Conditional Neural Fields. - Jian Peng 001; Liefeng Bo; Jinbo Xu (NIPS, 2009)

Boosting Protein Threading Accuracy. - Jian Peng 001; Jinbo Xu (RECOMB, 2009)

A Probabilistic Graphical Model for Ab Initio Folding. - Feng Zhao; Jian Peng 001; Joe DeBartolo; Karl F. Freed; Tobin R. Sosnick; Jinbo Xu (RECOMB, 2009)

Protein 8-class secondary structure prediction using Conditional Neural Fields. - Zhiyong Wang 005; Feng Zhao; Jian Peng 001; Jinbo Xu (BIBM, 2010)

Low-homology protein threading. - Jian Peng 001; Jinbo Xu (Bioinform., 2010)

Fragment-free approach to protein folding using conditional neural fields. - Feng Zhao; Jian Peng 001; Jinbo Xu (Bioinform., 2010)

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling. - Feng Zhao; Jian Peng 001; Joe DeBartolo; Karl F. Freed; Tobin R. Sosnick; Jinbo Xu (J. Comput. Biol., 2010)

Convex Max-Product over Compact Sets for Protein Folding. - Jian Peng 001; Tamir Hazan; David A. McAllester; Raquel Urtasun (ICML, 2011)

Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. - Sheng Wang 001; Jian Peng 001; Jinbo Xu (Bioinform., 2011)

Variational Inference for Crowdsourcing. - Qiang Liu 001; Jian Peng 001; Alexander Ihler (NIPS, 2012)

Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs. - Tamir Hazan; Jian Peng 001; Amnon Shashua (UAI, 2012)

A conditional neural fields model for protein threading. - Jianzhu Ma; Jian Peng 001; Sheng Wang 001; Jinbo Xu (Bioinform., 2012)

Approximate Inference by Intersecting Semidefinite Bound and Local Polytope. - Jian Peng 001; Tamir Hazan; Nathan Srebro; Jinbo Xu (AISTATS, 2012)

Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. - Jianzhu Ma; Jian Peng 001; Sheng Wang 001; Jinbo Xu (AISTATS, 2013)

Compressive genomics for protein databases. - Noah M. Daniels; Andrew Gallant; Jian Peng 001; Lenore J. Cowen; Michael Baym; Bonnie Berger (Bioinform., 2013)

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. - Emily Berger; Deniz Yörükoglu; Jian Peng 001; Bonnie Berger (PLoS Comput. Biol., 2014)

Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. - Qingming Tang; Sheng Wang 001; Jian Peng 001; Jianzhu Ma; Jinbo Xu (BCB, 2015)

Exact Hybrid Covariance Thresholding for Joint Graphical Lasso. - Qingming Tang; Chao Yang; Jian Peng 001; Jinbo Xu (ECML/PKDD (2), 2015)

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. - Hyunghoon Cho; Bonnie Berger; Jian Peng 001 (RECOMB, 2015)

Estimating the Partition Function by Discriminance Sampling. - Qiang Liu 001; Jian Peng 001; Alexander Ihler; John W. Fisher III (UAI, 2015)

Exploiting ontology graph for predicting sparsely annotated gene function. - Sheng Wang 001; Hyunghoon Cho; ChengXiang Zhai; Bonnie Berger; Jian Peng 001 (Bioinform., 2015)

Protein secondary structure prediction using deep convolutional neural fields. - Sheng Wang 001; Jian Peng 001; Jianzhu Ma; Jinbo Xu (CoRR, 2015)

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. - Sean Simmons 001; Jian Peng 001; Jadwiga R. Bienkowska; Bonnie Berger (J. Comput. Biol., 2015)

Exploiting temporal divergence of topic distributions for event detection. - Rongda Zhu; Aston Zhang; Jian Peng 001; Chengxiang Zhai (IEEE BigData, 2016)

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. - Yunan Luo; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (RECOMB, 2016)

Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining. - Xiuli Ma; Guangyu Zhou; Jingjing Wang; Jian Peng 001; Jiawei Han 001 (RECOMB, 2016)

MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance. - Jingbo Shang; Jian Peng 001; Jiawei Han 001 (SDM, 2016)

DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework. - Jingbo Shang; Wenzhu Tong; Jian Peng 001; Jiawei Han 001 (SDM, 2016)

Meta-Path Guided Embedding for Similarity Search in Large-Scale Heterogeneous Information Networks. - Jingbo Shang; Meng Qu; Jialu Liu; Lance M. Kaplan; Jiawei Han 001; Jian Peng 001 (CoRR, 2016)

On the Interpretability of Conditional Probability Estimates in the Agnostic Setting. - Yihan Gao; Aditya G. Parameswaran; Jian Peng 001 (AISTATS, 2017)

Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening. - Frank S. He; Yang Liu 097; Alexander G. Schwing; Jian Peng 001 (ICLR (Poster), 2017)

Scalable Visualization for High-dimensional Single-cell Data. - Juho Kim; Nate Russell; Jian Peng 001 (PSB, 2017)

ProSNet: integrating homology with molecular networks for protein function prediction. - Sheng Wang 001; Meng Qu; Jian Peng 001 (PSB, 2017)

A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. - Yunan Luo; Xinbin Zhao; Jingtian Zhou; Jinling Yang; Yanqing Zhang 010; Wenhua Kuang; Jian Peng 001; Ligong Chen; Jianyang Zeng 001 (RECOMB, 2017)

Stein Variational Policy Gradient. - Yang Liu 097; Prajit Ramachandran; Qiang Liu 001; Jian Peng 001 (UAI, 2017)

Stochastic Variance Reduction for Policy Gradient Estimation. - Tianbing Xu; Qiang Liu 001; Jian Peng 001 (CoRR, 2017)

Sample-efficient Policy Optimization with Stein Control Variate. - Hao Liu; Yihao Feng; Yi Mao; Dengyong Zhou; Jian Peng 001; Qiang Liu 001 (CoRR, 2017)

Genetic Policy Optimization. - Tanmay Gangwani; Jian Peng 001 (CoRR, 2017)

Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining. - Xiuli Ma; Guangyu Zhou; Jingbo Shang; Jingjing Wang; Jian Peng 001; Jiawei Han 001 (J. Comput. Biol., 2017)

Network-assisted target identification for haploinsufficiency and homozygous profiling screens. - Sheng Wang 001; Jian Peng 001 (PLoS Comput. Biol., 2017)

Empower Sequence Labeling with Task-Aware Neural Language Model. - Liyuan Liu; Jingbo Shang; Xiang Ren 001; Frank Fangzheng Xu; Huan Gui; Jian Peng 001; Jiawei Han 001 (AAAI, 2018)

Efficient Contextualized Representation: Language Model Pruning for Sequence Labeling. - Liyuan Liu; Xiang Ren 001; Jingbo Shang; Xiaotao Gu; Jian Peng 001; Jiawei Han 001 (EMNLP, 2018)

emrQA: A Large Corpus for Question Answering on Electronic Medical Records. - Anusri Pampari; Preethi Raghavan; Jennifer J. Liang; Jian Peng 001 (EMNLP, 2018)

SemRegex: A Semantics-Based Approach for Generating Regular Expressions from Natural Language Specifications. - Zexuan Zhong; Jiaqi Guo; Wei Yang 013; Jian Peng 001; Tao Xie 001; Jian-Guang Lou; Ting Liu 002; Dongmei Zhang 001 (EMNLP, 2018)

Policy Optimization by Genetic Distillation. - Tanmay Gangwani; Jian Peng 001 (ICLR (Poster), 2018)

Action-dependent Control Variates for Policy Optimization via Stein Identity. - Hao Liu; Yihao Feng; Yi Mao; Dengyong Zhou; Jian Peng 001; Qiang Liu 001 (ICLR (Poster), 2018)

Fast and Accurate Text Classification: Skimming, Rereading and Early Stopping. - Keyi Yu; Yang Liu 097; Alexander G. Schwing; Jian Peng 001 (ICLR (Workshop), 2018)

