Jian Peng

According to our database, Jian Peng authored at least 137 papers between 2009 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Categorical Flow Matching on Statistical Manifolds.

Chaoran Cheng, Jiahan Li, Jian Peng, Ge Liu

CoRR, 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, Yang You

Proceedings of the 29th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming, 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, Yunan Luo, Jian Peng

Proceedings of the Forty-first International Conference on Machine Learning, 2024

Projecting Molecules into Synthesizable Chemical Spaces.

Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma

Proceedings of the Forty-first International Conference on Machine Learning, 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, Jianzhu Ma

Proceedings of the Forty-first International Conference on Machine Learning, 2024

InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation.

Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu

Proceedings of the Twelfth International Conference on Learning Representations, 2024

2023

Calibrated geometric deep learning improves kinase-drug binding predictions.

Yunan Luo, Yang Liu, Jian Peng

Nat. Mac. Intell., December, 2023

LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion.

Jiaqi Guan, Xingang Peng, Peiqi Jiang, Yunan Luo, Jian Peng, Jianzhu Ma

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

Equivariant Neural Operator Learning with Graphon Convolution.

Chaoran Cheng, Jian Peng

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design.

Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu

Proceedings of the International Conference on Machine Learning, 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, Jianzhu Ma

Proceedings of the Eleventh International Conference on Learning Representations, 2023

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction.

Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma

Proceedings of the Eleventh International Conference on Learning Representations, 2023

2022

RECOMB 2021 Special Issue.

Jian Peng

J. Comput. Biol., 2022

Is Self-Supervised Learning More Robust Than Supervised Learning?

Yuanyi Zhong, Haoran Tang, Junkun Chen, Jian Peng, Yu-Xiong Wang

CoRR, 2022

A 3D Molecule Generative Model for Structure-Based Drug Design.

Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng

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, Yang You

CoRR, 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, Jianzhu Ma

CoRR, 2022

Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation.

Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures.

Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Proximal Exploration for Model-guided Protein Sequence Design.

Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma, Jian Peng

Proceedings of the International Conference on Machine Learning, 2022

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets.

Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma

Proceedings of the International Conference on Machine Learning, 2022

Off-Policy Reinforcement Learning with Delayed Rewards.

Beining Han, Zhizhou Ren, Zuofan Wu, Yuan Zhou, Jian Peng

Proceedings of the International Conference on Machine Learning, 2022

Hindsight Foresight Relabeling for Meta-Reinforcement Learning.

Michael Wan, Jian Peng, Tanmay Gangwani

Proceedings of the Tenth International Conference on Learning Representations, 2022

Learning Long-Term Reward Redistribution via Randomized Return Decomposition.

Zhizhou Ren, Ruihan Guo, Yuan Zhou, Jian Peng

Proceedings of the Tenth International Conference on Learning Representations, 2022

Energy-Inspired Molecular Conformation Optimization.

Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng

Proceedings of the Tenth International Conference on Learning Representations, 2022

Imitation Learning from Observations under Transition Model Disparity.

Tanmay Gangwani, Yuan Zhou, Jian Peng

Proceedings of the Tenth International Conference on Learning Representations, 2022

Equivariant Point Cloud Analysis via Learning Orientations for Message Passing.

Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2022

Characterizing Attacks on Deep Reinforcement Learning.

Xinlei Pan, Chaowei Xiao, Warren He, Shuang Yang, Jian Peng, Mingjie Sun, Mingyan Liu, Bo Li, Dawn Song

Proceedings of the 21st International Conference on Autonomous Agents and Multiagent Systems, 2022

2021

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity.

Xianggen Liu, Yunan Luo, Pengyong Li, Sen Song, Jian Peng

PLoS Comput. Biol., 2021

Coordinate-wise Control Variates for Deep Policy Gradients.

Yuanyi Zhong, Yuan Zhou, Jian Peng

CoRR, 2021

Bayesian information sharing enhances detection of regulatory associations in rare cell types.

Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho

Bioinform., 2021

PALM: Probabilistic area loss Minimization for Protein Sequence Alignment.

Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue

Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial Intelligence, 2021

A 3D Generative Model for Structure-Based Drug Design.

Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng

Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021

Learning Neural Generative Dynamics for Molecular Conformation Generation.

