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Fa Zhang 0001

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affiliation: Chinese Academy of Sciences, High Performance Computer Research Center, Beijing, China

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2020 – today

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2025
[j55]
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Hongmin Cai, Ranran Deng, Defu Yang, Fa Zhang, Guorong Wu, Jiazhou Chen:
Harmonic Wavelet Neural Network for Discovering Neuropathological Propagation Patterns in Alzheimer's Disease. IEEE J. Biomed. Health Informatics 29(1): 608-619 (2025)
2024
[j54]
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Chi Zhang, Yiran Cheng, Kaiwen Feng, Fa Zhang, Renmin Han, Jieqing Feng:
UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs. Briefings Bioinform. 26(1) (2024)
[j53]
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Junhai Qi, Chenjie Feng, Yulin Shi, Jianyi Yang, Fa Zhang, Guojun Li, Renmin Han:
FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval. Genom. Proteom. Bioinform. 22(1) (2024)
[j52]
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Zhidong Yang, Hongjia Li, Dawei Zang, Renmin Han, Fa Zhang:
Improved Denoising of Cryo-Electron Microscopy Micrographs with Simulation-Aware Pretraining. J. Comput. Biol. 31(6): 564-575 (2024)
[j51]
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Hongmin Cai, Weitian Huang, Sirui Yang, Siqi Ding, Yue Zhang, Bin Hu, Fa Zhang, Yiu-Ming Cheung:
Realize Generative Yet Complete Latent Representation for Incomplete Multi-View Learning. IEEE Trans. Pattern Anal. Mach. Intell. 46(5): 3637-3652 (2024)
[j50]
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Xiaohua Wan, Wenjing Zhang, Dehui Qiu, Sijia Li, Fa Zhang, Zhongchang Sun, Bin Hu:
MSTCA-Net: A Novel Impervious Surface Extraction Method Based on a Multistage Transformer. IEEE J. Sel. Top. Appl. Earth Obs. Remote. Sens. 17: 17945-17956 (2024)
[j49]
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Wenjian Qin, Tianming Liu, Fa Zhang:
Guest Editorial Computational Mathematics Modeling in Cancer Analysis. IEEE J. Biomed. Health Informatics 28(1): 4-6 (2024)
[j48]
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Rui Yan, Zhilong Lv, Zhidong Yang, Senlin Lin, Chun-Hou Zheng, Fa Zhang:
Sparse and Hierarchical Transformer for Survival Analysis on Whole Slide Images. IEEE J. Biomed. Health Informatics 28(1): 7-18 (2024)
[c99]
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  - conf/bcb/WangZWZFL0024
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Letian Wang, Yanbing Zhu, Xiaohua Wan, Yiming Zhang, Shuang Feng, Chang Li, Fa Zhang, Bin Hu:
Com-DNB: A novel method for identifying critical states of complex biological processes and its parallelization. BCB 2024: 29:1-29:10
[c98]
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Rongxu Guo, Cheng Chen, Jiaheng Sang, Guishan Cui, Fa Zhang, Xuefeng Cui, Shengying Li:
Advancing Template-Based Flexible Docking of P450-Heme Complexes via JAX MD. BIBM 2024: 675-680
[c97]
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Xuan Wang, Haofan Cao, Xinsheng Wang, Xiaohua Wan, Fa Zhang:
SelfAlign: Achieving Subtomogram Alignment with Self-Supervised Deep Learning. BIBM 2024: 2534-2541
[c96]
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Xuan Wang, Shiwei Liu, Xinsheng Wang, Xiaohua Wan, Fa Zhang:
Innovative 3D CTF Correction Techniques for Cryo-ET of Individual Particles. BIBM 2024: 2633-2638
[c95]
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  - conf/icic/FengWLWZH24
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Shuang Feng, Letian Wang, Chang Li, Xiaohua Wan, Fa Zhang, Bin Hu:
IG-GRD: A Model Based on Disentangled Graph Representation Learning for Imaging Genetic Data Fusion. ICIC (2) 2024: 142-153
[c94]
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Yaoyu Wang, Xiaohua Wan, Cheng Chen, Fa Zhang, Xuefeng Cui:
Central Feature Network Enables Accurate Detection of Both Small and Large Particles in Cryo-Electron Tomography. ISBRA (1) 2024: 212-223
[c93]
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Yiran Cheng, Bintao He, Fa Zhang, Renmin Han:
Serial Section Microscopy Image Inpainting Guided by Axial Optical Flow. ACM Multimedia 2024: 2964-2972
2023
[j47]
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Yutong Yu, Pengju Ding, Hongli Gao, Guozhu Liu, Fa Zhang, Bin Yu:
Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction. Briefings Bioinform. 24(2) (2023)
[j46]
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Hui Zhang, Hongjia Li, Fa Zhang, Ping Zhu:
A strategy combining denoising and cryo-EM single particle analysis. Briefings Bioinform. 24(3) (2023)
[j45]
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Dehui Qiu, Xinyue Zhang, Xiaohua Wan, Jiacheng Li, Ziheng Xu, Senlin Lin, Fa Zhang, Xuekun Song, Rui Zhang, Yulong Chen, Yuling Zheng:
A novel tongue feature extraction method on mobile devices. Biomed. Signal Process. Control. 80(Part): 104271 (2023)
[j44]
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Zhilong Lv, Yuexiao Lin, Rui Yan, Ying Wang, Fa Zhang:
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer. IEEE ACM Trans. Comput. Biol. Bioinform. 20(6): 3411-3420 (2023)
[c92]
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Cuiyuan Li, Fa Zhang, Kai Hu, Xuefeng Cui:
Variational Clustering and Denoising of Spatial Transcriptomics. BIBM 2023: 281-286
[c91]
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Tianci Li, Lulu Xie, Zhonghai Zhang, Xu Li, Bo Duan, Gang Niu, Shiwei Sun, Fa Zhang, Runting Zhang, Guangming Tan, Chunming Zhang:
Integrative Drug Discovery Platform: A Modular Approach for Efficient and Automated Virtual Screening. BIBM 2023: 365-372
[c90]
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  - conf/bibm/HuQWZWZH23
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Yulong Hu, Dehui Qiu, Xiaohua Wan, Juan Zhang, Xiaotong Wang, Fa Zhang, Bin Hu:
A Tongue Feature Extraction Method Based on a Sublingual Vein Segmentation. BIBM 2023: 1138-1143
[c89]
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  - conf/icic/FuWZ23
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Zi-Ang Fu, Xiaohua Wan, Fa Zhang:
GPU Optimization of Biological Macromolecule Multi-tilt Electron Tomography Reconstruction Algorithm. ICIC (3) 2023: 473-484
[c88]
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  - conf/igarss/ZhangQWZY23
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Wenjing Zhang, Dehui Qiu, Xiaohua Wan, Fa Zhang, Huimei Yuan:
A Novel Impervious Surface Extraction Method Based on Transformer. IGARSS 2023: 6851-6854
[c87]
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  - conf/isbra/YangLZHZ23
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Zhidong Yang, Hongjia Li, Dawei Zang, Renmin Han, Fa Zhang:
SaID: Simulation-Aware Image Denoising Pre-trained Model for Cryo-EM Micrographs. ISBRA 2023: 325-336
[i14]
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  - journals/corr/abs-2309-09217
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Bintao He, Fa Zhang, Chenjie Feng, Jianyi Yang, Xin Gao, Renmin Han:
CryoAlign: feature-based method for global and local 3D alignment of EM density maps. CoRR abs/2309.09217 (2023)
2022
[j43]
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  - journals/bioinformatics/LiZWYLLHZZ22
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Hongjia Li, Hui Zhang, Xiaohua Wan, Zhidong Yang, Chengmin Li, Jintao Li, Renmin Han, Ping Zhu, Fa Zhang:
Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling and transfer. Bioinform. 38(7): 2022-2029 (2022)
[j42]
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  - journals/bioinformatics/HeZZH22
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Bintao He, Yan Zhang, Fa Zhang, Renmin Han:
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network. Bioinform. 38(20): 4797-4805 (2022)
[j41]
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  - journals/cmpb/HaoWYLLZCZ22
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Yu Hao, Xiaohua Wan, Rui Yan, Zhiyong Liu, Jintao Li, Shihua Zhang, Xuefeng Cui, Fa Zhang:
VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms. Comput. Methods Programs Biomed. 221: 106871 (2022)
[j40]
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Hongjia Li, Ge Chen, Shan Gao, Jintao Li, Xiaohua Wan, Fa Zhang:
A Transfer Learning-Based Classification Model for Particle Pruning in Cryo-Electron Microscopy. J. Comput. Biol. 29(10): 1117-1131 (2022)
[j39]
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  - journals/sensors/YanRLRLZZ22
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Rui Yan, Fei Ren, Jintao Li, Xiaosong Rao, Zhilong Lv, Chunhou Zheng, Fa Zhang:
Nuclei-Guided Network for Breast Cancer Grading in HE-Stained Pathological Images. Sensors 22(11): 4061 (2022)
[j38]
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  - journals/tcbb/GaoHZLXZ22
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Shan Gao, Renmin Han, Xiangrui Zeng, Zhiyong Liu, Min Xu, Fa Zhang:
Macromolecules Structural Classification With a 3D Dilated Dense Network in Cryo-Electron Tomography. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 209-219 (2022)
[c86]
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Jing Gao, Fa Zhang, Kai Hu, Xuefeng Cui:
Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification. BIBM 2022: 200-205
[c85]
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Shuo Li, Hongjia Li, Chi Zhang, Fa Zhang, Xiaohua Wan:
A Segmentation-aware Synergy Network for Single Particle Recognition in Cryo-EM. BIBM 2022: 1066-1071
[c84]
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  - conf/bibm/XuQLZSZZW22
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Ziheng Xu, Dehui Qiu, Senlin Lin, Xinyue Zhang, Sheng Shi, Shengtao Zhu, Fa Zhang, Xiaohua Wan:
Temporal Correlation Network for Video Polyp Segmentation. BIBM 2022: 1317-1322
[c83]
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  - conf/icic/LiZZYZZ22
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Xiaoguang Li, Qiang Zhang, Zonglan Zuo, Rui Yan, Chunhou Zheng, Fa Zhang:
Predicting Drug-Disease Associations by Self-topological Generalized Matrix Factorization with Neighborhood Constraints. ICIC (2) 2022: 138-149
[c82]
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  - conf/igarss/ZhaoWLSZQ0LT22
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Fangyuan Zhao, Xiaohua Wan, Sijia Li, Zhongchang Sun, Wenjing Zhang, Dehui Qiu, Fa Zhang, Xinyu Liu, Guangming Tan:
CSAM: A Channel and Spatial Attention Mechanism for Impervious Surface Extraction in Difficult Areas. IGARSS 2022: 1360-1363
[c81]
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  - conf/miccai/LvYLWZ22
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Zhilong Lv, Rui Yan, Yuexiao Lin, Ying Wang, Fa Zhang:
Joint Region-Attention and Multi-scale Transformer for Microsatellite Instability Detection from Whole Slide Images in Gastrointestinal Cancer. MICCAI (2) 2022: 293-302
[i13]
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  - journals/corr/abs-2203-10035
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Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak, Giorgos Papoulias, Stavros Gerolymatos, Evangelia I. Zacharaki, Konstantinos Moustakas, Xiangrui Zeng, Sinuo Liu, Min Xu, Yaoyu Wang, Cheng Chen, Xuefeng Cui, Fa Zhang:
SHREC 2021: Classification in cryo-electron tomograms. CoRR abs/2203.10035 (2022)
2021
[j37]
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  - journals/bioinformatics/HanLYZG21
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Renmin Han, Lun Li, Peng Yang, Fa Zhang, Xin Gao:
A novel constrained reconstruction model towards high-resolution subtomogram averaging. Bioinform. 37(11): 1616-1626 (2021)
[j36]
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  - journals/bmcbi/ZhangZHZLW21
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Enze Zhang, Boheng Zhang, Shaohan Hu, Fa Zhang, Zhiyong Liu, Xiaohua Wan:
Multi-labelled proteins recognition for high-throughput microscopy images using deep convolutional neural networks. BMC Bioinform. 22-S(3): 327 (2021)
[j35]
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Yi Pan, De-Shuang Huang, Jian-Xin Wang, Fa Zhang:
Preface. J. Comput. Sci. Technol. 36(2): 231-233 (2021)
[j34]
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  - journals/midm/YanZRLLZLLRZL21
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Rui Yan, Fa Zhang, Xiaosong Rao, Zhilong Lv, Jintao Li, Lingling Zhang, Shuang Liang, Yilin Li, Fei Ren, Chunhou Zheng, Jun Liang:
Richer fusion network for breast cancer classification based on multimodal data. BMC Medical Informatics Decis. Mak. 21(1): 134 (2021)
[j33]
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  - journals/suscom/ChiZJML21
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Ce Chi, Fa Zhang, Kaixuan Ji, Avinab Marahatta, Zhiyong Liu:
Improving energy efficiency in colocation data centers for demand response. Sustain. Comput. Informatics Syst. 29(Part): 100476 (2021)
[j32]
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Kaixuan Ji, Fa Zhang, Ce Chi, Penglei Song, Biyu Zhou, Avinab Marahatta, Zhiyong Liu:
A joint energy efficiency optimization scheme based on marginal cost and workload prediction in data centers. Sustain. Comput. Informatics Syst. 32: 100596 (2021)
[j31]
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Jingrong Zhang, Zihao Wang, Zhiyong Liu, Fa Zhang:
Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI. IEEE ACM Trans. Comput. Biol. Bioinform. 18(2): 583-595 (2021)
[j30]
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Avinab Marahatta, Sandeep Pirbhulal, Fa Zhang, Reza M. Parizi, Kim-Kwang Raymond Choo, Zhiyong Liu:
Classification-Based and Energy-Efficient Dynamic Task Scheduling Scheme for Virtualized Cloud Data Center. IEEE Trans. Cloud Comput. 9(4): 1376-1390 (2021)
[j29]
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Avinab Marahatta, Qin Xin, Ce Chi, Fa Zhang, Zhiyong Liu:
PEFS: AI-Driven Prediction Based Energy-Aware Fault-Tolerant Scheduling Scheme for Cloud Data Center. IEEE Trans. Sustain. Comput. 6(4): 655-666 (2021)
[c80]
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  - conf/3dor/GubinsCSTVF0KMN21
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Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak, Giorgos Papoulias, Stavros Gerolymatos, Evangelia I. Zacharaki, Konstantinos Moustakas, Xiangrui Zeng, Sinuo Liu, Min Xu, Yaoyu Wang, Cheng Chen, Xuefeng Cui, Fa Zhang:
SHREC 2021: Classification in Cryo-electron Tomograms. 3DOR 2021: 5-17
[c79]
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  - conf/bibm/LvLYYW021
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Zhilong Lv, Yuexiao Lin, Rui Yan, Zhenghe Yang, Ying Wang, Fa Zhang:
PG-TFNet: Transformer-based Fusion Network Integrating Pathological Images and Genomic Data for Cancer Survival Analysis. BIBM 2021: 491-496
[c78]
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Senlin Lin, Xuekun Song, Ziheng Xu, Xinyue Zhang, Yingqing Lin, Rui Zhang, Yulong Chen, Fa Zhang, Dehui Qiu, Yuling Zheng, Xiaohua Wan:
Moment Invariants with Data Augmentation for Tongue Image Segmentation. BIBM 2021: 988-993
[c77]
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Chi Zhang, Hongjia Li, Xiaohua Wan, Xuemei Chen, Zhenghe Yang, Jieqing Feng, Fa Zhang:
TransPicker: a Transformer-based Framework for Particle Picking in cryoEM Micrographs. BIBM 2021: 1179-1184
[c76]
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Penglei Song, Ce Chi, Kaixuan Ji, Zhiyong Liu, Fa Zhang, Shikui Zhang, Dehui Qiu, Xiaohua Wan:
A Deep Reinforcement Learning-based Task Scheduling Algorithm for Energy Efficiency in Data Centers. ICCCN 2021: 1-9
[c75]
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Bintao He, Fa Zhang, Huanshui Zhang, Renmin Han:
A Hybrid Frequency-Spatial Domain Model for Sparse Image Reconstruction in Scanning Transmission Electron Microscopy. ICCV 2021: 2662-2671
[c74]
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Zhidong Yang, Fa Zhang, Renmin Han:
Self-Supervised Cryo-Electron Tomography Volumetric Image Restoration from Single Noisy Volume with Sparsity Constraint. ICCV 2021: 4036-4045
[c73]
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Rui Yan, Jintao Li, S. Kevin Zhou, Zhilong Lv, Xueyuan Zhang, Xiaosong Rao, Chunhou Zheng, Fei Ren, Fa Zhang:
Decomposition-and-Fusion Network for HE-Stained Pathological Image Classification. ICIC (3) 2021: 198-207
[c72]
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Qiang Zhang, Zonglan Zuo, Rui Yan, Chunhou Zheng, Fa Zhang:
Predicting Drug-Disease Associations Based on Network Consistency Projection. ICIC (3) 2021: 591-602
[c71]
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Zihao Yang, Zhaobin Cao, Xiaohua Wan, Fa Zhang, Guangming Tan:
Spatio-Temporal Features Processing Network for Change Detection in Remote Sensing Images. IGARSS 2021: 3344-3347
