Publications

Publications

Professor Phoebe Chen

"The more I learn, the more I realize how much I don't know." - Albert Einstein

"It's simply a matter of doing what you do best and not worrying about what the other fellow is going to do." -- John R. Amos

"Happiness depends upon ourselves." - Aristotle

2023
Journals: 293. SQ Abbas, L Chi, YPP Chen (2023) Transformed domain convolutional neural network for alzheimer's disease diagnosis using structural MRI, Pattern Recognition 133, 109031. 292. Tung MH, Chen YPP, Liu CY, Liao CS (2023) A Fast and More Accurate Seed-and-Extension Density-based Clustering Algorithm, IEEE Transactions on Knowledge and Data Engineering. 291. B Yuan, Y Sheng, BK Bao, YPP Chen, C Xu (2023) Semantic Distance Adversarial Learning for Text-to-Image Synthesis, IEEE Transactions on Multimedia 290. P Cheng, Y Chen, M Ding, Z Chen, S Liu, YPP Chen (2023) Deep Reinforcement Learning for Online Resource Allocation in IoT Networks: Technology, Development, and Future Challenges, IEEE Communications Magazine 61 (6), 111-117 289. L Yu, W Xiang, J Fang, YPP Chen, L Chi (2023) eX-ViT: A Novel explainable vision transformer for weakly supervised semantic segmentation, Pattern Recognition 142, 109666. 288. W Lan, Y Dong, H Zhang, C Li, Q Chen, J Liu, J Wang, YPP Chen (2023) Benchmarking of computational methods for predicting circRNA-disease associations, Briefings in Bioinformatics 24 (1), bbac613 1 2023 287. T McIntosh, ASM Kayes, YPP Chen, A Ng, P Watters (2023) Applying staged event-driven access control to combat ransomware, Computers & Security 128, 103160 2 2023 286. M Luo, Z He, H Cui, YPP Chen, P Ward (2023) Class activation attention transfer neural networks for MCI conversion prediction, Computers in Biology and Medicine 156, 106700 1 2023 285. SQ Abbas, L Chi, YPP Chen (2023) DeepMNF: Deep Multimodal Neuroimaging Framework for Diagnosing Autism Spectrum Disorder Artificial Intelligence in Medicine 136, 102475 2 2023 284. R Halawani, M Buchert, YPP Chen (2023) Deep learning exploration of single-cell and spatially resolved cancer transcriptomics to unravel tumour heterogeneity, Computers in Biology and Medicine 164, 107274. Refereed conference papers: 283. Z Song, R Luo, J Yu, YPP Chen, W Yang (2023) Compact Transformer Tracker with Correlative Masked Modeling , AAAI2023 Full Accepted Paper, 2023 282. G Sharma, MAP Chamikara, MB Chhetri, YPP Chen (2023) SoK: Systematizing Attack Studies in Federated Learning–From Sparseness to Completeness, Proceedings of the 2023 ACM Asia Conference on Computer and Communications Security, 579-592
2022
Journals: 281. McIntosh T, Kayes ASM, Chen YPP, Ng A, and Watters P (2022) Ransomware Mitigation in the Modern Era: A Comprehensive Review, Research Challenges, and Future Directions. ACM Computing Surveys 54(9), Dec 2022 Article No.: 197, 1-36 280. Yu L, Xiang W, Fang J, Chen YPP, Zhu R (2022), A novel explainable neural network for Alzheimer's disease diagnosis, Pattern Recognition, 131(2022), 108876. 279. Mohammed YA, Chen YPP (2022) A blockchain-based application for genomic access and variant discovery using smart contracts and homomorphic encryption, Future Generation Computer Systems, 137(Dec): 234-247. 278. Lan W, Wu X, Chen Q, Peng W, Wang J, Chen YPP (2022), GANLDA: Graph attention network for lncRNA-disease associations prediction, Neurocomputing, 469:384-393. 277. Naz S, Phan KT, Chen YPP (2022) A comprehensive review of federated learning for COVID-19 detection, International Journal of Intelligent Systems, 37(3): 2371-2392. 