Minkai Xu, Shitong Luo, Yoshua Bengio, Jian Peng, Jian Tang

Proceedings of the 9th International Conference on Learning Representations, 2021

Pixel Contrastive-Consistent Semi-Supervised Semantic Segmentation.

Yuanyi Zhong, Bodi Yuan, Hong Wu, Zhiqiang Yuan, Jian Peng, Yu-Xiong Wang

Proceedings of the 2021 IEEE/CVF International Conference on Computer Vision, 2021

DAP: Detection-Aware Pre-Training With Weak Supervision.

Yuanyi Zhong, Jianfeng Wang, Lijuan Wang, Jian Peng, Yu-Xiong Wang, Lei Zhang

Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2021

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, Sibo Wang, Yizhi Huang

Remote. Sens., 2020

When causal inference meets deep learning.

Yunan Luo, Jian Peng, Jianzhu Ma

Nat. Mach. Intell., 2020

Efficient Competitive Self-Play Policy Optimization.

Yuanyi Zhong, Yuan Zhou, Jian Peng

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

CoRR, 2020

cube2net: Efficient Query-Specific Network Construction with Data Cube Organization.

Carl Yang, Mengxiong Liu, Frank He, Jian Peng, Jiawei Han

CoRR, 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, William Gropp

Proceedings of the PEARC '20: Practice and Experience in Advanced Research Computing, 2020

Anchor Box Optimization for Object Detection.

Yuanyi Zhong, Jianfeng Wang, Jian Peng, Lei Zhang

Proceedings of the IEEE Winter Conference on Applications of Computer Vision, 2020

Mutual Information Based Knowledge Transfer Under State-Action Dimension Mismatch.

Michael Wan, Tanmay Gangwani, Jian Peng

Proceedings of the Thirty-Sixth Conference on Uncertainty in Artificial Intelligence, 2020

Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering.

Yunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu, Wesley Wei Qian, Huimin Zhao, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2020

Off-Policy Interval Estimation with Lipschitz Value Iteration.

Ziyang Tang, Yihao Feng, Na Zhang, Jian Peng, Qiang Liu

Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020

Learning Guidance Rewards with Trajectory-space Smoothing.

Tanmay Gangwani, Yuan Zhou, Jian Peng

Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020

A Chance-Constrained Generative Framework for Sequence Optimization.

Xianggen Liu, Qiang Liu, Sen Song, Jian Peng

Proceedings of the 37th International Conference on Machine Learning, 2020

State-only Imitation with Transition Dynamics Mismatch.

Tanmay Gangwani, Jian Peng

Proceedings of the 8th International Conference on Learning Representations, 2020

Disentangling Controllable Object Through Video Prediction Improves Visual Reinforcement Learning.

Yuanyi Zhong, Alexander G. Schwing, Jian Peng

Proceedings of the 2020 IEEE International Conference on Acoustics, 2020

Boosting Weakly Supervised Object Detection with Progressive Knowledge Transfer.

Yuanyi Zhong, Jianfeng Wang, Jian Peng, Lei Zhang

Proceedings of the Computer Vision - ECCV 2020, 2020

Harnessing Distribution Ratio Estimators for Learning Agents with Quality and Diversity.

Tanmay Gangwani, Jian Peng, Yuan Zhou

Proceedings of the 4th Conference on Robot Learning, 2020

Root-n-Regret for Learning in Markov Decision Processes with Function Approximation and Low Bellman Rank.

Kefan Dong, Jian Peng, Yining Wang, Yuan Zhou

Proceedings of the Conference on Learning Theory, 2020

A PTAS for the Bayesian Thresholding Bandit Problem.

Yue Qin, Jian Peng, Yuan Zhou

Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics, 2020

Stein Variational Inference for Discrete Distributions.

Jun Han, Fan Ding, Xianglong Liu, Lorenzo Torresani, Jian Peng, Qiang Liu

Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics, 2020

2019

Identification of pathways associated with chemosensitivity through network embedding.

Sheng Wang, Edward W. Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha

PLoS Comput. Biol., 2019

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction.

Yufeng Su, Yunan Luo, Xiaoming Zhao, Yang Liu, Jian Peng

PLoS Comput. Biol., 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, Yunan Luo, Sibo Wang

CoRR, 2019

√n-Regret for Learning in Markov Decision Processes with Function Approximation and Low Bellman Rank.