[c70]
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Zihao Wang, Xiaohua Wan, Zhiyong Liu, Qianshuo Fan, Fa Zhang, Guangming Tan:
A Multi-GPU Design for Large Size Cryo-EM 3D Reconstruction. IPDPS 2021: 847-858
[c69]
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Hongjia Li, Ge Chen, Shan Gao, Jintao Li, Fa Zhang:
PickerOptimizer: A Deep Learning-Based Particle Optimizer for Cryo-Electron Microscopy Particle-Picking Algorithms. ISBRA 2021: 549-560
[c68]
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Shikui Zhang, Ce Chi, Kaixuan Ji, Zhiyong Liu, Fa Zhang, Penglei Song, Huimei Yuan, Dehui Qiu, Xiaohua Wan:
A new meta-heuristic task scheduling algorithm for optimizing energy efficiency in data centers. ISPA/BDCloud/SocialCom/SustainCom 2021: 947-954
2020
[j28]
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Lun Li, Renmin Han, Zhaotian Zhang, Tiande Guo, Zhiyong Liu, Fa Zhang:
Compressed sensing improved iterative reconstruction-reprojection algorithm for electron tomography. BMC Bioinform. 21-S(6): 202 (2020)
[j27]
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  - journals/cg/GubinsCSVFHWCZM20
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Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, Remco C. Veltkamp, Friedrich Förster, Yu Hao, Xiaohua Wan, Xuefeng Cui, Fa Zhang, Emmanuel Moebel, Xiao Wang, Daisuke Kihara, Xiangrui Zeng, Min Xu, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak:
SHREC 2020: Classification in cryo-electron tomograms. Comput. Graph. 91: 279-289 (2020)
[j26]
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Zihao Wang, Jingrong Zhang, Weifang Gao, Zhiyong Liu, Xiaohua Wan, Fa Zhang:
A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography. J. Comput. Biol. 27(2): 212-222 (2020)
[c67]
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Rui Yan, Jintao Li, Xiaosong Rao, Zhilong Lv, Chunhou Zheng, Jinjin Dou, Xiaowen Wang, Fei Ren, Fa Zhang:
NANet: Nuclei-Aware Network for Grading of Breast Cancer in HE Stained Pathological Images. BIBM 2020: 865-870
[c66]
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Baorong Shi, Hong Zhang, Rui Yan, Wang Jing, Jinfeng Zang, Fa Zhang:
LR-Net: A Multi-task Model Using Relationship-based Contour Information to Enhance the Semantic Segmentation of Cancer Regions. BIBM 2020: 2371-2378
[c65]
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Kaixuan Ji, Ce Chi, Avinab Marahatta, Fa Zhang, Zhiyong Liu:
Energy Efficient Scheduling Based on Marginal Cost and Task Grouping in Data Centers. e-Energy 2020: 482-488
[c64]
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Ce Chi, Kaixuan Ji, Avinab Marahatta, Penglei Song, Fa Zhang, Zhiyong Liu:
Jointly Optimizing the IT and Cooling Systems for Data Center Energy Efficiency based on Multi-Agent Deep Reinforcement Learning. e-Energy 2020: 489-495
[c63]
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Avinab Marahatta, Ce Chi, Kaixuan Ji, Carlos Juiz, Fa Zhang, Zhiyong Liu:
Eco-friendly Dynamic Task Scheduling for Regional Data Center. e-Energy 2020: 566-571
[c62]
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Xiang Shi, Fa Zhang, Zhiyong Liu:
PriorityBucket: A Multipath-QUIC Scheduler on Accelerating First Rendering Time in Page Loading. e-Energy 2020: 572-577
[c61]
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Ce Chi, Kaixuan Ji, Avinab Marahatta, Fa Zhang, Youshi Wang, Zhiyong Liu:
An Energy Saving-Oriented Incentive Mechanism in Colocation Data Centers. ICCCN 2020: 1-6
[c60]
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Xiang Shi, Lin Wang, Fa Zhang, Biyu Zhou, Zhiyong Liu:
PStream: Priority-Based Stream Scheduling for Heterogeneous Paths in Multipath-QUIC. ICCCN 2020: 1-8
[c59]
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Zhonglie Wang, Rui Yan, Jie Liu, Yudong Liu, Fei Ren, Chunhou Zheng, Fa Zhang:
An Integration Framework for Liver Cancer Subtype Classification and Survival Prediction Based on Multi-omics Data. ICIC (3) 2020: 247-257
[c58]
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Shan Gao, Renmin Han, Xiangrui Zeng, Xuefeng Cui, Zhiyong Liu, Min Xu, Fa Zhang:
Dilated-DenseNet for Macromolecule Classification in Cryo-electron Tomography. ISBRA 2020: 82-94
[c57]
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Ce Chi, Kaixuan Ji, Avinab Marahatta, Fa Zhang, Youshi Wang, Zhiyong Liu:
An Incentive Mechanism for Improving Energy Efficiency of Colocation Data Centers Based on Power Prediction. ISCC 2020: 1-6

2010 – 2019

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2019
[j25]
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Renmin Han, Xiaohua Wan, Lun Li, Albert F. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang:
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. Bioinform. 35(2): 319-328 (2019)
[j24]
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Renmin Han, Zhipeng Bao, Xiangrui Zeng, Tongxin Niu, Fa Zhang, Min Xu, Xin Gao:
A joint method for marker-free alignment of tilt series in electron tomography. Bioinform. 35(14): i249-i259 (2019)
[j23]
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Jingrong Zhang, Zihao Wang, Yu Chen, Renmin Han, Zhiyong Liu, Fei Sun, Fa Zhang:
PIXER: an automated particle-selection method based on segmentation using a deep neural network. BMC Bioinform. 20(1): 41:1-41:14 (2019)
[j22]
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Xiang Shi, Lin Wang, Fa Zhang, Kai Zheng, Max Mühlhäuser, Zhiyong Liu:
PABO: Mitigating congestion via packet bounce in data center networks. Comput. Commun. 140-141: 1-14 (2019)
[j21]
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Avinab Marahatta, Youshi Wang, Fa Zhang, Arun Kumar Sangaiah, Sumarga Kumar Sah Tyagi, Zhiyong Liu:
Energy-Aware Fault-Tolerant Dynamic Task Scheduling Scheme for Virtualized Cloud Data Centers. Mob. Networks Appl. 24(3): 1063-1077 (2019)
[j20]
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Youshi Wang, Fa Zhang, Ce Chi, Shaolei Ren, Fangming Liu, Rui Wang, Zhiyong Liu:
A market-oriented incentive mechanism for emergency demand response in colocation data centers. Sustain. Comput. Informatics Syst. 22: 13-25 (2019)
[c56]
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Ilja Gubins, Gijs van der Schot, Remco C. Veltkamp, Friedrich Förster, Xuefeng Du, Xiangrui Zeng, Zhenxi Zhu, Lufan Chang, Min Xu, Emmanuel Moebel, Antonio Martínez-Sánchez, Charles Kervrann, Tuan Manh Lai, Xusi Han, Genki Terashi, Daisuke Kihara, Benjamin A. Himes, Xiaohua Wan, Jingrong Zhang, Shan Gao, Yu Hao, Zhilong Lv, Xiaohua Wan, Zhidong Yang, Zijun Ding, Xuefeng Cui, Fa Zhang:
Classification in Cryo-Electron Tomograms. 3DOR@Eurographics 2019: 49-54
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Zhilong Lv, Rui Yan, Xinyu Liu, Zhongke Wu, Yicheng Zhu, Shiwei Sun, Fa Zhang, Xingce Wang, Xiaohua Wan:
Cerebrovascular Segmentation Algorithm Based on Focused Multi-Gaussians Model and Weighted 3D Markov Random Field. BIBM 2019: 846-851
[c54]
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Hong Zhang, Fa Zhang, Fei Ren, Zhonglie Wang, Xiaosong Rao, Li Li, Junbo Hao, Rui Yan, Jiancheng Luo, Ming Du:
Predicting Tumor Mutational Burden from Liver Cancer Pathological Images Using Convolutional Neural Network. BIBM 2019: 920-925
[c53]
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Enze Zhang, Boheng Zhang, Shaohan Hu, Fa Zhang, Xiaohua Wan:
Classifying Mixed Patterns of Proteins in High-Throughput Microscopy Images Using Deep Neural Networks. ICIC (1) 2019: 448-459
[c52]
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Rui Yan, Fei Ren, Xiaosong Rao, Baorong Shi, Tiange Xiang, Lingling Zhang, Yudong Liu, Jun Liang, Chunhou Zheng, Fa Zhang:
Integration of Multimodal Data for Breast Cancer Classification Using a Hybrid Deep Learning Method. ICIC (1) 2019: 460-469
[c51]
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Xiang Shi, Lin Wang, Fa Zhang, Zhiyong Liu:
FStream: Flexible Stream Scheduling and Prioritizing in Multipath-QUIC. ICPADS 2019: 921-924
[c50]
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Zihao Wang, Jingrong Zhang, Xintong Liu, Zhiyong Liu, Xiaohua Wan, Fa Zhang:
DM-SIRT: A Distributed Method for Multi-tilt Reconstruction in Electron Tomography. ISBRA 2019: 220-231
2018
[j19]
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Renmin Han, Fa Zhang, Xin Gao:
A fast fiducial marker tracking model for fully automatic alignment in electron tomography. Bioinform. 34(5): 853-863 (2018)
[j18]
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Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han:
DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. Bioinform. 34(13): i284-i294 (2018)
[j17]
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Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang:
ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer. J. Comput. Biol. 25(3): 270-281 (2018)
[c49]
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Yu Hao, Renmin Han, Xiaohua Wan, Fa Zhang, Shiwei Sun:
Fiducial marker detection via deep learning approach for electron tomography. BIBM 2018: 642-645
[c48]
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Zihao Wang, Mingzhe Zhang, Jingrong Zhang, Rui Yan, Xiaohua Wan, Zhiyong Liu, Fa Zhang, Xuefeng Cui:
Mmalloc: A Dynamic Memory Management on Many-core Coprocessor for the Acceleration of Storage-intensive Bioinformatics Application. BIBM 2018: 771-774
[c47]
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Rui Yan, Fei Ren, Zihao Wang, Lihua Wang, Yubo Ren, Yudong Liu, Xiaosong Rao, Chunhou Zheng, Fa Zhang:
A Hybrid Convolutional and Recurrent Deep Neural Network for Breast Cancer Pathological Image Classification. BIBM 2018: 957-962
[c46]
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Avinab Marahatta, Ce Chi, Fa Zhang, Zhiyong Liu:
Energy-aware Fault-tolerant Scheduling Scheme based on Intelligent Prediction Model for Cloud Data Center. IGSC 2018: 1-8
[c45]
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Jingrong Zhang, Zihao Wang, Yu Chen, Zhiyong Liu, Fa Zhang:
Memory-Efficient and Stabilizing Management System and Parallel Methods for RELION Using CUDA and MPI. ISBRA 2018: 205-216
[e1]
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Fa Zhang, Zhipeng Cai, Pavel Skums, Shihua Zhang:
Bioinformatics Research and Applications - 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. Lecture Notes in Computer Science 10847, Springer 2018, ISBN 978-3-319-94967-3 [contents]
[i12]
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Xiang Shi, Lin Wang, Fa Zhang, Kai Zheng, Max Mühlhäuser, Zhiyong Liu:
PABO: A Link-Layer Congestion Mitigation Mechanism Based on Packet Bounce. CoRR abs/1802.07429 (2018)
[i11]
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Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han:
DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. CoRR abs/1805.07777 (2018)
[i10]
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  - journals/corr/abs-1811-11729
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Enze Zhang, Fa Zhang, Zhiyong Liu, Xiaohua Wan, Lifa Zhu:
SegET: Deep Neural Network with Rich Contextual Features for Cellular Structures Segmentation in Electron Tomography Image. CoRR abs/1811.11729 (2018)
2017
[j16]
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Fa Zhang, Yu Chen, Fei Ren, Xuan Wang, Zhiyong Liu, Xiaohua Wan:
A Two-Phase Improved Correlation Method for Automatic Particle Selection in Cryo-EM. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 316-325 (2017)
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Xibo Jin, Fa Zhang, Lin Wang, Songlin Hu, Biyu Zhou, Zhiyong Liu:
Joint Optimization of Operational Cost and Performance Interference in Cloud Data Centers. IEEE Trans. Cloud Comput. 5(4): 697-711 (2017)
[j14]
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Dawei Li, Jie Wu, Zhiyong Liu, Fa Zhang:
Towards the Tradeoffs in Designing Data Center Network Architectures. IEEE Trans. Parallel Distributed Syst. 28(1): 260-273 (2017)
[c44]
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Biyu Zhou, Jie Wu, Lin Wang, Fa Zhang, Zhiyong Liu:
Joint Optimization of Server and Network Resource Utilization in Cloud Data Centers. GLOBECOM 2017: 1-6
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Youshi Wang, Fa Zhang, Shaolei Ren, Fangming Liu, Rui Wang, Zhiyong Liu:
Energy efficiency in colocation data centers: A joint incentive mechanism approach. IGSC 2017: 1-8
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Xiang Shi, Lin Wang, Fa Zhang, Kai Zheng, Zhiyong Liu:
PABO: Congestion mitigation via packet bounce. ICC 2017: 1-6
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Biyu Zhou, Fa Zhang, Jie Wu, Zhiyong Liu:
Cost Reduction in Hybrid Clouds for Enterprise Computing. ICDCS Workshops 2017: 270-274
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Biyu Zhou, Jie Wu, Lin Wang, Fa Zhang, Zhiyong Liu:
Online Flow Scheduling with Deadline for Energy Conservation in Data Center Networks. ICPADS 2017: 578-585
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Biyu Zhou, Jie Wu, Fa Zhang, Zhiyong Liu:
Resource optimization for survivable embedding of virtual clusters in cloud data centers. IPCCC 2017: 1-8
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Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang:
Accelerating Electron Tomography Reconstruction Algorithm ICON Using the Intel Xeon Phi Coprocessor on Tianhe-2 Supercomputer. ISBRA 2017: 258-269
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Yu Chen, Zihao Wang, Lun Li, Xiaohua Wan, Fei Sun, Fa Zhang:
A Fully Automatic Geometric Parameters Determining Method for Electron Tomography. ISBRA 2017: 385-389
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Youshi Wang, Fa Zhang, Rui Wang, Yangguang Shi, Hua Guo, Zhiyong Liu:
Real-time Task Scheduling for joint energy efficiency optimization in data centers. ISCC 2017: 838-843
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Yangguang Shi, Fa Zhang, Zhiyong Liu:
Hardness of Routing for Minimizing Superlinear Polynomial Cost in Directed Graphs. TAMC 2017: 571-585
2016
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Biyu Zhou, Fa Zhang, Lin Wang, Chenying Hou, Antonio Fernández Anta, Athanasios V. Vasilakos, Youshi Wang, Jie Wu, Zhiyong Liu:
HDEER: A Distributed Routing Scheme for Energy-Efficient Networking. IEEE J. Sel. Areas Commun. 34(5): 1713-1727 (2016)
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Xiujuan Sun, Fa Zhang, Xiaohua Wan, Jinzhi Zhang:
aWGRS: Automates paired-end whole genome re-sequencing data analysis framework. BIBM 2016: 910-916
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Mingzhe Zhang, Yangguang Shi, Fa Zhang, Zhiyong Liu:
COMRANCE: A rapid method for Network-on-Chip design space exploration. IGSC 2016: 1-8
[i9]
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Xibo Jin, Fa Zhang, Athanasios V. Vasilakos, Zhiyong Liu:
Green Data Centers: A Survey, Perspectives, and Future Directions. CoRR abs/1608.00687 (2016)
2015
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Xibo Jin, Fa Zhang, Liya Fan, Ying Song, Zhiyong Liu:
Scheduling for energy minimization on restricted parallel processors. J. Parallel Distributed Comput. 81-82: 36-46 (2015)
[j11]
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Yangguang Shi, Fa Zhang, Jie Wu, Zhiyong Liu:
Randomized oblivious integral routing for minimizing power cost. Theor. Comput. Sci. 607: 221-246 (2015)
[c32]
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Youshi Wang, Fa Zhang, Zhiyong Liu:
Truthful Strategy and Resource Integration for Multi-tenant Data Center Demand Response. FAW 2015: 259-270
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Dawei Li, Jie Wu, Zhiyong Liu, Fa Zhang:
Dual-centric Data Center Network Architectures. ICPP 2015: 679-688
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Lin Wang, Antonio Fernández Anta, Fa Zhang, Jie Wu, Zhiyong Liu:
Multi-resource energy-efficient routing in cloud data centers with network-as-a-service. ISCC 2015: 694-699
[i8]
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Lin Wang, Antonio Fernández Anta, Fa Zhang, Jie Wu, Zhiyong Liu:
Multi-resource Energy-efficient Routing in Cloud Data Centers with Networks-as-a-Service. CoRR abs/1501.05086 (2015)
2014
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Lin Wang, Fa Zhang, Jordi Arjona Aroca, Athanasios V. Vasilakos, Kai Zheng, Chenying Hou, Dan Li, Zhiyong Liu:
GreenDCN: A General Framework for Achieving Energy Efficiency in Data Center Networks. IEEE J. Sel. Areas Commun. 32(1): 4-15 (2014)
[c29]
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Yangguang Shi, Fa Zhang, Zhiyong Liu:
Oblivious Integral Routing for Minimizing the Quadratic Polynomial Cost. FAW 2014: 216-228
[c28]
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Lin Wang, Fa Zhang, Kai Zheng, Athanasios V. Vasilakos, Shaolei Ren, Zhiyong Liu:
Energy-Efficient Flow Scheduling and Routing with Hard Deadlines in Data Center Networks. ICDCS 2014: 248-257
