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2020 – today
- 2024
[c39]Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu:
InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. ICLR 2024- [c38]Jiahan Li, Chaoran Cheng, Zuofan Wu, Ruihan Guo, Shitong Luo, Zhizhou Ren, Jian Peng, Jianzhu Ma:
Full-Atom Peptide Design based on Multi-modal Flow Matching. ICML 2024 - [c37]Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang:
Selecting Large Language Model to Fine-tune via Rectified Scaling Law. ICML 2024 - [c36]Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma:
Projecting Molecules into Synthesizable Chemical Spaces. ICML 2024 - [c35]Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng:
FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. ICML 2024 - [i33]Haowei Lin, Baizhou Huang, Haotian Ye, Qinyu Chen, Zihao Wang, Sujian Li, Jianzhu Ma, Xiaojun Wan, James Zou, Yitao Liang:
Selecting Large Language Model to Fine-tune via Rectified Scaling Law. CoRR abs/2402.02314 (2024) - [i32]Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu:
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. CoRR abs/2403.07902 (2024) - [i31]Jiahan Li, Chaoran Cheng, Zuofan Wu, Ruihan Guo, Shitong Luo, Zhizhou Ren, Jian Peng, Jianzhu Ma:
Full-Atom Peptide Design based on Multi-modal Flow Matching. CoRR abs/2406.00735 (2024) - [i30]Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor W. Coley, Jianzhu Ma:
Projecting Molecules into Synthesizable Chemical Spaces. CoRR abs/2406.04628 (2024) - [i29]Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li, Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng:
FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. CoRR abs/2407.01649 (2024) - [i28]Haotian Ye, Haowei Lin, Jiaqi Han, Minkai Xu, Sheng Liu, Yitao Liang, Jianzhu Ma, James Zou, Stefano Ermon:
TFG: Unified Training-Free Guidance for Diffusion Models. CoRR abs/2409.15761 (2024) - [i27]Xiangxin Zhou, Jiaqi Guan, Yijia Zhang, Xingang Peng, Liang Wang, Jianzhu Ma:
Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design. CoRR abs/2410.20688 (2024) - 2023
- [j24]Ruiyang Chen
, Yingheng Tang, Jianzhu Ma, Weilu Gao:
Scientific Computing with Diffractive Optical Neural Networks. Adv. Intell. Syst. 5(12) (2023) - [j23]Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li:
Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. Bioinform. 39(4) (2023) - [j22]Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao, Jianyang Zeng:
Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. Nat. Mac. Intell. 5(4): 395-407 (2023) - [j21]Addie Woicik, Mingxin Zhang, Janelle Chan, Jianzhu Ma, Sheng Wang:
Extrapolating heterogeneous time-series gene expression data using Sagittarius. Nat. Mac. Intell. 5(7): 699-713 (2023) - [c34]Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma:
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. ICLR 2023 - [c33]Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang:
Boosting the Cycle Counting Power of Graph Neural Networks with I$^2$-GNNs. ICLR 2023 - [c32]Shitong Luo, Yufeng Su, Zuofan Wu, Chenpeng Su, Jian Peng, Jianzhu Ma:
Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction. ICLR 2023 - [c31]Yijie Wang, Yuan Zhou, Xiaoqing Huang, Kun Huang, Jie Zhang, Jianzhu Ma:
Learning Sparse Group Models Through Boolean Relaxation. ICLR 2023 - [c30]Jiaqi Guan, Xiangxin Zhou, Yuwei Yang, Yu Bao, Jian Peng, Jianzhu Ma, Qiang Liu, Liang Wang, Quanquan Gu:
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design. ICML 2023: 11827-11846 - [c29]Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma:
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. ICML 2023: 27611-27629 - [c28]Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu:
ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. NeurIPS 2023 - [c27]Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song:
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. NeurIPS 2023 - [c26]Jiaqi Guan, Xingang Peng, Peiqi Jiang, Yunan Luo, Jian Peng, Jianzhu Ma:
LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion. NeurIPS 2023 - [i26]Ruiyang Chen, Yingheng Tang, Jianzhu Ma, Weilu Gao:
Scientific Computing with Diffractive Optical Neural Networks. CoRR abs/2302.10905 (2023) - [i25]Jiaqi Guan, Wesley Wei Qian, Xingang Peng, Yufeng Su, Jian Peng, Jianzhu Ma:
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction. CoRR abs/2303.03543 (2023) - [i24]Xingang Peng, Jiaqi Guan, Qiang Liu, Jianzhu Ma:
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation. CoRR abs/2305.07508 (2023) - [i23]Xingchao Liu, Xiwen Zhang, Jianzhu Ma, Jian Peng, Qiang Liu:
InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation. CoRR abs/2309.06380 (2023) - [i22]Haowei Lin, Zihao Wang, Jianzhu Ma, Yitao Liang:
MCU: A Task-centric Framework for Open-ended Agent Evaluation in Minecraft. CoRR abs/2310.08367 (2023) - [i21]Jieming Cui, Ziren Gong, Baoxiong Jia, Siyuan Huang, Zilong Zheng, Jianzhu Ma, Yixin Zhu:
ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab. CoRR abs/2311.00556 (2023) - [i20]Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song:
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. CoRR abs/2311.15156 (2023) - 2022
- [j20]Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma:
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Briefings Bioinform. 23(5) (2022) - [j19]Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang:
scPretrain: multi-task self-supervised learning for cell-type classification. Bioinform. 38(6): 1607-1614 (2022) - [j18]Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish V. Ukkusuri, Jianzhu Ma:
Quantifying the spatial homogeneity of urban road networks via graph neural networks. Nat. Mach. Intell. 4(3): 246-257 (2022) - [j17]Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao:
Physics-informed recurrent neural network for time dynamics in optical resonances. Nat. Comput. Sci. 2(3): 169-178 (2022) - [j16]Yubo Shao, Kaikai Zhao, Zhiwen Cao, Zhehao Peng, Xingang Peng, Pan Li, Yijie Wang, Jianzhu Ma:
MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System. Sensors 22(11): 4081 (2022) - [c25]Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma:
Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. CVPR 2022: 18910-18919 - [c24]Jiaqi Guan, Wesley Wei Qian, Qiang Liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng:
Energy-Inspired Molecular Conformation Optimization. ICLR 2022 - [c23]Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang:
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design. ICML 2022: 9280-9294 - [c22]Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma:
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. ICML 2022: 17644-17655 - [c21]Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma, Jian Peng:
Proximal Exploration for Model-guided Protein Sequence Design. ICML 2022: 18520-18536 - [c20]Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri:
Multiwave COVID-19 Prediction from Social Awareness Using Web Search and Mobility Data. KDD 2022: 4279-4289 - [c19]Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma:
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. NeurIPS 2022 - [c18]Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma:
Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. NeurIPS 2022 - [c17]Juan Shu, Bowei Xi, Yu Li, Fan Wu, Charles A. Kamhoua, Jianzhu Ma:
Understanding Dropout for Graph Neural Networks. WWW (Companion Volume) 2022: 1128-1138 - [c16]Yunyu Liu, Jianzhu Ma, Pan Li:
Neural Predicting Higher-order Patterns in Temporal Networks. WWW 2022: 1340-1351 - [i19]Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma:
Directed Weight Neural Networks for Protein Structure Representation Learning. CoRR abs/2201.13299 (2022) - [i18]Yingheng Tang, Princess Tara Zamani, Ruiyang Chen, Jianzhu Ma, Minghao Qi, Cunxi Yu, Weilu Gao:
Device-system Co-design of Photonic Neuromorphic Processor using Reinforcement Learning. CoRR abs/2203.06061 (2022) - [i17]Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng:
A 3D Molecule Generative Model for Structure-Based Drug Design. CoRR abs/2203.10446 (2022) - [i16]Fan Ding, Yijie Wang, Jianzhu Ma, Yexiang Xue:
Provable Constrained Stochastic Convex Optimization with XOR-Projected Gradient Descent. CoRR abs/2203.11829 (2022) - [i15]Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma:
Equivariant Point Cloud Analysis via Learning Orientations for Message Passing. CoRR abs/2203.14486 (2022) - [i14]Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma:
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets. CoRR abs/2205.07249 (2022) - [i13]Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang:
3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design. CoRR abs/2205.07309 (2022) - [i12]Yinan Huang, Xingang Peng, Jianzhu Ma, Muhan Zhang:
Boosting the Cycle Counting Power of Graph Neural Networks with I2-GNNs. CoRR abs/2210.13978 (2022) - [i11]Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma:
Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation. CoRR abs/2211.10861 (2022) - 2021
- [j15]Peiyuan Feng, Jianyang Zeng, Jianzhu Ma:
Predicting MHC-peptide binding affinity by differential boundary tree. Bioinform. 37(Supplement): 254-261 (2021) - [j14]Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma:
Disease gene prediction with privileged information and heteroscedastic dropout. Bioinform. 37(Supplement): 410-417 (2021) - [j13]Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma:
Modeling gene regulatory networks using neural network architectures. Nat. Comput. Sci. 1(7): 491-501 (2021) - [j12]Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma:
AirSign: Smartphone Authentication by Signing in the Air. Sensors 21(1): 104 (2021) - [c15]Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue:
XOR-CD: Linearly Convergent Constrained Structure Generation. ICML 2021: 2728-2738 - [c14]Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma:
Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. KDD 2021: 1541-1551 - [c13]Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng:
