Jian Peng

Orcid: 0000-0002-1736-2978

Affiliations:
  • HeliXon, Beijing, China
  • University of Illinois at Urbana-Champaign, Department of Computer Science, IL, USA (former)
  • Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA (former)
  • Toyota Technological Institute at Chicago, IL, USA (former)


According to our database1, Jian Peng authored at least 137 papers between 2009 and 2024.

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Bibliography

2024
Categorical Flow Matching on Statistical Manifolds.
CoRR, 2024

FastFold: Optimizing AlphaFold Training and Inference on GPU Clusters.
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.
Proceedings of the Forty-first International Conference on Machine Learning, 2024

Projecting Molecules into Synthesizable Chemical Spaces.
Proceedings of the Forty-first International Conference on Machine Learning, 2024

Full-Atom Peptide Design based on Multi-modal Flow Matching.
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.
Proceedings of the Twelfth International Conference on Learning Representations, 2024

2023
Calibrated geometric deep learning improves kinase-drug binding predictions.
Nat. Mac. Intell., December, 2023

LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion.
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.
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.
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.
Proceedings of the Eleventh International Conference on Learning Representations, 2023

3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction.
Proceedings of the Eleventh International Conference on Learning Representations, 2023

2022
RECOMB 2021 Special Issue.
J. Comput. Biol., 2022

Is Self-Supervised Learning More Robust Than Supervised Learning?
CoRR, 2022

A 3D Molecule Generative Model for Structure-Based Drug Design.
CoRR, 2022

FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours.
CoRR, 2022

Directed Weight Neural Networks for Protein Structure Representation Learning.
CoRR, 2022

Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation.
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.
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.
Proceedings of the International Conference on Machine Learning, 2022

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets.
Proceedings of the International Conference on Machine Learning, 2022

Off-Policy Reinforcement Learning with Delayed Rewards.
Proceedings of the International Conference on Machine Learning, 2022

Hindsight Foresight Relabeling for Meta-Reinforcement Learning.
Proceedings of the Tenth International Conference on Learning Representations, 2022

Learning Long-Term Reward Redistribution via Randomized Return Decomposition.
Proceedings of the Tenth International Conference on Learning Representations, 2022

Energy-Inspired Molecular Conformation Optimization.
Proceedings of the Tenth International Conference on Learning Representations, 2022

Imitation Learning from Observations under Transition Model Disparity.
Proceedings of the Tenth International Conference on Learning Representations, 2022

Equivariant Point Cloud Analysis via Learning Orientations for Message Passing.
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2022

Characterizing Attacks on Deep Reinforcement Learning.
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.
PLoS Comput. Biol., 2021

Coordinate-wise Control Variates for Deep Policy Gradients.
CoRR, 2021

Bayesian information sharing enhances detection of regulatory associations in rare cell types.
Bioinform., 2021

PALM: Probabilistic area loss Minimization for Protein Sequence Alignment.
Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial Intelligence, 2021

A 3D Generative Model for Structure-Based Drug Design.
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.
Proceedings of the 9th International Conference on Learning Representations, 2021

Pixel Contrastive-Consistent Semi-Supervised Semantic Segmentation.
Proceedings of the 2021 IEEE/CVF International Conference on Computer Vision, 2021

DAP: Detection-Aware Pre-Training With Weak Supervision.
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.
Remote. Sens., 2020

When causal inference meets deep learning.
Nat. Mach. Intell., 2020

Efficient Competitive Self-Play Policy Optimization.
CoRR, 2020

Pre-training of Graph Neural Network for Modeling Effects of Mutations on Protein-Protein Binding Affinity.
CoRR, 2020

cube2net: Efficient Query-Specific Network Construction with Data Cube Organization.
CoRR, 2020

HAL: Computer System for Scalable Deep Learning.
Proceedings of the PEARC '20: Practice and Experience in Advanced Research Computing, 2020

Anchor Box Optimization for Object Detection.
Proceedings of the IEEE Winter Conference on Applications of Computer Vision, 2020

