Pengyi Yang

44 papers A* 1C 2Journal 35Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data.
Bioinform.
Daniel Kim, Carissa Chen, Lijia Yu, Jean Yee Hwa Yang, Pengyi Yang
2025 J jnl
Multi-view gene panel characterization for spatially resolved omics.
Briefings Bioinform.
Daniel Kim, Wenze Ding, Akira Nguyen Shaw, Marni Torkel, Cameron J. Turtle, Pengyi Yang, Jean Y. H. Yang
2025 J jnl
The current landscape and emerging challenges of benchmarking single-cell methods.
Briefings Bioinform.
Yue Cao, Lijia Yu, Marni Torkel, Sanghyun Kim, Yingxin Lin, Pengyi Yang, Terence P. Speed, Shila Ghazanfar, Jean Yee Hwa Yang
2024 J jnl
Interpretable deep learning in single-cell omics.
Bioinform.
Manoj M. Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
2024 J jnl
Interpretable deep learning in single-cell omics.
CoRR
Manoj M. Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
2023 J jnl
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.
Briefings Bioinform.
Yue Cao, Shila Ghazanfar, Pengyi Yang, Jean Y. H. Yang
2023 J jnl
Ensemble deep learning of embeddings for clustering multimodal single-cell omics data.
Bioinform.
Lijia Yu, Chunlei Liu, Jean Yee Hwa Yang, Pengyi Yang
2022 J jnl
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities.
Bioinform.
Di Xiao, Hani Jieun Kim, Ignatius Pang, Pengyi Yang
2022 J jnl
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction.
Bioinform.
Yue Cao, Yingxin Lin, Ellis Patrick, Pengyi Yang, Jean Yee Hwa Yang
2021 J jnl
Feature selection revisited in the single-cell era.
CoRR
Pengyi Yang, Hao Huang, Chunlei Liu
2021 J jnl
Uncovering cell identity through differential stability with Cepo.
Nat. Comput. Sci.
Hani Jieun Kim, Kevin Y. X. Wang, Carissa Chen, Yingxin Lin, Patrick P. L. Tam, David M. Lin, Jean Y. H. Yang, Pengyi Yang
2020 J jnl
CiteFuse enables multi-modal analysis of CITE-seq data.
Bioinform.
Hani Jieun Kim, Yingxin Lin, Thomas Andrew Geddes, Jean Yee Hwa Yang, Pengyi Yang
2020 J jnl
Ensemble deep learning in bioinformatics.
Nat. Mach. Intell.
Yue Cao, Thomas Andrew Geddes, Jean Yee Hwa Yang, Pengyi Yang
2019 J jnl
AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications.
IEEE Trans. Cybern.
Pengyi Yang, John T. Ormerod, Wei Liu, Chendong Ma, Albert Y. Zomaya, Jean Yee Hwa Yang
2019 J jnl
An Uncertainty Visual Analytics Framework for fMRI Functional Connectivity.
Neuroinformatics
Michael de Ridder, Karsten Klein, Jean Yee Hwa Yang, Pengyi Yang, Jim Lagopoulos, Ian B. Hickie, Max Bennett, Jinman Kim
2019 J jnl
Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis.
BMC Bioinform.
Thomas Andrew Geddes, Taiyun Kim, Lihao Nan, James G. Burchfield, Jean Yee Hwa Yang, Dacheng Tao, Pengyi Yang
2019 J jnl
Impact of similarity metrics on single-cell RNA-seq data clustering.
Briefings Bioinform.
Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang, Pengyi Yang
2019 C conf
New Parallel Algorithms for All Pairwise Computation on Large HPC Clusters.
PDCAT
Tao Tang, Hao Wu, Wei Bao, Pengyi Yang, Dong Yuan, Bing Bing Zhou
2019 J jnl
scDC: single cell differential composition analysis.
BMC Bioinform.
Yue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Yee Hwa Yang, Kitty K. Lo
2017 J jnl
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells.
Bioinform.
Pengyi Yang, Andrew J. Oldfield, Taiyun Kim, Andrian Yang, Jean Yee Hwa Yang, Joshua Wing Kei Ho
2017 A* conf
Positive unlabeled learning via wrapper-based adaptive sampling.
IJCAI
Pengyi Yang, Wei Liu, Jean Yee Hwa Yang
2016 J jnl
Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015.