Learning to Explore via Meta-Policy Gradient. - Tianbing Xu; Qiang Liu 001; Liang Zhao 006; Jian Peng 001 (ICML, 2018)

Efficient Localized Inference for Large Graphical Models. - Jinglin Chen; Jian Peng 001; Qiang Liu 001 (IJCAI, 2018)

Energy-efficient Amortized Inference with Cascaded Deep Classifiers. - Jiaqi Guan; Yang Liu 097; Qiang Liu 001; Jian Peng 001 (IJCAI, 2018)

Similarity Modeling on Heterogeneous Networks via Automatic Path Discovery. - Carl Yang 001; Mengxiong Liu; Frank He; Xikun Zhang 001; Jian Peng 001; Jiawei Han 001 (ECML/PKDD (2), 2018)

Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action. - Yunan Luo; Sheng Wang 001; Jinfeng Xiao; Jian Peng 001 (PSB, 2018)

Annotating gene sets by mining large literature collections with protein networks. - Sheng Wang 001; Jianzhu Ma; Michael Ku Yu; Fan Zheng; Edward W. Huang; Jiawei Han 001; Jian Peng 001; Trey Ideker (PSB, 2018)

Generalizable Visualization of Mega-Scale Single-Cell Data. - Hyunghoon Cho; Bonnie Berger; Jian Peng 001 (RECOMB, 2018)

Deciphering Signaling Specificity with Deep Neural Networks. - Yunan Luo; Jianzhu Ma; Yang Liu 097; Qing Ye; Trey Ideker; Jian Peng 001 (RECOMB, 2018)

Learning structural motif representations for efficient protein structure search. - Yang Liu 097; Qing Ye; Liwei Wang 009; Jian Peng 001 (Bioinform., 2018)

Low-Norm Graph Embedding. - Yihan Gao; Chao Zhang 014; Jian Peng 001; Aditya G. Parameswaran (CoRR, 2018)

Learning to Explore with Meta-Policy Gradient. - Tianbing Xu; Qiang Liu 001; Liang Zhao 006; Jian Peng 001 (CoRR, 2018)

Efficient Contextualized Representation: Language Model Pruning for Sequence Labeling. - Liyuan Liu; Xiang Ren 001; Jingbo Shang; Jian Peng 001; Jiawei Han 001 (CoRR, 2018)

DPPred: An Effective Prediction Framework with Concise Discriminative Patterns. - Jingbo Shang; Meng Jiang 001; Wenzhu Tong; Jinfeng Xiao; Jian Peng 001; Jiawei Han 001 (IEEE Trans. Knowl. Data Eng., 2018)

Large-Margin Classification in Hyperbolic Space. - Hyunghoon Cho; Benjamin Demeo; Jian Peng 001; Bonnie Berger (AISTATS, 2019)

Stochastic Variance Reduction for Deep Q-learning. - Wei-Ye Zhao; Jian Peng 001 (AAMAS, 2019)

HeteSpaceyWalk: A Heterogeneous Spacey Random Walk for Heterogeneous Information Network Embedding. - Yu He; Yangqiu Song; Jianxin Li 002; Cheng Ji 001; Jian Peng 001; Hao Peng 001 (CIKM, 2019)

Accelerating Nonconvex Learning via Replica Exchange Langevin diffusion. - Yi Chen; Jinglin Chen; Jing Dong 007; Jian Peng 001; Zhaoran Wang 001 (ICLR (Poster), 2019)

Learning Self-Imitating Diverse Policies. - Tanmay Gangwani; Qiang Liu 001; Jian Peng 001 (ICLR (Poster), 2019)

Knowledge Flow: Improve Upon Your Teachers. - Iou-Jen Liu; Jian Peng 001; Alexander G. Schwing (ICLR (Poster), 2019)

Off-Policy Evaluation and Learning from Logged Bandit Feedback: Error Reduction via Surrogate Policy. - Yuan Xie 005; Boyi Liu 001; Qiang Liu 001; Zhaoran Wang 001; Yuan Zhou 007; Jian Peng 001 (ICLR (Poster), 2019)