Mutual Information Based Knowledge Transfer Under State-Action Dimension Mismatch.
Proceedings of the Thirty-Sixth Conference on Uncertainty in Artificial Intelligence, 2020

Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering.
Proceedings of the Research in Computational Molecular Biology, 2020

Off-Policy Interval Estimation with Lipschitz Value Iteration.
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.
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.
Proceedings of the 37th International Conference on Machine Learning, 2020

State-only Imitation with Transition Dynamics Mismatch.
Proceedings of the 8th International Conference on Learning Representations, 2020

Disentangling Controllable Object Through Video Prediction Improves Visual Reinforcement Learning.
Proceedings of the 2020 IEEE International Conference on Acoustics, 2020

Boosting Weakly Supervised Object Detection with Progressive Knowledge Transfer.
Proceedings of the Computer Vision - ECCV 2020, 2020

Harnessing Distribution Ratio Estimators for Learning Agents with Quality and Diversity.
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.
Proceedings of the Conference on Learning Theory, 2020

A PTAS for the Bayesian Thresholding Bandit Problem.
Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics, 2020

Stein Variational Inference for Discrete Distributions.
Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics, 2020

2019
Identification of pathways associated with chemosensitivity through network embedding.
PLoS Comput. Biol., 2019

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction.
PLoS Comput. Biol., 2019

DeepMask: an algorithm for cloud and cloud shadow detection in optical satellite remote sensing images using deep residual network.
CoRR, 2019

√n-Regret for Learning in Markov Decision Processes with Function Approximation and Low Bellman Rank.
CoRR, 2019

Characterizing Attacks on Deep Reinforcement Learning.
CoRR, 2019

Sequence Modeling of Temporal Credit Assignment for Episodic Reinforcement Learning.
CoRR, 2019

Stochastic Variance Reduction for Deep Q-learning.
CoRR, 2019

Metagenomic binning through low-density hashing.
Bioinform., 2019

Learning Belief Representations for Imitation Learning in POMDPs.
Proceedings of the Thirty-Fifth Conference on Uncertainty in Artificial Intelligence, 2019

REINAM: reinforcement learning for input-grammar inference.
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.
Proceedings of the Research in Computational Molecular Biology, 2019

Thresholding Bandit with Optimal Aggregate Regret.
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

Exploration via Hindsight Goal Generation.
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.
Proceedings of the 36th International Conference on Machine Learning, 2019

A Gradual, Semi-Discrete Approach to Generative Network Training via Explicit Wasserstein Minimization.
Proceedings of the 36th International Conference on Machine Learning, 2019

Off-Policy Evaluation and Learning from Logged Bandit Feedback: Error Reduction via Surrogate Policy.
Proceedings of the 7th International Conference on Learning Representations, 2019

Knowledge Flow: Improve Upon Your Teachers.
Proceedings of the 7th International Conference on Learning Representations, 2019

Learning Self-Imitating Diverse Policies.
Proceedings of the 7th International Conference on Learning Representations, 2019

Accelerating Nonconvex Learning via Replica Exchange Langevin diffusion.
Proceedings of the 7th International Conference on Learning Representations, 2019

HeteSpaceyWalk: A Heterogeneous Spacey Random Walk for Heterogeneous Information Network Embedding.
Proceedings of the 28th ACM International Conference on Information and Knowledge Management, 2019

Stochastic Variance Reduction for Deep Q-learning.
Proceedings of the 18th International Conference on Autonomous Agents and MultiAgent Systems, 2019

Large-Margin Classification in Hyperbolic Space.
Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 2019

2018
DPPred: An Effective Prediction Framework with Concise Discriminative Patterns.
IEEE Trans. Knowl. Data Eng., 2018

Efficient Contextualized Representation: Language Model Pruning for Sequence Labeling.
CoRR, 2018