Kefan Dong, Jian Peng, Yining Wang, Yuan Zhou

CoRR, 2019

Characterizing Attacks on Deep Reinforcement Learning.

Chaowei Xiao, Xinlei Pan, Warren He, Jian Peng, Mingjie Sun, Jinfeng Yi, Mingyan Liu, Bo Li, Dawn Song

CoRR, 2019

Sequence Modeling of Temporal Credit Assignment for Episodic Reinforcement Learning.

Yang Liu, Yunan Luo, Yuanyi Zhong, Xi Chen, Qiang Liu, Jian Peng

CoRR, 2019

Stochastic Variance Reduction for Deep Q-learning.

Wei-Ye Zhao, Xiya Guan, Yang Liu, Xiaoming Zhao, Jian Peng

CoRR, 2019

Metagenomic binning through low-density hashing.

Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng

Bioinform., 2019

Learning Belief Representations for Imitation Learning in POMDPs.

Tanmay Gangwani, Joel Lehman, Qiang Liu, Jian Peng

Proceedings of the Thirty-Fifth Conference on Uncertainty in Artificial Intelligence, 2019

REINAM: reinforcement learning for input-grammar inference.

Zhengkai Wu, Evan Johnson, Wei Yang, Osbert Bastani, Dawn Song, Jian Peng, Tao Xie

Proceedings of the ACM Joint Meeting on European Software Engineering Conference and Symposium on the Foundations of Software Engineering, 2019

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning.

Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2019

Thresholding Bandit with Optimal Aggregate Regret.

Chao Tao, Saúl A. Blanco, Jian Peng, Yuan Zhou

Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

Exploration via Hindsight Goal Generation.

Zhizhou Ren, Kefan Dong, Yuan Zhou, Qiang Liu, Jian Peng

Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

Quantile Stein Variational Gradient Descent for Batch Bayesian Optimization.

ChengYue Gong, Jian Peng, Qiang Liu

Proceedings of the 36th International Conference on Machine Learning, 2019

A Gradual, Semi-Discrete Approach to Generative Network Training via Explicit Wasserstein Minimization.

Yucheng Chen, Matus Telgarsky, Chao Zhang, Bolton Bailey, Daniel Hsu, Jian Peng

Proceedings of the 36th International Conference on Machine Learning, 2019

Off-Policy Evaluation and Learning from Logged Bandit Feedback: Error Reduction via Surrogate Policy.

Yuan Xie, Boyi Liu, Qiang Liu, Zhaoran Wang, Yuan Zhou, Jian Peng

Proceedings of the 7th International Conference on Learning Representations, 2019

Knowledge Flow: Improve Upon Your Teachers.

Iou-Jen Liu, Jian Peng, Alexander G. Schwing

Proceedings of the 7th International Conference on Learning Representations, 2019

Learning Self-Imitating Diverse Policies.

Tanmay Gangwani, Qiang Liu, Jian Peng

Proceedings of the 7th International Conference on Learning Representations, 2019

Accelerating Nonconvex Learning via Replica Exchange Langevin diffusion.

Yi Chen, Jinglin Chen, Jing Dong, Jian Peng, Zhaoran Wang

Proceedings of the 7th International Conference on Learning Representations, 2019

HeteSpaceyWalk: A Heterogeneous Spacey Random Walk for Heterogeneous Information Network Embedding.

Yu He, Yangqiu Song, Jianxin Li, Cheng Ji, Jian Peng, Hao Peng

Proceedings of the 28th ACM International Conference on Information and Knowledge Management, 2019

Stochastic Variance Reduction for Deep Q-learning.

Wei-Ye Zhao, Jian Peng

Proceedings of the 18th International Conference on Autonomous Agents and MultiAgent Systems, 2019

Large-Margin Classification in Hyperbolic Space.

Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger

Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 2019

2018

DPPred: An Effective Prediction Framework with Concise Discriminative Patterns.

Jingbo Shang, Meng Jiang, Wenzhu Tong, Jinfeng Xiao, Jian Peng, Jiawei Han

IEEE Trans. Knowl. Data Eng., 2018

Efficient Contextualized Representation: Language Model Pruning for Sequence Labeling.

Liyuan Liu, Xiang Ren, Jingbo Shang, Jian Peng, Jiawei Han

CoRR, 2018

Learning to Explore with Meta-Policy Gradient.