A Gradual, Semi-Discrete Approach to Generative Network Training via Explicit Wasserstein Minimization. - Yucheng Chen; Matus Telgarsky; Chao Zhang 014; Bolton Bailey; Daniel Hsu 001; Jian Peng 001 (ICML, 2019)

Quantile Stein Variational Gradient Descent for Batch Bayesian Optimization. - ChengYue Gong; Jian Peng 001; Qiang Liu 001 (ICML, 2019)

Exploration via Hindsight Goal Generation. - Zhizhou Ren; Kefan Dong; Yuan Zhou 007; Qiang Liu 001; Jian Peng 001 (NeurIPS, 2019)

Thresholding Bandit with Optimal Aggregate Regret. - Chao Tao 003; Saúl A. Blanco; Jian Peng 001; Yuan Zhou 007 (NeurIPS, 2019)

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. - Yunan Luo; Jianzhu Ma; Xiaoming Zhao 001; Yufeng Su; Yang Liu 097; Trey Ideker; Jian Peng 001 (RECOMB, 2019)

REINAM: reinforcement learning for input-grammar inference. - Zhengkai Wu; Evan Johnson 001; Wei Yang 013; Osbert Bastani; Dawn Song; Jian Peng 001; Tao Xie 001 (ESEC/SIGSOFT FSE, 2019)

Learning Belief Representations for Imitation Learning in POMDPs. - Tanmay Gangwani; Joel Lehman; Qiang Liu 001; Jian Peng 001 (UAI, 2019)

Metagenomic binning through low-density hashing. - Yunan Luo; Yun William Yu; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (Bioinform., 2019)

Stochastic Variance Reduction for Deep Q-learning. - Wei-Ye Zhao; Xiya Guan; Yang Liu 097; Xiaoming Zhao 001; Jian Peng 001 (CoRR, 2019)

Sequence Modeling of Temporal Credit Assignment for Episodic Reinforcement Learning. - Yang Liu 097; Yunan Luo; Yuanyi Zhong; Xi Chen; Qiang Liu 001; Jian Peng 001 (CoRR, 2019)

Characterizing Attacks on Deep Reinforcement Learning. - Chaowei Xiao; Xinlei Pan; Warren He; Jian Peng 001; Mingjie Sun; Jinfeng Yi; Mingyan Liu; Bo Li 026; Dawn Song (CoRR, 2019)

√n-Regret for Learning in Markov Decision Processes with Function Approximation and Low Bellman Rank. - Kefan Dong; Jian Peng 001; Yining Wang 001; Yuan Zhou 007 (CoRR, 2019)

DeepMask: an algorithm for cloud and cloud shadow detection in optical satellite remote sensing images using deep residual network. - Ke Xu; Kaiyu Guan; Jian Peng 001; Yunan Luo; Sibo Wang 005 (CoRR, 2019)

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction. - Yufeng Su; Yunan Luo; Xiaoming Zhao 001; Yang Liu 097; Jian Peng 001 (PLoS Comput. Biol., 2019)

Identification of pathways associated with chemosensitivity through network embedding. - Sheng Wang 001; Edward W. Huang; Junmei Cairns; Jian Peng 001; Liewei Wang; Saurabh Sinha (PLoS Comput. Biol., 2019)

Stein Variational Inference for Discrete Distributions. - Jun Han 002; Fan Ding; Xianglong Liu 001; Lorenzo Torresani; Jian Peng 001; Qiang Liu 001 (AISTATS, 2020)

A PTAS for the Bayesian Thresholding Bandit Problem. - Yue Qin; Jian Peng 001; Yuan Zhou 007 (AISTATS, 2020)

Root-n-Regret for Learning in Markov Decision Processes with Function Approximation and Low Bellman Rank. - Kefan Dong; Jian Peng 001; Yining Wang 001; Yuan Zhou 007 (COLT, 2020)

