Ensemble Learning in Bioinformatics |
Objective
Ensemble classifiers performed well on the weak classification problems. I try to select heterogeneous classifers (eg. SVM, RF, kNN...) and vote for the last results. A friendly plug-in to weka, named libD3C, was developed and maintained.- Friendly plug-in to weka, libD3C, was developed and maintained.
- We try our methods on several bioinformatics problems.
- Baidu Tieba has employed our method for spamming filtering.
Awards
2019年度福建省自然科学奖三等奖: 集成分类和降维方法及生物信息学应用Fundings
国家自然科学基金青年基金: 基于投票机制的非编码RNA“从头预测”识别方法研究Software
libD3CPublications
1. Shixiang Wan, Yucong Duan, Quan Zou*. HPSLPred: An Ensemble Multi-label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source. Proteomics. 2017, 17: 1700262. (SCI, IF2015=4.079, PMID: 28776938)
2. Wei Chen, Pengwei Xing, Quan Zou*. Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines. Scientific Reports. 2017, 7: 40242.
3. Chen Lin*, Ying Zou, Ji Qin, Xiangrong Liu, Yi Jiang, Caihuan Ke, Quan Zou*. Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier. PLOS ONE. 2013, 8(2):e56499. (SCI, IF2010=4.411, PMID: 23437146)
4. Quan Zou, Jiasheng Guo, Ying Ju, Meihong Wu, Xiangxiang Zeng, Zhiling Hong. Improving tRNAscan-SE annotation results via ensemble classifiers. Molecular Informatics. 2015, 34(11-12):761-770. (SCI, IF2014=1.647, PMID: 28155714)
5. Quan Zou, Zhen Wang, Xinjun Guan, Bin Liu, Yunfeng Wu, Ziyu Lin. An Approach for Identifying Cytokines Based On a Novel Ensemble Classifier. BioMed Research International. 2013, 2013:686090 (SCI, IF2012=2.88, PMID: 24027761)
6. Chen Lin, Wenqiang Chen, Cheng Qiu, Yunfeng Wu, Sridhar Krishnan, Quan Zou*. LibD3C: Ensemble Classifiers with a Clustering and Dynamic Selection Strategy. Neurocomputing. 2014, 123:424-435 (SCI, IF2013=2.005)
7. Jun Wang, Quan Zou, Maozu Guo. Mining SNPs from EST sequences using filters and ensemble classifiers. Genetics and Molecular Research. 2010,9(2):820-834. (SCI, IF2010=1.013)
8. Ruifeng Xu, Jiyun Zhou, Bin Liu, Lin Yao, Yulan He, Quan Zou, Xiaolong Wang. enDNA-Prot: Identification of DNA-binding Proteins by Applying Ensemble Learning. BioMed Research International. 2014, 2014: 294279. (SCI, IF2012=2.88)
9. Weicheng Chen, Xiangrong Liu, Yong Huang, Yi Jiang, Quan Zou, Chen Lin. Improved method for predicting protein fold patterns with ensemble classifiers. Genetics and Molecular Research. 2012,11(1):174-181.(SCI, IF2010=1.013)
10. Chunyu Wang, Lingling Hu, Maozu Guo, Xiaoyan Liu, Quan Zou. imDC: an ensemble learning method for imbalanced classification with miRNA data. Genetics and Molecular Research. 2015, 14(1): 123-133 (SCI, IF2010=1.013, PMID: 25729943)
11. Xiaoqing Ru, Peigang Cao, Lihong Li, Quan Zou*. Selecting essential microRNAs using a novel voting method. Molecular Therapy-Nucleic Acids. 2019, 18: 16-23. (SCI, IF2018=5.919)
12. Jing Li, Leyi Wei, Fei Guo*, Quan Zou*. EP3: An ensemble predictor that accurately identifies type III secreted effectors. Briefings in Bioinformatics. 2021: 22(2): 1918-1928
13. Juntao Chen, Quan Zou*, Jing Li. DeepM6ASeq-EL: Prediction of Human N6-Methyladenosine (m6A) Sites with LSTM and Ensemble Learning. Frontiers of Computer Science. 2022, 16(2): 162302
14. Mengting Niu, Yuan Lin*, Quan Zou*. SgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks. Plant Molecular Biology. 2021, 105(4-5): 483-495
15. Jing Li, Lichao Zhang, Shida He, Fei Guo*, Quan Zou*. SubLocEP: A novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning. Briefings in Bioinformatics. 2021, 22(5): bbaa401
16. Kaiyang Qu, Quan Zou, Hua Shi*. Prediction of diabetic protein markers based on an ensemble method. Frontiers in Bioscience-Landmark. 2021, 26(7): 207-221.
