, Shengchao Liu, Hongyu Guo, Anima Anandkumar

NeurIPSW 2024 Language Models for Text-Guided Protein Evolution Zhanghan Ni, Shengchao Liu, Hongyu Guo, Anima Anandkumar

ICMLW 2024 Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design Shengchao Liu, Liang Yan, Weitao Du, Weiyang Liu, Hongyu Guo, Christian Borgs, Jennifer T Chayes, Anima Anandkumar

NeurIPSW 2024 Structure Language Models for Protein Conformation Generation Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu, Chence Shi, Hongyu Guo, Yoshua Bengio, Jian Tang

NeurIPSW 2024 Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models Dhruva Rajwade, Erica Wang, Aryan Satpathy, Alexander Brace, Hongyu Guo, Arvind Ramanathan, Shengchao Liu, Anima Anandkumar

NeurIPSW 2024 Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models Dhruva Rajwade, Erica Wang, Aryan Satpathy, Alexander Brace, Hongyu Guo, Arvind Ramanathan, Shengchao Liu, Anima Anandkumar

TMLR 2023 $f$-MICL: Understanding and Generalizing InfoNCE-Based Contrastive Learning Yiwei Lu, Guojun Zhang, Sun Sun, Hongyu Guo, Yaoliang Yu

ICML 2023 A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-Modal Pretraining Shengchao Liu, Weitao Du, Zhi-Ming Ma, Hongyu Guo, Jian Tang

ICMLW 2023 ChatGPT-Powered Conversational Drug Editing Using Retrieval and Domain Feedback Shengchao Liu, Jiongxiao Wang, Yijin Yang, Chengpeng Wang, Ling Liu, Hongyu Guo, Chaowei Xiao

NeurIPSW 2023 ChatPathway: Conversational Large Language Models for Biology Pathway Detection Yanjing Li, Hannan Xu, Haiteng Zhao, Hongyu Guo, Shengchao Liu

NeurIPSW 2023 ChatPathway: Conversational Large Language Models for Biology Pathway Detection Yanjing Li, Hannan Xu, Haiteng Zhao, Hongyu Guo, Shengchao Liu

NeurIPS 2023 Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering Tianxiao Li, Hongyu Guo, Filippo Grazioli, Mark Gerstein, Martin Renqiang Min

AAAI 2023 Interpolating Graph Pair to Regularize Graph Classification Hongyu Guo, Yongyi Mao

ICLR 2023 Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching Shengchao Liu, Hongyu Guo, Jian Tang

ICLR 2023 Over-Training with Mixup May Hurt Generalization Zixuan Liu, Ziqiao Wang, Hongyu Guo, Yongyi Mao

NeurIPS 2023 Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu, Weitao Du, Yanjing Li, Zhuoxinran Li, Zhiling Zheng, Chenru Duan, Zhi-Ming Ma, Omar Yaghi, Animashree Anandkumar, Christian Borgs, Jennifer Chayes, Hongyu Guo, Jian Tang

NeurIPSW 2022 Over-Training with Mixup May Hurt Generalization Zixuan Liu, Ziqiao Wang, Hongyu Guo, Yongyi Mao

ICLR 2022 Pre-Training Molecular Graph Representation with 3D Geometry Shengchao Liu, Hanchen Wang, Weiyang Liu, Joan Lasenby, Hongyu Guo, Jian Tang

ICLRW 2022 Pre-Training Molecular Graph Representation with 3D Geometry Shengchao Liu, Hanchen Wang, Weiyang Liu, Joan Lasenby, Hongyu Guo, Jian Tang

ECML-PKDD 2021 Midpoint Regularization: From High Uncertainty Training Labels to Conservative Classification Decisions Hongyu Guo

ICML 2021 Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction Hangrui Bi, Hengyi Wang, Chence Shi, Connor Coley, Jian Tang, Hongyu Guo

ICML 2021 Self-Supervised Graph-Level Representation Learning with Local and Global Structure Minghao Xu, Hang Wang, Bingbing Ni, Hongyu Guo, Jian Tang

UAI 2021 Symmetric Wasserstein Autoencoders Sun Sun, Hongyu Guo

ICML 2020 A Graph to Graphs Framework for Retrosynthesis Prediction Chence Shi, Minkai Xu, Hongyu Guo, Ming Zhang, Jian Tang

AAAI 2020 Aggregated Learning: A Vector-Quantization Approach to Learning Neural Network Classifiers Masoumeh Soflaei, Hongyu Guo, Ali Al-Bashabsheh, Yongyi Mao, Richong Zhang

ICLR 2020 MixUp as Directional Adversarial Training Guillaume P. Archambault, Yongyi Mao, Hongyu Guo, Richong Zhang

AAAI 2020 Nonlinear Mixup: Out-of-Manifold Data Augmentation for Text Classification Hongyu Guo

IJCAI 2019 Learning K-Way D-Dimensional Discrete Embedding for Hierarchical Data Visualization and Retrieval Xiaoyuan Liang, Martin Renqiang Min, Hongyu Guo, Guiling Wang

AAAI 2019 MixUp as Locally Linear Out-of-Manifold Regularization Hongyu Guo, Yongyi Mao, Richong Zhang

IJCAI 2019 Modeling Noisy Hierarchical Types in Fine-Grained Entity Typing: A Content-Based Weighting Approach Junshuang Wu, Richong Zhang, Yongyi Mao, Hongyu Guo, Jinpeng Huai

ECML-PKDD 2018 Parametric T-Distributed Stochastic Exemplar-Centered Embedding Martin Renqiang Min, Hongyu Guo, Dinghan Shen

IJCAI 2017 Exemplar-Centered Supervised Shallow Parametric Data Embedding Martin Renqiang Min, Hongyu Guo, Dongjin Song

ICML 2015 Long Short-Term Memory over Recursive Structures Xiaodan Zhu, Parinaz Sobihani, Hongyu Guo

ECML-PKDD 2013 Modeling Short-Term Energy Load with Continuous Conditional Random Fields Hongyu Guo

CVPR 2004 A New Joint Clustering and Diffeomorphism Estimation Algorithm for Non-Rigid Shape Matching Hongyu Guo, Anand Rangarajan, Sarang C. Joshi, Laurent Younes

CVPRW 2004 A New Joint Clustering and Diffeomorphism Estimation Algorithm for Non-Rigid Shape Matching Hongyu Guo, Anand Rangarajan, Sarang C. Joshi, Laurent Younes