Harnessing Distribution Ratio Estimators for Learning Agents with Quality and Diversity. - Tanmay Gangwani; Jian Peng 001; Yuan Zhou 007 (CoRL, 2020)

Boosting Weakly Supervised Object Detection with Progressive Knowledge Transfer. - Yuanyi Zhong; Jianfeng Wang; Jian Peng 001; Lei Zhang 001 (ECCV (26), 2020)

Disentangling Controllable Object Through Video Prediction Improves Visual Reinforcement Learning. - Yuanyi Zhong; Alexander G. Schwing; Jian Peng 001 (ICASSP, 2020)

State-only Imitation with Transition Dynamics Mismatch. - Tanmay Gangwani; Jian Peng 001 (ICLR, 2020)

A Chance-Constrained Generative Framework for Sequence Optimization. - Xianggen Liu; Qiang Liu 001; Sen Song; Jian Peng 001 (ICML, 2020)

Learning Guidance Rewards with Trajectory-space Smoothing. - Tanmay Gangwani; Yuan Zhou 007; Jian Peng 001 (NeurIPS, 2020)

Off-Policy Interval Estimation with Lipschitz Value Iteration. - Ziyang Tang; Yihao Feng; Na Zhang; Jian Peng 001; Qiang Liu 001 (NeurIPS, 2020)

Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering. - Yunan Luo; Lam Vo; Hantian Ding; Yufeng Su; Yang Liu 097; Wesley Wei Qian; Huimin Zhao 007; Jian Peng 001 (RECOMB, 2020)

Mutual Information Based Knowledge Transfer Under State-Action Dimension Mismatch. - Michael Wan; Tanmay Gangwani; Jian Peng 001 (UAI, 2020)

Anchor Box Optimization for Object Detection. - Yuanyi Zhong; Jianfeng Wang; Jian Peng 001; Lei Zhang 001 (WACV, 2020)

HAL: Computer System for Scalable Deep Learning. - Volodymyr V. Kindratenko; Dawei Mu; Yan Zhan; John Maloney; Sayed Hadi Hashemi; Benjamin Rabe; Ke Xu; Roy H. Campbell; Jian Peng 001; William Gropp (PEARC, 2020)

Batch equalization with a generative adversarial network. - Wesley Wei Qian; Cassandra Xia; Subhashini Venugopalan; Arunachalam Narayanaswamy; Michelle Dimon; George W. Ashdown; Jake Baum; Jian Peng 001; D. Michael Ando (Bioinform., 2020)

cube2net: Efficient Query-Specific Network Construction with Data Cube Organization. - Carl Yang 001; Mengxiong Liu; Frank He; Jian Peng 001; Jiawei Han 001 (CoRR, 2020)

Pre-training of Graph Neural Network for Modeling Effects of Mutations on Protein-Protein Binding Affinity. - Xianggen Liu; Yunan Luo; Sen Song; Jian Peng 001 (CoRR, 2020)

Efficient Competitive Self-Play Policy Optimization. - Yuanyi Zhong; Yuan Zhou 007; Jian Peng 001 (CoRR, 2020)

When causal inference meets deep learning. - Yunan Luo; Jian Peng 001; Jianzhu Ma (Nat. Mach. Intell., 2020)

STAIR 2.0: A Generic and Automatic Algorithm to Fuse Modis, Landsat, and Sentinel-2 to Generate 10 m, Daily, and Cloud-/Gap-Free Surface Reflectance Product. - Yunan Luo; Kaiyu Guan; Jian Peng 001; Sibo Wang 005; Yizhi Huang (Remote. Sens., 2020)

DAP: Detection-Aware Pre-Training With Weak Supervision. - Yuanyi Zhong; Jianfeng Wang; Lijuan Wang; Jian Peng 001; Yu-Xiong Wang; Lei Zhang 001 (CVPR, 2021)

Pixel Contrastive-Consistent Semi-Supervised Semantic Segmentation. - Yuanyi Zhong; Bodi Yuan; Hong Wu; Zhiqiang Yuan; Jian Peng 001; Yu-Xiong Wang (ICCV, 2021)