[c27]
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Yangguang Shi, Fa Zhang, Zhiyong Liu:
Polylogarithmic Competitive Algorithm for Energy Minimization in Optical WDM Networks. ICNP 2014: 197-202
[c26]
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Dawei Li, Jie Wu, Zhiyong Liu, Fa Zhang:
Joint power optimization through VM placement and flow scheduling in data centers. IPCCC 2014: 1-8
[c25]
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Jingrong Zhang, Xiaohua Wan, Fa Zhang, Fei Ren, Xuan Wang, Zhiyong Liu:
A Parallel Scheme for Three-Dimensional Reconstruction in Large-Field Electron Tomography. ISBRA 2014: 102-113
[c24]
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Yu Chen, Fei Ren, Xiaohua Wan, Xuan Wang, Fa Zhang:
An Improved Correlation Method Based on Rotation Invariant Feature for Automatic Particle Selection. ISBRA 2014: 114-125
[c23]
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Biyu Zhou, Lin Wang, Fa Zhang, Xibo Jin, Zhiyong Liu:
DEER: A distributed routing scheme for achieving network energy efficiency. LANMAN 2014: 1-6
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Liya Fan, Bo Gao, Xi Sun, Fa Zhang, Zhiyong Liu:
Improving the Load Balance of MapReduce Operations based on the Key Distribution of Pairs. CoRR abs/1401.0355 (2014)
[i6]
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Xibo Jin, Fa Zhang, Lin Wang, Songlin Hu, Biyu Zhou, Zhiyong Liu:
A Joint Optimization of Operational Cost and Performance Interference in Cloud Data Centers. CoRR abs/1404.2842 (2014)
[i5]
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Lin Wang, Fa Zhang, Kai Zheng, Athanasios V. Vasilakos, Shaolei Ren, Zhiyong Liu:
Energy-Efficient Flow Scheduling and Routing with Hard Deadlines in Data Center Networks. CoRR abs/1405.7484 (2014)
[i4]
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Liya Fan, Bo Gao, Fa Zhang, Zhiyong Liu:
OS4M: Achieving Global Load Balance of MapReduce Workload by Scheduling at the Operation Level. CoRR abs/1406.3901 (2014)
2013
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Gongming Wang, Fa Zhang, Qi Chu, Liya Fan, Fei Sun, Zhiyong Liu:
A fast calculation strategy of density function in ISAF reconstruction algorithm. Sci. China Inf. Sci. 56(9): 1-12 (2013)
[j8]
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Xiaohua Wan, Sebastien Phan, Albert F. Lawrence, Fa Zhang, Renmin Han, Zhiyong Liu, Mark H. Ellisman:
Iterative Methods in Large Field Electron Microscope Tomography. SIAM J. Sci. Comput. 35(5) (2013)
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Chenying Hou, Fa Zhang, Antonio Fernández Anta, Lin Wang, Zhiyong Liu:
A hop-by-hop energy efficient distributed routing scheme. SIGMETRICS Perform. Evaluation Rev. 41(3): 101-106 (2013)
[j6]
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Lin Wang, Fa Zhang, Athanasios V. Vasilakos, Chenying Hou, Zhiyong Liu:
Joint virtual machine assignment and traffic engineering for green data center networks. SIGMETRICS Perform. Evaluation Rev. 41(3): 107-112 (2013)
[c22]
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Xibo Jin, Fa Zhang, Ying Song, Liya Fan, Zhiyong Liu:
Energy-Efficient Scheduling with Time and Processors Eligibility Restrictions. Euro-Par 2013: 66-77
[c21]
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Xibo Jin, Fa Zhang, Songlin Hu, Zhiyong Liu:
Risk management for virtual machines consolidation in data centers. GLOBECOM 2013: 2872-2878
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Lin Wang, Fa Zhang, Zhiyong Liu:
Improving the Network Energy Efficiency in MapReduce Systems. ICCCN 2013: 1-7
[c19]
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Xibo Jin, Fa Zhang, Zhiyong Liu:
Discrete Min-Energy Scheduling on Restricted Parallel Processors. IPDPS Workshops 2013: 2226-2229
[c18]
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Lin Wang, Fa Zhang, Chenying Hou, Jordi Arjona Aroca, Zhiyong Liu:
Incorporating Rate Adaptation Into Green Networking for Future Data Centers. NCA 2013: 106-109
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Yangguang Shi, Fa Zhang, Zhiyong Liu:
A Universally Stable and Energy-Efficient Scheduling Protocol for Packet Switching Network. NCA 2013: 118-126
[i3]
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  - journals/corr/abs-1301-4131
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Xibo Jin, Fa Zhang, Ying Song, Liya Fan, Zhiyong Liu:
Energy-Efficient Scheduling with Time and Processors Eligibility Restrictions. CoRR abs/1301.4131 (2013)
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Lin Wang, Antonio Fernández Anta, Fa Zhang, Chenying Hou, Zhiyong Liu:
Routing for Energy Minimization with Discrete Cost Functions. CoRR abs/1302.0234 (2013)
[i1]
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Lin Wang, Fa Zhang, Jordi Arjona Aroca, Athanasios V. Vasilakos, Kai Zheng, Chenying Hou, Dan Li, Zhiyong Liu:
A General Framework for Achieving Energy Efficiency in Data Center Networks. CoRR abs/1304.3519 (2013)
2012
[j5]
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Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu:
High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs. BMC Bioinform. 13(S-10): S4 (2012)
[j4]
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Gongming Wang, Fa Zhang, Fei Sun, Zhiyong Liu:
An Accelerated ISAF Algorithm with the Fast Mapping Strategy. J. Comput. 7(2): 528-533 (2012)
[j3]
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Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu:
An effective approximation algorithm for the Malleable Parallel Task Scheduling problem. J. Parallel Distributed Comput. 72(5): 693-704 (2012)
[c16]