Tianbing Xu, Qiang Liu, Liang Zhao, Jian Peng

CoRR, 2018

Low-Norm Graph Embedding.

Yihan Gao, Chao Zhang, Jian Peng, Aditya G. Parameswaran

CoRR, 2018

Learning structural motif representations for efficient protein structure search.

Yang Liu, Qing Ye, Liwei Wang, Jian Peng

Bioinform., 2018

Deciphering Signaling Specificity with Deep Neural Networks.

Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2018

Generalizable Visualization of Mega-Scale Single-Cell Data.

Hyunghoon Cho, Bonnie Berger, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2018

Annotating gene sets by mining large literature collections with protein networks.

Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action.

Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Similarity Modeling on Heterogeneous Networks via Automatic Path Discovery.

Carl Yang, Mengxiong Liu, Frank He, Xikun Zhang, Jian Peng, Jiawei Han

Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2018

Energy-efficient Amortized Inference with Cascaded Deep Classifiers.

Jiaqi Guan, Yang Liu, Qiang Liu, Jian Peng

Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Efficient Localized Inference for Large Graphical Models.

Jinglin Chen, Jian Peng, Qiang Liu

Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Learning to Explore via Meta-Policy Gradient.

Tianbing Xu, Qiang Liu, Liang Zhao, Jian Peng

Proceedings of the 35th International Conference on Machine Learning, 2018

Fast and Accurate Text Classification: Skimming, Rereading and Early Stopping.

Keyi Yu, Yang Liu, Alexander G. Schwing, Jian Peng

Proceedings of the 6th International Conference on Learning Representations, 2018

Action-dependent Control Variates for Policy Optimization via Stein Identity.

Hao Liu, Yihao Feng, Yi Mao, Dengyong Zhou, Jian Peng, Qiang Liu

Proceedings of the 6th International Conference on Learning Representations, 2018

Policy Optimization by Genetic Distillation.

Tanmay Gangwani, Jian Peng

Proceedings of the 6th International Conference on Learning Representations, 2018

SemRegex: A Semantics-Based Approach for Generating Regular Expressions from Natural Language Specifications.

Zexuan Zhong, Jiaqi Guo, Wei Yang, Jian Peng, Tao Xie, Jian-Guang Lou, Ting Liu, Dongmei Zhang

Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, Brussels, Belgium, October 31, 2018

emrQA: A Large Corpus for Question Answering on Electronic Medical Records.

Anusri Pampari, Preethi Raghavan, Jennifer J. Liang, Jian Peng

Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, Brussels, Belgium, October 31, 2018

Efficient Contextualized Representation: Language Model Pruning for Sequence Labeling.

Liyuan Liu, Xiang Ren, Jingbo Shang, Xiaotao Gu, Jian Peng, Jiawei Han

Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, Brussels, Belgium, October 31, 2018

Empower Sequence Labeling with Task-Aware Neural Language Model.

Liyuan Liu, Jingbo Shang, Xiang Ren, Frank Fangzheng Xu, Huan Gui, Jian Peng, Jiawei Han

Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence, 2018

2017

Network-assisted target identification for haploinsufficiency and homozygous profiling screens.

Sheng Wang, Jian Peng

PLoS Comput. Biol., 2017

Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining.

Xiuli Ma, Guangyu Zhou, Jingbo Shang, Jingjing Wang, Jian Peng, Jiawei Han

J. Comput. Biol., 2017

Genetic Policy Optimization.

Tanmay Gangwani, Jian Peng

CoRR, 2017

Sample-efficient Policy Optimization with Stein Control Variate.

Hao Liu, Yihao Feng, Yi Mao, Dengyong Zhou, Jian Peng, Qiang Liu

CoRR, 2017

Stochastic Variance Reduction for Policy Gradient Estimation.

Tianbing Xu, Qiang Liu, Jian Peng

CoRR, 2017

Stein Variational Policy Gradient.

Yang Liu, Prajit Ramachandran, Qiang Liu, Jian Peng

Proceedings of the Thirty-Third Conference on Uncertainty in Artificial Intelligence, 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, Wenhua Kuang, Jian Peng, Ligong Chen, Jianyang Zeng

Proceedings of the Research in Computational Molecular Biology, 2017

ProSNet: integrating homology with molecular networks for protein function prediction.

