Jianzhu Ma

According to our database, Jianzhu Ma authored at least 78 papers between 2010 and 2024.

Collaborative distances:

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

2024

Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design.

Xiangxin Zhou, Jiaqi Guan, Yijia Zhang, Xingang Peng, Liang Wang, Jianzhu Ma

CoRR, 2024

TFG: Unified Training-Free Guidance for Diffusion Models.

Haotian Ye, Haowei Lin, Jiaqi Han, Minkai Xu, Sheng Liu, Yitao Liang, Jianzhu Ma, James Zou, Stefano Ermon

CoRR, 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

Selecting Large Language Model to Fine-tune via Rectified Scaling Law.

Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang

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

Scientific Computing with Diffractive Optical Neural Networks.

Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao

Adv. Intell. Syst., December, 2023

Extrapolating heterogeneous time-series gene expression data using Sagittarius.

Addie Woicik, Mingxin Zhang, Janelle Chan, Jianzhu Ma, Sheng Wang

Nat. Mac. Intell., July, 2023

Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning.

Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao, Jianyang Zeng

Nat. Mac. Intell., April, 2023

Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration.

Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li

Bioinform., April, 2023

MCU: A Task-centric Framework for Open-ended Agent Evaluation in Minecraft.

Haowei Lin, Zihao Wang, Jianzhu Ma, Yitao Liang

CoRR, 2023

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

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

CoRR, 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

xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data.

Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song

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

ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab.

Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu

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

MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation.

Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma

Proceedings of the International Conference on Machine Learning, 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

Learning Sparse Group Models Through Boolean Relaxation.

Yijie Wang, Yuan Zhou, Xiaoqing Huang, Kun Huang, Jie Zhang, Jianzhu Ma

Proceedings of the Eleventh International Conference on Learning Representations, 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

Boosting the Cycle Counting Power of Graph Neural Networks with I$^2$-GNNs.

Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

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

MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System.

Yubo Shao, Kaikai Zhao, Zhiwen Cao, Zhehao Peng, Xingang Peng, Pan Li, Yijie Wang, Jianzhu Ma

Sensors, 2022

Physics-informed recurrent neural network for time dynamics in optical resonances.

Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao

Nat. Comput. Sci., 2022

Quantifying the spatial homogeneity of urban road networks via graph neural networks.

Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish V. Ukkusuri, Jianzhu Ma

Nat. Mach. Intell., 2022

Boosting the Cycle Counting Power of Graph Neural Networks with I²-GNNs.

Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

CoRR, 2022

Provable Constrained Stochastic Convex Optimization with XOR-Projected Gradient Descent.

Fan Ding, Yijie Wang, Jianzhu Ma, Yexiang Xue

CoRR, 2022

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

Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng

CoRR, 2022

Device-system Co-design of Photonic Neuromorphic Processor using Reinforcement Learning.

Yingheng Tang, Princess Tara Zamani, Ruiyang Chen, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao

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

scPretrain: multi-task self-supervised learning for cell-type classification.

Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang

Bioinform., 2022

Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.

Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma

Briefings Bioinform., 2022

Understanding Dropout for Graph Neural Networks.

Juan Shu, Bowei Xi, Yu Li, Fan Wu, Charles A. Kamhoua, Jianzhu Ma

Proceedings of the Companion of The Web Conference 2022, Virtual Event / Lyon, France, April 25, 2022

Neural Predicting Higher-order Patterns in Temporal Networks.

Yunyu Liu, Jianzhu Ma, Pan Li

Proceedings of the WWW '22: The ACM Web Conference 2022, Virtual Event, Lyon, France, April 25, 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

Multiwave COVID-19 Prediction from Social Awareness Using Web Search and Mobility Data.

Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri

Proceedings of the KDD '22: The 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 14, 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

3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design.

Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang

Proceedings of the International Conference on Machine Learning, 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

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

2021

AirSign: Smartphone Authentication by Signing in the Air.

Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma

Sensors, 2021

Modeling gene regulatory networks using neural network architectures.

Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma

Nat. Comput. Sci., 2021

Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration.

Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li

CoRR, 2021

Multiwave COVID-19 Prediction via Social Awareness-Based Graph Neural Networks using Mobility and Web Search Data.

Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri

CoRR, 2021

Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics.

Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang

CoRR, 2021

Neural Higher-order Pattern (Motif) Prediction in Temporal Networks.

Yunyu Liu, Jianzhu Ma, Pan Li

CoRR, 2021

Quantifying spatial homogeneity of urban road networks via graph neural networks.

Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Satish V. Ukkusuri, Jianzhu Ma

CoRR, 2021

Disease gene prediction with privileged information and heteroscedastic dropout.

Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma

Bioinform., 2021

Predicting MHC-peptide binding affinity by differential boundary tree.

Peiyuan Feng, Jianyang Zeng, Jianzhu Ma

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

Fast Projection onto the Capped Simplex with Applications to Sparse Regression in Bioinformatics.

Andersen Man Shun Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang

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

Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns.

Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma

Proceedings of the KDD '21: The 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2021

XOR-CD: Linearly Convergent Constrained Structure Generation.

Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue

Proceedings of the 38th International Conference on Machine Learning, 2021

2020

When causal inference meets deep learning.

Yunan Luo, Jian Peng, Jianzhu Ma

Nat. Mach. Intell., 2020

Artificial-cell-type aware cell-type classification in CITE-seq.

Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen

Bioinform., 2020

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

2018

Classifying tumors by supervised network propagation.

Wei Zhang, Jianzhu Ma, Trey Ideker

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

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

2017

DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields.

Mingfu Shao, Jianzhu Ma, Sheng Wang

Bioinform., 2017

2016

AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.

Sheng Wang, Jianzhu Ma, Jinbo Xu

Bioinform., 2016

ModuleAlign: module-based global alignment of protein-protein interaction networks.

Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu

Bioinform., 2016

2015

Protein Homology Detection Through Alignment of Markov Random Fields - Using MRFalign

Jinbo Xu, Sheng Wang, Jianzhu Ma

Springer Briefs in Computer Science, Springer, ISBN: 978-3-319-14914-1, 2015

Protein secondary structure prediction using deep convolutional neural fields.

Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu

CoRR, 2015

Protein Structure Prediction by Protein Alignments.

Jianzhu Ma

CoRR, 2015

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.

Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

Bioinform., 2015

Structure Learning Constrained by Node-Specific Degree Distribution.

Jianzhu Ma, Feng Zhao, Jinbo Xu

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

Predicting diverse M-best protein contact maps.

Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 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

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields.

Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

PLoS Comput. Biol., 2014

2013

Protein contact prediction by joint evolutionary coupling analysis across multiple families.

Jianzhu Ma, Sheng Wang, Jinbo Xu

CoRR, 2013

Protein threading using context-specific alignment potential.

Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu

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

A conditional neural fields model for protein threading.

Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu

Bioinform., 2012

2010

A browser-based framework for data cache in Web-delivered service composition.

Jiyu Huang, Xuanzhe Liu, Qi Zhao, Jianzhu Ma, Gang Huang

Proceedings of the IEEE International Conference on Service-Oriented Computing and Applications, 2010