Learning Neural Generative Dynamics for Molecular Conformation Generation. - Minkai Xu; Shitong Luo; Yoshua Bengio; Jian Peng 001; Jian Tang 005 (ICLR, 2021)

A 3D Generative Model for Structure-Based Drug Design. - Shitong Luo; Jiaqi Guan; Jianzhu Ma; Jian Peng 001 (NeurIPS, 2021)

PALM: Probabilistic area loss Minimization for Protein Sequence Alignment. - Fan Ding; Nan Jiang 012; Jianzhu Ma; Jian Peng 001; Jinbo Xu; Yexiang Xue (UAI, 2021)

Bayesian information sharing enhances detection of regulatory associations in rare cell types. - Alexander P. Wu; Jian Peng 001; Bonnie Berger; Hyunghoon Cho (Bioinform., 2021)

Coordinate-wise Control Variates for Deep Policy Gradients. - Yuanyi Zhong; Yuan Zhou 007; Jian Peng 001 (CoRR, 2021)

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity. - Xianggen Liu; Yunan Luo; Pengyong Li; Sen Song; Jian Peng 001 (PLoS Comput. Biol., 2021)

Characterizing Attacks on Deep Reinforcement Learning. - Xinlei Pan; Chaowei Xiao; Warren He; Shuang Yang; Jian Peng 001; Mingjie Sun; Mingyan Liu; Bo Li 026; Dawn Song (AAMAS, 2022)

Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. - Shitong Luo; Jiahan Li; Jiaqi Guan; Yufeng Su; Chaoran Cheng; Jian Peng 001; Jianzhu Ma (CVPR, 2022)

Imitation Learning from Observations under Transition Model Disparity. - Tanmay Gangwani; Yuan Zhou 007; Jian Peng 001 (ICLR, 2022)

Energy-Inspired Molecular Conformation Optimization. - Jiaqi Guan; Wesley Wei Qian; Qiang Liu 001; Wei-Ying Ma; Jianzhu Ma; Jian Peng 001 (ICLR, 2022)

Learning Long-Term Reward Redistribution via Randomized Return Decomposition. - Zhizhou Ren; Ruihan Guo; Yuan Zhou 007; Jian Peng 001 (ICLR, 2022)

Hindsight Foresight Relabeling for Meta-Reinforcement Learning. - Michael Wan; Jian Peng 001; Tanmay Gangwani (ICLR, 2022)

Off-Policy Reinforcement Learning with Delayed Rewards. - Beining Han; Zhizhou Ren; Zuofan Wu; Yuan Zhou 007; Jian Peng 001 (ICML, 2022)

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. - Xingang Peng; Shitong Luo; Jiaqi Guan; Qi Xie; Jian Peng 001; Jianzhu Ma (ICML, 2022)

Proximal Exploration for Model-guided Protein Sequence Design. - Zhizhou Ren; Jiahan Li; Fan Ding; Yuan Zhou 007; Jianzhu Ma; Jian Peng 001 (ICML, 2022)

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. - Shitong Luo; Yufeng Su; Xingang Peng; Sheng Wang 001; Jian Peng 001; Jianzhu Ma (NeurIPS, 2022)

Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. - Zhizhou Ren; Anji Liu; Yitao Liang; Jian Peng 001; Jianzhu Ma (NeurIPS, 2022)

Directed Weight Neural Networks for Protein Structure Representation Learning. - Jiahan Li; Shitong Luo; Congyue Deng; Chaoran Cheng; Jiaqi Guan; Leonidas J. Guibas; Jian Peng 001; Jianzhu Ma (CoRR, 2022)

FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours. - Shenggan Cheng; Ruidong Wu; Zhongming Yu; Bin-Rui Li; Xiwen Zhang; Jian Peng 001; Yang You 001 (CoRR, 2022)

A 3D Molecule Generative Model for Structure-Based Drug Design. - Shitong Luo; Jiaqi Guan; Jianzhu Ma; Jian Peng 001 (CoRR, 2022)