BMC Bioinform.
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, Raju Nagarajan, 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
2016 J jnl
NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity.
Comput. Biol. Chem.
Chang Lu, Jun Wang, Zili Zhang, Pengyi Yang, Guo-Xian Yu
2016 J jnl
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data.
Bioinform.
Pengyi Yang, Sean J. Humphrey, David E. James, Yee Hwa Yang, Raja Jothi
2015 J jnl
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.
PLoS Comput. Biol.
Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi
2014 J jnl
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway.
Bioinform.
Pengyi Yang, Ellis Patrick, Shi-Xiong Tan, Daniel J. Fazakerley, James G. Burchfield, Christopher Gribben, Matthew J. Prior, David E. James, Yee Hwa Yang
2014 J jnl
Sample Subset Optimization Techniques for Imbalanced and Ensemble Learning Problems in Bioinformatics Applications.
IEEE Trans. Cybern.
Pengyi Yang, Paul D. Yoo, Juanita I. Fernando, Bing Bing Zhou, Zili Zhang, Albert Y. Zomaya
2013 — conf
Ensemble-Based Wrapper Methods for Feature Selection and Class Imbalance Learning.
PAKDD (1)
Pengyi Yang, Wei Liu, Bing Bing Zhou, Sanjay Chawla, Albert Y. Zomaya
2012 J jnl
Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pengyi Yang, Jie Ma, Penghao Wang, Yunping Zhu, Bing Bing Zhou, Jean Yee Hwa Yang
2012 J jnl
OCAP: an open comprehensive analysis pipeline for iTRAQ.
Bioinform.
Penghao Wang, Pengyi Yang, Jean Yee Hwa Yang
2011 J jnl
Gene-gene interaction filtering with ensemble of filters.
BMC Bioinform.
Pengyi Yang, Joshua Wing Kei Ho, Jean Yee Hwa Yang, Bing Bing Zhou
2011 — conf
Sample Subset Optimization for Classifying Imbalanced Biological Data.
PAKDD (2)
Pengyi Yang, Zili Zhang, Bing Bing Zhou, Albert Y. Zomaya
2010 J jnl
A clustering based hybrid system for biomarker selection and sample classification of mass spectrometry data.
Neurocomputing
Pengyi Yang, Zili Zhang, Bing Bing Zhou, Albert Y. Zomaya
2010 J jnl
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data.
Bioinform.
Penghao Wang, Pengyi Yang, Jonathan Arthur, Jean Yee Hwa Yang
2010 J jnl
A genetic ensemble approach for gene-gene interaction identification.
BMC Bioinform.
Pengyi Yang, Joshua Wing Kei Ho, Albert Y. Zomaya, Bing Bing Zhou
2010 J jnl
A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data.
BMC Bioinform.
Pengyi Yang, Bing Bing Zhou, Zili Zhang, Albert Y. Zomaya
2010 C conf
Genetic Algorithm-Based Multi-objective Optimisation for QoS-Aware Web Services Composition.
KSEM
Li Li, Pengyi Yang, Ling Ou, Zili Zhang, Peng Cheng
2009 J jnl
An Agent-Based Hybrid System for Microarray Data Analysis.
IEEE Intell. Syst.
Zili Zhang, Pengyi Yang, Xindong Wu, Chengqi Zhang
2009 J jnl
An Embedded Two-Layer Feature Selection Approach for Microarray Data Analysis.
IEEE Intell. Informatics Bull.
Pengyi Yang, Zili Zhang
2009 — conf
Multiagent Framework for Bio-data Mining.
RSKT
Pengyi Yang, Li Tao, Liang Xu, Zili Zhang
2008 — conf
A Clustering Based Hybrid System for Mass Spectrometry Data Analysis.
PRIB
Pengyi Yang, Zili Zhang
2008 — conf
A Hybrid Approach to Selecting Susceptible Single Nucleotide Polymorphisms for Complex Disease Analysis.
BMEI (1)
Pengyi Yang, Zili Zhang
2008 J jnl
An Ensemble of Classifiers with Genetic Algorithm Based Feature Selection.
IEEE Intell. Informatics Bull.
Zili Zhang, Pengyi Yang
2007 — conf
Hybrid Methods to Select Informative Gene Sets in Microarray Data Classification.
Australian Conference on Artificial Intelligence
Pengyi Yang, Zili Zhang