Learning to Explore with Meta-Policy Gradient.
CoRR, 2018

Low-Norm Graph Embedding.
CoRR, 2018

Learning structural motif representations for efficient protein structure search.
Bioinform., 2018

Deciphering Signaling Specificity with Deep Neural Networks.
Proceedings of the Research in Computational Molecular Biology, 2018

Generalizable Visualization of Mega-Scale Single-Cell Data.
Proceedings of the Research in Computational Molecular Biology, 2018

Annotating gene sets by mining large literature collections with protein networks.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Similarity Modeling on Heterogeneous Networks via Automatic Path Discovery.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2018

Energy-efficient Amortized Inference with Cascaded Deep Classifiers.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Efficient Localized Inference for Large Graphical Models.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Learning to Explore via Meta-Policy Gradient.
Proceedings of the 35th International Conference on Machine Learning, 2018

Fast and Accurate Text Classification: Skimming, Rereading and Early Stopping.
Proceedings of the 6th International Conference on Learning Representations, 2018

Action-dependent Control Variates for Policy Optimization via Stein Identity.
Proceedings of the 6th International Conference on Learning Representations, 2018

Policy Optimization by Genetic Distillation.
Proceedings of the 6th International Conference on Learning Representations, 2018

SemRegex: A Semantics-Based Approach for Generating Regular Expressions from Natural Language Specifications.
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.
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.
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.
Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence, 2018

2017
Network-assisted target identification for haploinsufficiency and homozygous profiling screens.
PLoS Comput. Biol., 2017

Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining.
J. Comput. Biol., 2017

Genetic Policy Optimization.
CoRR, 2017

Sample-efficient Policy Optimization with Stein Control Variate.
CoRR, 2017

Stochastic Variance Reduction for Policy Gradient Estimation.
CoRR, 2017

Stein Variational Policy Gradient.
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.
Proceedings of the Research in Computational Molecular Biology, 2017

ProSNet: integrating homology with molecular networks for protein function prediction.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Scalable Visualization for High-dimensional Single-cell Data.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening.
Proceedings of the 5th International Conference on Learning Representations, 2017

On the Interpretability of Conditional Probability Estimates in the Agnostic Setting.
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.
CoRR, 2016

DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework.
Proceedings of the 2016 SIAM International Conference on Data Mining, 2016

MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance.
Proceedings of the 2016 SIAM International Conference on Data Mining, 2016

Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Exploiting temporal divergence of topic distributions for event detection.
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.
J. Comput. Biol., 2015

Protein secondary structure prediction using deep convolutional neural fields.
CoRR, 2015

Exploiting ontology graph for predicting sparsely annotated gene function.
Bioinform., 2015

Estimating the Partition Function by Discriminance Sampling.
Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 2015

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.
Proceedings of the Research in Computational Molecular Biology, 2015

Exact Hybrid Covariance Thresholding for Joint Graphical Lasso.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2015

Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.
PLoS Comput. Biol., 2014

2013
Compressive genomics for protein databases.
Bioinform., 2013

Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling.
Proceedings of the Sixteenth International Conference on Artificial Intelligence and Statistics, 2013

2012
Approximate Inference by Intersecting Semidefinite Bound and Local Polytope.
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012

A conditional neural fields model for protein threading.
Bioinform., 2012

Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs.
Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence, 2012

Variational Inference for Crowdsourcing.
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.
Bioinform., 2011

Convex Max-Product over Compact Sets for Protein Folding.
Proceedings of the 28th International Conference on Machine Learning, 2011

2010
A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling.
J. Comput. Biol., 2010

Fragment-free approach to protein folding using conditional neural fields.
Bioinform., 2010

Low-homology protein threading.
Bioinform., 2010

Protein 8-class secondary structure prediction using Conditional Neural Fields.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009
A Probabilistic Graphical Model for Ab Initio Folding.
Proceedings of the Research in Computational Molecular Biology, 2009

Boosting Protein Threading Accuracy.
Proceedings of the Research in Computational Molecular Biology, 2009

Conditional Neural Fields.
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


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