Is Self-Supervised Learning More Robust Than Supervised Learning? - Yuanyi Zhong; Haoran Tang; Jun-Kun Chen; Jian Peng 001; Yu-Xiong Wang (CoRR, 2022)

RECOMB 2021 Special Issue. - Jian Peng 001 (J. Comput. Biol., 2022)

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. - Jiaqi Guan; Wesley Wei Qian; Xingang Peng; Yufeng Su; Jian Peng 001; Jianzhu Ma (ICLR, 2023)

Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction. - Shitong Luo; Yufeng Su; Zuofan Wu; Chenpeng Su; Jian Peng 001; Jianzhu Ma (ICLR, 2023)

DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. - Jiaqi Guan; Xiangxin Zhou; Yuwei Yang; Yu Bao; Jian Peng 001; Jianzhu Ma; Qiang Liu 006; Liang Wang 001; Quanquan Gu (ICML, 2023)

Equivariant Neural Operator Learning with Graphon Convolution. - Chaoran Cheng; Jian Peng 001 (NeurIPS, 2023)

LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion. - Jiaqi Guan; Xingang Peng; Peiqi Jiang; Yunan Luo; Jian Peng 001; Jianzhu Ma (NeurIPS, 2023)

Calibrated geometric deep learning improves kinase-drug binding predictions. - Yunan Luo; Yang Liu 097; Jian Peng 001 (Nat. Mac. Intell., 2023)

InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. - Xingchao Liu; Xiwen Zhang; Jianzhu Ma; Jian Peng 001; Qiang Liu 001 (ICLR, 2024)

Full-Atom Peptide Design based on Multi-modal Flow Matching. - Jiahan Li; Chaoran Cheng; Zuofan Wu; Ruihan Guo; Shitong Luo; Zhizhou Ren; Jian Peng 001; Jianzhu Ma (ICML, 2024)

Projecting Molecules into Synthesizable Chemical Spaces. - Shitong Luo; Wenhao Gao 001; Zuofan Wu; Jian Peng 001; Connor W. Coley; Jianzhu Ma (ICML, 2024)

FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. - Ruidong Wu; Ruihan Guo; Rui Wang; Shitong Luo; Yue Xu; Jiahan Li; Jianzhu Ma; Qiang Liu 001; Yunan Luo; Jian Peng 001 (ICML, 2024)

Categorical Flow Matching on Statistical Manifolds. - Chaoran Cheng; Jiahan Li; Jian Peng 001; Ge Liu (NeurIPS, 2024)

Enhancing Protein Mutation Effect Prediction through a Retrieval-Augmented Framework. - Ruihan Guo; Rui Wang; Ruidong Wu; Zhizhou Ren; Jiahan Li; Shitong Luo; Zuofan Wu; Qiang Liu 001; Jian Peng 001; Jianzhu Ma (NeurIPS, 2024)

FastFold: Optimizing AlphaFold Training and Inference on GPU Clusters. - Shenggan Cheng; Xuanlei Zhao; Guangyang Lu; Jiarui Fang; Tian Zheng; Ruidong Wu; Xiwen Zhang; Jian Peng 001; Yang You 001 (PPoPP, 2024)

Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension. - Jiahan Li; Tong Chen; Shitong Luo; Chaoran Cheng; Jiaqi Guan; Ruihan Guo; Sheng Wang 001; Ge Liu; Jian Peng 001; Jianzhu Ma (CoRR, 2024)

Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset. - Khalid Usman; Fangping Wan; Dan Zhao 004; Jian Peng 001; Jianyang Zeng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Group Ligands Docking to Protein Pockets. - Jiaqi Guan; Jiahan Li; Xiangxin Zhou; Xingang Peng; Sheng Wang 001; Yunan Luo; Jian Peng 001; Jianzhu Ma (ICLR, 2025)

Orientation-Aware Networks for Protein Structure Representation Learning. - Jiahan Li; Shitong Luo; Congyue Deng; Chaoran Cheng; Jiaqi Guan; Leonidas J. Guibas; Jian Peng 001; Jianzhu Ma (RECOMB, 2025)