A 3D Generative Model for Structure-Based Drug Design. NeurIPS 2021: 6229-6239 - [c12]Andersen Man Shun Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang:
Fast Projection onto the Capped Simplex with Applications to Sparse Regression in Bioinformatics. NeurIPS 2021: 9990-9999 - [c11]Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue:
PALM: Probabilistic area loss Minimization for Protein Sequence Alignment. UAI 2021: 1100-1109 - [i10]Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Satish V. Ukkusuri, Jianzhu Ma:
Quantifying spatial homogeneity of urban road networks via graph neural networks. CoRR abs/2101.00307 (2021) - [i9]Yunyu Liu, Jianzhu Ma, Pan Li:
Neural Higher-order Pattern (Motif) Prediction in Temporal Networks. CoRR abs/2106.06039 (2021) - [i8]Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma:
Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns. CoRR abs/2106.06586 (2021) - [i7]Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang:
Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics. CoRR abs/2110.08471 (2021) - [i6]Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma, Satish V. Ukkusuri:
Multiwave COVID-19 Prediction via Social Awareness-Based Graph Neural Networks using Mobility and Web Search Data. CoRR abs/2110.11584 (2021) - [i5]Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li:
Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration. CoRR abs/2112.03266 (2021) - 2020
- [j11]Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen:
Artificial-cell-type aware cell-type classification in CITE-seq. Bioinform. 36(Supplement-1): i542-i550 (2020) - [j10]Yunan Luo, Jian Peng, Jianzhu Ma:
When causal inference meets deep learning. Nat. Mach. Intell. 2(8): 426-427 (2020)
2010 – 2019
- 2019
- [j9]Wei Zhang, Jianzhu Ma, Trey Ideker:
Classifying tumors by supervised network propagation. Bioinform. 35(14): 2528 (2019) - [c10]Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng:
Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. RECOMB 2019: 305-307 - 2018
- [j8]Wei Zhang, Jianzhu Ma, Trey Ideker:
Classifying tumors by supervised network propagation. Bioinform. 34(13): i484-i493 (2018) - [c9]Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker:
Annotating gene sets by mining large literature collections with protein networks. PSB 2018: 601-613 - [c8]Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng:
Deciphering Signaling Specificity with Deep Neural Networks. RECOMB 2018: 266-268 - 2017
- [j7]Mingfu Shao, Jianzhu Ma, Sheng Wang:
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. Bioinform. 33(14): i267-i273 (2017) - 2016
- [j6]Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu:
ModuleAlign: module-based global alignment of protein-protein interaction networks. Bioinform. 32(17): 658-664 (2016) - [j5]Sheng Wang, Jianzhu Ma, Jinbo Xu:
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. Bioinform. 32(17): 672-679 (2016) - 2015
- [b1]Jinbo Xu, Sheng Wang, Jianzhu Ma:
Protein Homology Detection Through Alignment of Markov Random Fields - Using MRFalign. Springer Briefs in Computer Science, Springer 2015, ISBN 978-3-319-14913-4, pp. 1-48 - [j4]Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinform. 31(21): 3506-3513 (2015) - [c7]Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu:
Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. BCB 2015: 166-175 - [c6]Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu:
Predicting diverse M-best protein contact maps. BIBM 2015: 1287-1295 - [c5]Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. RECOMB 2015: 218-221 - [c4]Jianzhu Ma, Feng Zhao, Jinbo Xu:
Structure Learning Constrained by Node-Specific Degree Distribution. UAI 2015: 533-541 - [i4]Jianzhu Ma:
Protein Structure Prediction by Protein Alignments. CoRR abs/1510.05682 (2015) - [i3]Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu:
Protein secondary structure prediction using deep convolutional neural fields. CoRR abs/1512.00843 (2015) - 2014
- [j3]Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. PLoS Comput. Biol. 10(3) (2014) - [c3]Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. RECOMB 2014: 173-174 - [i2]Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. CoRR abs/1401.2668 (2014) - 2013
- [j2]Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu:
Protein threading using context-specific alignment potential. Bioinform. 29(13): 257-265 (2013) - [c2]Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu:
Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. AISTATS 2013: 433-441 - [i1]Jianzhu Ma, Sheng Wang, Jinbo Xu:
Protein contact prediction by joint evolutionary coupling analysis across multiple families. CoRR abs/1312.2988 (2013) - 2012
- [j1]Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu:
A conditional neural fields model for protein threading. Bioinform. 28(12): 59-66 (2012) - 2010
- [c1]Jiyu Huang, Xuanzhe Liu, Qi Zhao, Jianzhu Ma, Gang Huang:
A browser-based framework for data cache in Web-delivered service composition. SOCA 2010: 1-8
Coauthor Index
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