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Lin Wang, Antonio Fernández Anta, Fa Zhang, Chenying Hou, Zhiyong Liu:
Energy-Efficient Network Routing with Discrete Cost Functions. TAMC 2012: 307-318
2011
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Gongming Wang, Fa Zhang, Qi Chu, Fei Sun, Zhiyong Liu:
A fast mapping method in the ISAF reconstruction algorithm. EMBC 2011: 3930-3933
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Chenying Hou, Fa Zhang, Lin Wang, Zhiyong Liu:
Time-Slot Energy-Efficient Scheduling Algorithm for Capacity Limited Networks. GreenCom 2011: 16-21
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Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu:
High-Performance Blob-Based Iterative Reconstruction of Electron Tomography on Multi-GPUs. ISBRA 2011: 61-72
2010
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Qi Chu, Fa Zhang, Kai Zhang, Xiaohua Wan, Mingwei Chen, Zhiyong Liu:
An accurate, automatic method for markerless alignment of electron tomographic images. BIBM 2010: 393-396
[c11]
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Yan Jia, Ziyang Chen, Xuan Wang, Fa Zhang:
Protein Sequence Alignment Algorithm Based on Hybrid Profile Information. BIOCOMP 2010: 220-224
[c10]
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Yugang Li, Yao Lu, Fa Zhang, ZhenGe Qiu, Zhiyong Liu:
Protein classification using family profiles. FSKD 2010: 2212-2216

2000 – 2009

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2009
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  - journals/bioinformatics/FanZWL09
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Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu:
A framework to refine particle clusters produced by EMAN. Bioinform. 25(12) (2009)
[c9]
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Yugang Li, Zhiyong Liu, Fa Zhang, ZhenGe Qiu:
A New Method for Remote Protein Classification. BMEI 2009: 1-5
[c8]
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  - conf/hipc/FanZWL09
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Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu:
An effective scheduling algorithm for Linear Makespan Minimization on Unrelated Parallel Machines. HiPC 2009: 40-49
[c7]
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  - conf/icpads/WanZL09
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Xiaohua Wan, Fa Zhang, Zhiyong Liu:
Modified Simultaneous Algebraic Reconstruction Technique and its Parallelization in Cryo-electron Tomography. ICPADS 2009: 384-390
[p3]
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  - series/sci/FanZWYL09
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Liya Fan, Fa Zhang, Gongming Wang, Bo Yuan, Zhiyong Liu:
A Self-adaptive Greedy Scheduling Scheme for a Multi-Objective Optimization on Identical Parallel Machines. Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing 2009: 43-55
2008
[c6]
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  - conf/biocomp/QueZFYL08
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Xinyu Que, Fa Zhang, Shengzhong Feng, Bo Yuan, Zhiyong Liu:
An improvement method based on OrthoMCL by adding the domain information. BIOCOMP 2008: 418-423
2007
[c5]
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  dblp key:
  - conf/bibe/ZhangMLY07
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Fa Zhang, Zhaoyun Ma, Zhiyong Liu, Bo Yuan:
Using Domain-Based Structural Ensemble to Improve Structure Modeling. BIBE 2007: 835-841
[c4]
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  - conf/sac/ZhangXLY07
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Fa Zhang, Lin Xu, Zhiyong Liu, Bo Yuan:
Improved structural modeling based on conserved domain clusters and structure-anchored alignments. SAC 2007: 128-132
2006
[c3]
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  - conf/cibcb/XuZL06
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Lin Xu, Fa Zhang, Zhiyong Liu:
A profile-based protein sequence alignment algorithm for a domain clustering database. CIBCB 2006: 1-8
[c2]
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  - conf/cibcb/ZhangXCLY06
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Fa Zhang, Lin Xu, Jingchun Chen, Zhiyong Liu, Bo Yuan:
A method to integrate, assess and characterize the protein-protein interactions. CIBCB 2006: 1-7
[c1]
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  - conf/ipps/ZhangXY06
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Fa Zhang, Lin Xu, Bo Yuan:
A method to improve structural modeling based on conserved domain clusters. IPDPS 2006
2005
[p2]
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  - books/ws/05/OzerCZY05
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Hatice Gulcin Ozer, Jingchun Chen, Fa Zhang, Bo Yuan:
Clustering of eukaryotic orthologs based on sequence and Domain Similarities using the Markov Graph-Flow Algorithm. Advances in Bioinformatics and Its Applications 2005
[p1]
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  - books/ws/05/ZhangCLY05
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Fa Zhang, Jingchun Chen, Zhiyong Liu, Bo Yuan:
The Construction of Structural Templates for the Modeling of conserved protein Domains. Advances in Bioinformatics and Its Applications 2005
2004
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  - journals/chinaf/ZhangQL04
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Fa Zhang, Xiangzhen Qiao, Zhiyong Liu:
Parallel divide and conquer bio-sequence comparison based on smith-waterman algorithm. Sci. China Ser. F Inf. Sci. 47(2): 221-231 (2004)

Coauthor Index

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