2. Wei Chen, Pengwei Xing, Quan Zou*. Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines. Scientific Reports. 2017, 7: 40242.
3. Chen Lin*, Ying Zou, Ji Qin, Xiangrong Liu, Yi Jiang, Caihuan Ke, Quan Zou*. Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier. PLOS ONE. 2013, 8(2):e56499. (SCI, IF2010=4.411, PMID: 23437146)
4. Quan Zou, Jiasheng Guo, Ying Ju, Meihong Wu, Xiangxiang Zeng, Zhiling Hong. Improving tRNAscan-SE annotation results via ensemble classifiers. Molecular Informatics. 2015, 34(11-12):761-770. (SCI, IF2014=1.647, PMID: 28155714)
5. Quan Zou, Zhen Wang, Xinjun Guan, Bin Liu, Yunfeng Wu, Ziyu Lin. An Approach for Identifying Cytokines Based On a Novel Ensemble Classifier. BioMed Research International. 2013, 2013:686090 (SCI, IF2012=2.88, PMID: 24027761)
6. Chen Lin, Wenqiang Chen, Cheng Qiu, Yunfeng Wu, Sridhar Krishnan, Quan Zou*. LibD3C: Ensemble Classifiers with a Clustering and Dynamic Selection Strategy. Neurocomputing. 2014, 123:424-435 (SCI, IF2013=2.005)
7. Jun Wang, Quan Zou, Maozu Guo. Mining SNPs from EST sequences using filters and ensemble classifiers. Genetics and Molecular Research. 2010,9(2):820-834. (SCI, IF2010=1.013)
8. Ruifeng Xu, Jiyun Zhou, Bin Liu, Lin Yao, Yulan He, Quan Zou, Xiaolong Wang. enDNA-Prot: Identification of DNA-binding Proteins by Applying Ensemble Learning. BioMed Research International. 2014, 2014: 294279. (SCI, IF2012=2.88)
9. Weicheng Chen, Xiangrong Liu, Yong Huang, Yi Jiang, Quan Zou, Chen Lin. Improved method for predicting protein fold patterns with ensemble classifiers. Genetics and Molecular Research. 2012,11(1):174-181.(SCI, IF2010=1.013)
10. Chunyu Wang, Lingling Hu, Maozu Guo, Xiaoyan Liu, Quan Zou. imDC: an ensemble learning method for imbalanced classification with miRNA data. Genetics and Molecular Research. 2015, 14(1): 123-133 (SCI, IF2010=1.013, PMID: 25729943)
11. Xiaoqing Ru, Peigang Cao, Lihong Li, Quan Zou*. Selecting essential microRNAs using a novel voting method. Molecular Therapy-Nucleic Acids. 2019, 18: 16-23. (SCI, IF2018=5.919)
12. Jing Li, Leyi Wei, Fei Guo*, Quan Zou*. EP3: An ensemble predictor that accurately identifies type III secreted effectors. Briefings in Bioinformatics. 2021: 22(2): 1918-1928
13. Juntao Chen, Quan Zou*, Jing Li. DeepM6ASeq-EL: Prediction of Human N6-Methyladenosine (m6A) Sites with LSTM and Ensemble Learning. Frontiers of Computer Science. 2022, 16(2): 162302
14. Mengting Niu, Yuan Lin*, Quan Zou*. SgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks. Plant Molecular Biology. 2021, 105(4-5): 483-495
15. Jing Li, Lichao Zhang, Shida He, Fei Guo*, Quan Zou*. SubLocEP: A novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning. Briefings in Bioinformatics. 2021, 22(5): bbaa401
16. Kaiyang Qu, Quan Zou, Hua Shi*. Prediction of diabetic protein markers based on an ensemble method. Frontiers in Bioscience-Landmark. 2021, 26(7): 207-221.
Last revised：2021.9.22