Code & Data


The code or data listed below were developed or collected by MLDA members. They are shared here for facilitating the research community. They can be freely used at your own risk, given that the contributions are appropriatedly cited or acknowledged in your publications.

Note: They can only be used for academic purpose. For other purposes, please contact with Dr. Yu(guoxian85@gmail.com;gxyu@swu.edu.cn).

Data



Code


  • NetBC
    Reference: Yu G, Yu X, Wang J. Network-aided Bi-Clustering for discovering cancer subtypes[J]. Scientific Reports, 2017, 7(1): 1046.

  • NoGOA
    Reference: Yu G, Chang L, Wang J. NoGOA: predicting noisy GO annotations using evidences and sparse representation[J]. Bmc Bioinformatics, 2017, 18:350.

  • NewGOA
    Reference: Yu G, Fu G, Wang J, et al. NewGOA: Predicting new GO annotations of proteins by bi-random walks on a hybrid graph[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2018, 15(4): 1390-1402.

  • MFLDA
    Reference: Fu G, Wang J, Domeniconi C, et al. Matrix factorization-based data fusion for the prediction of lncRNA-disease associations[J]. Bioinformatics, 2017, 34(9): 1529-1537.

  • TrioMDR
    Reference: Liu J, Yu G, Ren Y, et al. TrioMDR: Detecting SNP interactions in trio families with model-based multifactor dimensionality reduction[J]. Genomics, 2018.

  • BMC3C
    Reference: Yu G, Jiang Y, Wang J, et al. BMC3C: Binning Metagenomic Contigs using Codon usage, sequence Composition and read Coverage[J]. Bioinformatics, 2018, 1: 8.

  • McWL
    Reference: Tan Q, Yu G, Domeniconi C, et al. Multi-view Weak-label Learning based on Matrix Completion[C]//Proceedings of the 2018 SIAM International Conference on Data Mining. Society for Industrial and Applied Mathematics, 2018: 450-458.

  • DRW
    Reference: Guoxian Yu, Hailong Zhu, Carlotta Domeniconi, Jiming Liu. Predicting protein function via downward random walks on a gene ontology, BMC Bioinformatics, 2015, 16: 271.

  • SimNet
    Reference: Guoxian Yu*, Guangyuan Fu+, Jun Wang, Hailong Zhu. Predicting Protein Function via Semantic Integration of Multiple Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2016, 13(2): 220-232.

  • PILL
    Reference: Guoxian Yu, Hailong Zhu, Carlotta Domeniconi. Predicting Protein Function using Incomplete Hierarchical Labels, BMC Bioinformatics, 2015, 16: 1.

  • MNet
    Reference: Guoxian Yu, Hailong Zhu, Carlotta Domeniconi, Maozu Guo. Integrating Multiple Networks for Protein Function Prediction, BMC Systems Biology, 2015, 9(S1): S3.

  • ProMK
    Reference: Guoxian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zili Zhang. Predicting Protein Function using Multiple Kernels, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (CCF Rank C), 2015, 12(1): 219-233.

  • TMEC
    Reference: Guoxian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zhiwen Yu. Protein Function Prediction using Multi-label Ensemble Classification, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (CCF Rank C), 2013, 10(4): 1045-1057.

  • NMFGO
    Reference: Guoxian Yu, Keyao Wang, Guangyuan Fu, Maozu Guo, Jun Wang. NMFGO: Gene function prediction via nonnegative matrix factorization with Gene Ontology [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018.

  • iMVWL
    Reference: Tan Q, Yu G, Domeniconi C, et al. Incomplete Multi-View Weak-Label Learning[C]//IJCAI. 2018: 2703-2709.

  • NegGOA
    Reference: Fu G, Wang J, Yang B, et al. NegGOA: negative GO annotations selection using ontology structure[J]. Bioinformatics, 2016, 32(19): 2996-3004.

  • SelMFDF
    Reference: Yuehui Wang, Guoxian Yu*, Carlotta Domeniconi, Jun Wang, Xiangliang Zhang, Maozu Guo. Selective Matrix Factorization for Multi-Relational Data Fusion. 24th International Conference on Database Systems for Advanced Applications (DASFAA), In print.

  • CoDP
    Reference: CoDP: Cooperative driver pathways discovery based on matrix factorization and tri-random walk

  • SMILE
    Reference: Qiaoyu Tan+, Yanming Yu+, Guoxian Yu, Jun Wang*. Semi-supervised multi-label classification using incomplete label information, Neurcomputing, 2017, 260: 192-202.

  • SSCDR
    Reference: Jun Wang ,Guangjun Yao+, Guoxian Yu*. Semi-supervised classification by discriminative regularization, Applied Soft Computing, 2017, 58: 245-255.

  • DeepGOA
    Reference: Guangjie Zhou+, Jun Wang, Xiangliang Zhang, and Guoxian Yu*. DeepGOA: Predicting Gene Ontology Annotations of Proteins via Graph Convolutional Network, IEEE International Conference on Bioinformatics and Biomedicine (BIBM) BiOK.

  • WSM3L
    Reference: Weakly-Supervised Multi-view Multi-instance Multi-label Learning