Pengyi Yang

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 19

Top Topics

Ensemble Learning

Similarity Metric

Top Venues

IEEE Trans. Cybern.

Publications

Manoj M. Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
Interpretable deep learning in single-cell omics. CoRR (2024)
Yue Cao, Shila Ghazanfar, Pengyi Yang, Jean Y. H. Yang
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. Briefings Bioinform. 24 (3) (2023)
Di Xiao, Hani Jieun Kim, Ignatius Pang, Pengyi Yang
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. Bioinform. 38 (7) (2022)
Yue Cao, Yingxin Lin, Ellis Patrick, Pengyi Yang, Jean Yee Hwa Yang
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. Bioinform. 38 (20) (2022)
Hani Jieun Kim, Kevin Y. X. Wang, Carissa Chen, Yingxin Lin, Patrick P. L. Tam, David M. Lin, Jean Y. H. Yang, Pengyi Yang
Uncovering cell identity through differential stability with Cepo. Nat. Comput. Sci. 1 (12) (2021)
Pengyi Yang, Hao Huang, Chunlei Liu
Feature selection revisited in the single-cell era. CoRR (2021)
Yue Cao, Thomas Andrew Geddes, Jean Yee Hwa Yang, Pengyi Yang
Ensemble deep learning in bioinformatics. Nat. Mach. Intell. 2 (9) (2020)
Hani Jieun Kim, Yingxin Lin, Thomas Andrew Geddes, Jean Yee Hwa Yang, Pengyi Yang
CiteFuse enables multi-modal analysis of CITE-seq data. Bioinform. 36 (14) (2020)
Thomas Andrew Geddes, Taiyun Kim, Lihao Nan, James G. Burchfield, Jean Yee Hwa Yang, Dacheng Tao, Pengyi Yang
Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis. BMC Bioinform. (19) (2019)
Tao Tang, Hao Wu, Wei Bao, Pengyi Yang, Dong Yuan, Bing Bing Zhou
New Parallel Algorithms for All Pairwise Computation on Large HPC Clusters. PDCAT (2019)
Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang, Pengyi Yang
Impact of similarity metrics on single-cell RNA-seq data clustering. Briefings Bioinform. 20 (6) (2019)
Yue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Yee Hwa Yang, Kitty K. Lo
scDC: single cell differential composition analysis. BMC Bioinform. (19) (2019)
Michael de Ridder, Karsten Klein, Jean Yee Hwa Yang, Pengyi Yang, Jim Lagopoulos, Ian B. Hickie, Max Bennett, Jinman Kim
An Uncertainty Visual Analytics Framework for fMRI Functional Connectivity. Neuroinformatics 17 (2) (2019)
Pengyi Yang, John T. Ormerod, Wei Liu, Chendong Ma, Albert Y. Zomaya, Jean Yee Hwa Yang
AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications. IEEE Trans. Cybern. 49 (5) (2019)
Pengyi Yang, Andrew J. Oldfield, Taiyun Kim, Andrian Yang, Jean Yee Hwa Yang, Joshua Wing Kei Ho
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. Bioinform. 33 (13) (2017)
Pengyi Yang, Wei Liu, Jean Yee Hwa Yang
Positive unlabeled learning via wrapper-based adaptive sampling. IJCAI (2017)
Chang Lu, Jun Wang, Zili Zhang, Pengyi Yang, Guo-Xian Yu
NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity. Comput. Biol. Chem. 65 (2016)
Pengyi Yang, Sean J. Humphrey, David E. James, Yee Hwa Yang, Raja Jothi
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinform. 32 (2) (2016)
Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob B. Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan F. DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman, Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau, Nagarajan Raju, Sonia P. Chothani, C. Ramakrishnan, Masakazu Sekijima, M. Michael Gromiha, Paddy J. Slator, Nigel J. Burroughs, Przemyslaw Szalaj, Zhonghui Tang, Paul J. Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski, Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens, Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic
Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. BMC Bioinform. 17 (S-3) (2016)
Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. PLoS Comput. Biol. 11 (8) (2015)
Pengyi Yang, Paul D. Yoo, Juanita I. Fernando, Bing Bing Zhou, Zili Zhang, Albert Y. Zomaya
Sample Subset Optimization Techniques for Imbalanced and Ensemble Learning Problems in Bioinformatics Applications. IEEE Trans. Cybern. 44 (3) (2014)
Pengyi Yang, Ellis Patrick, Shi-Xiong Tan, Daniel J. Fazakerley, James G. Burchfield, Christopher Gribben, Matthew J. Prior, David E. James, Yee Hwa Yang
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. Bioinform. 30 (6) (2014)
Pengyi Yang, Wei Liu, Bing Bing Zhou, Sanjay Chawla, Albert Y. Zomaya
Ensemble-Based Wrapper Methods for Feature Selection and Class Imbalance Learning. PAKDD (1) (2013)
Penghao Wang, Pengyi Yang, Jean Yee Hwa Yang
OCAP: an open comprehensive analysis pipeline for iTRAQ. Bioinform. 28 (10) (2012)
Pengyi Yang, Jie Ma, Penghao Wang, Yunping Zhu, Bing Bing Zhou, Jean Yee Hwa Yang
Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (5) (2012)
Pengyi Yang, Joshua Wing Kei Ho, Jean Yee Hwa Yang, Bing Bing Zhou
Gene-gene interaction filtering with ensemble of filters. BMC Bioinform. 12 (S-1) (2011)
Pengyi Yang, Zili Zhang, Bing Bing Zhou, Albert Y. Zomaya
Sample Subset Optimization for Classifying Imbalanced Biological Data. PAKDD (2) (2011)
Penghao Wang, Pengyi Yang, Jonathan Arthur, Jean Yee Hwa Yang
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinform. 26 (18) (2010)
Pengyi Yang, Joshua Wing Kei Ho, Albert Y. Zomaya, Bing Bing Zhou
A genetic ensemble approach for gene-gene interaction identification. BMC Bioinform. 11 (2010)
Pengyi Yang, Zili Zhang, Bing Bing Zhou, Albert Y. Zomaya
A clustering based hybrid system for biomarker selection and sample classification of mass spectrometry data. Neurocomputing 73 (13-15) (2010)
Li Li, Pengyi Yang, Ling Ou, Zili Zhang, Peng Cheng
Genetic Algorithm-Based Multi-objective Optimisation for QoS-Aware Web Services Composition. KSEM (2010)
Pengyi Yang, Bing Bing Zhou, Zili Zhang, Albert Y. Zomaya
A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data. BMC Bioinform. 11 (S-1) (2010)
Pengyi Yang, Zili Zhang
An Embedded Two-Layer Feature Selection Approach for Microarray Data Analysis. IEEE Intell. Informatics Bull. 10 (1) (2009)
Zili Zhang, Pengyi Yang, Xindong Wu, Chengqi Zhang
An Agent-Based Hybrid System for Microarray Data Analysis. IEEE Intell. Syst. 24 (5) (2009)
Pengyi Yang, Li Tao, Liang Xu, Zili Zhang
Multiagent Framework for Bio-data Mining. RSKT (2009)
Pengyi Yang, Zili Zhang
A Clustering Based Hybrid System for Mass Spectrometry Data Analysis. PRIB (2008)
Zili Zhang, Pengyi Yang
An Ensemble of Classifiers with Genetic Algorithm Based Feature Selection. IEEE Intell. Informatics Bull. 9 (1) (2008)
Pengyi Yang, Zili Zhang
A Hybrid Approach to Selecting Susceptible Single Nucleotide Polymorphisms for Complex Disease Analysis. BMEI (1) (2008)
Pengyi Yang, Zili Zhang
Hybrid Methods to Select Informative Gene Sets in Microarray Data Classification. Australian Conference on Artificial Intelligence (2007)