Sheng Wang, Meng Qu, Jian Peng

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Scalable Visualization for High-dimensional Single-cell Data.

Juho Kim, Nate Russell, Jian Peng

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening.

Frank S. He, Yang Liu, Alexander G. Schwing, Jian Peng

Proceedings of the 5th International Conference on Learning Representations, 2017

On the Interpretability of Conditional Probability Estimates in the Agnostic Setting.

Yihan Gao, Aditya G. Parameswaran, Jian Peng

Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 2017

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, Jian Peng

CoRR, 2016

DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework.

Jingbo Shang, Wenzhu Tong, Jian Peng, Jiawei Han

Proceedings of the 2016 SIAM International Conference on Data Mining, 2016

MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance.

Jingbo Shang, Jian Peng, Jiawei Han

Proceedings of the 2016 SIAM International Conference on Data Mining, 2016

Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining.

Xiuli Ma, Guangyu Zhou, Jingjing Wang, Jian Peng, Jiawei Han

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning.

Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Exploiting temporal divergence of topic distributions for event detection.

Rongda Zhu, Aston Zhang, Jian Peng, Chengxiang Zhai

Proceedings of the 2016 IEEE International Conference on Big Data (IEEE BigData 2016), 2016

2015

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.

Sean Simmons, Jian Peng, Jadwiga R. Bienkowska, Bonnie Berger

J. Comput. Biol., 2015

Protein secondary structure prediction using deep convolutional neural fields.

Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu

CoRR, 2015

Exploiting ontology graph for predicting sparsely annotated gene function.

Sheng Wang, Hyunghoon Cho, ChengXiang Zhai, Bonnie Berger, Jian Peng

Bioinform., 2015

Estimating the Partition Function by Discriminance Sampling.

Qiang Liu, Jian Peng, Alexander Ihler, John W. Fisher III

Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 2015

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.

Hyunghoon Cho, Bonnie Berger, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2015

Exact Hybrid Covariance Thresholding for Joint Graphical Lasso.

Qingming Tang, Chao Yang, Jian Peng, Jinbo Xu

Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2015

Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage.

Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.

Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger

PLoS Comput. Biol., 2014

2013

Compressive genomics for protein databases.

Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger

Bioinform., 2013

Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling.

Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu

Proceedings of the Sixteenth International Conference on Artificial Intelligence and Statistics, 2013

2012

Approximate Inference by Intersecting Semidefinite Bound and Local Polytope.

Jian Peng, Tamir Hazan, Nathan Srebro, Jinbo Xu

Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012

A conditional neural fields model for protein threading.

Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu

Bioinform., 2012

Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs.

Tamir Hazan, Jian Peng, Amnon Shashua

Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence, 2012

Variational Inference for Crowdsourcing.

Qiang Liu, Jian Peng, Alexander Ihler

Proceedings of the Advances in Neural Information Processing Systems 25: 26th Annual Conference on Neural Information Processing Systems 2012. Proceedings of a meeting held December 3-6, 2012

2011

Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling.

Sheng Wang, Jian Peng, Jinbo Xu

Bioinform., 2011

Convex Max-Product over Compact Sets for Protein Folding.

Jian Peng, Tamir Hazan, David A. McAllester, Raquel Urtasun

Proceedings of the 28th International Conference on Machine Learning, 2011

2010

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling.

Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu

J. Comput. Biol., 2010

Fragment-free approach to protein folding using conditional neural fields.

Feng Zhao, Jian Peng, Jinbo Xu

Bioinform., 2010

Low-homology protein threading.

Jian Peng, Jinbo Xu

Bioinform., 2010

Protein 8-class secondary structure prediction using Conditional Neural Fields.

Zhiyong Wang, Feng Zhao, Jian Peng, Jinbo Xu

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009

A Probabilistic Graphical Model for Ab Initio Folding.

Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu

Proceedings of the Research in Computational Molecular Biology, 2009

Boosting Protein Threading Accuracy.

Jian Peng, Jinbo Xu

Proceedings of the Research in Computational Molecular Biology, 2009

Conditional Neural Fields.

Jian Peng, Liefeng Bo, Jinbo Xu

Proceedings of the Advances in Neural Information Processing Systems 22: 23rd Annual Conference on Neural Information Processing Systems 2009. Proceedings of a meeting held 7-10 December 2009, 2009