276. Lan W, Dong Y, Chen Q, Zheng R, Liu J, Pan Y, Chen YPP (2022), KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network, Briefings in Bioinformatics, 23(1): bbab494. 275. Tran L, Bonti A, Chi L, Abdelrazek M, Chen YPP, (2022) Advanced calibration of mortality prediction on cardiovascular disease using feature-based artificial neural network, Expert Systems with Applications, 203, 1 Oct 2022, 117393. 274. Lan W, Lai D, Chen Q, Wu X, Chen B, Liu J, Wang J, Chen Y-PP (2022) LDICDL: LncRNA-Disease Association Identification Based on Collaborative Deep Learning, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(3):1715-1723. 273. Salem OAM, Liu F, Chen YPP, Hamed A, Chen X (2022) Fuzzy joint mutual information feature selection based on ideal vector, Expert Systems with Applications, 272. Karri R, Chen YPP, Drummond KJ, Using machine learning to predict health-related quality of life outcomes in patients with low grade glioma, meningioma, and acoustic neuroma, PLoS ONE, 17(5 May). Refereed conference papers: 271. Zhu J, Wang Z, Chen J, Chen YPP, Jiang YG (2022) Balanced Contrastive Learning for Long-Tailed Visual Recognition, IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2022, Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2022, 6908-6917. 270. Song Z, Yu J, Chen Y-PP, Yang W (2022) Transformer Tracking with Cyclic Shifting Window Attention, IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2022, Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2022, 8791-8800.
2021
Journals: 269. CY Lee and YPP Chen (2021), Prediction of Drug Adverse Events using Deep Learning in Pharmaceutical Discovery, Briefings in Bioinformatics (In Press). 268. Tang R, Yu Z, Ma Y, Wu Y, Chen YPP, Wong L, Li J (2021) Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning, Bioinformatics (In Press). 267. Rahmani M, Chen YPP (2021) Tracking neutrophil migration in zebrafish model using multi-channel feature learning. IEEE Journal of Biomedical and Health Informatics. PP:1-9. 2021. 266. Anees A, Dillon T, Wallis S, Chen YPP (2021) Optimization of day-ahead and real-time prices for smart home community. International Journal of Electrical Power and Energy Systems. 124(2021) 106403. 265. McIntosh T, Watters P, Kayes ASM, Ng A, Chen YPP (2021) Enforcing situation-aware access control to build malware-resilient file systems. Future Generation Computer Systems: the international journal of grid computing: theory, methods and applications. 115:568-582. 2021 264. Rabab S, Badenhorst P, Chen YPP, Daetwyler HD (2021) A template-free machine vision-based crop row detection algorithm. Precision Agriculture. 2021 (In Press). 263. N Amin, A McGrath, Chen YPP (2021), FexRNA: Exploratory Data Analysis and Feature Selection of non-coding RNA, IEEE/ACM Transactions on Computational Biology and Bioinformatics, (In Press). 262. W Lan, D Lai, Q Chen, X Wu, B Chen, J Liu, J Wang, YPP Chen (2021), LDICDL: LncRNA-disease association identification based on Collaborative Deep Learning, IEEE/ACM Transactions on Computational Biology and Bioinformatics, (In Press). 261. Chen Q, Lai D, Lan W, Wu X, Chen B, Chen YPP, Wang J (2021) ILDMSF: Inferring Associations between Long non-coding RNA and Disease Based on Multi-similarity Fusion, IEEE/ACM Transactions on Computational Biology and Bioinformatics (In Press). 260. Lan W, Zhu M, Chen Q, Chen B, Liu J, Chen YPP (2021) CircR2Cancer: a manually curated database of associations between circRNAs and cancers. Database: the journal of biological databases and curation. 2021. 259. Abbas SQ, Ahmed F, Chen YPP (2021) Perceptual image hashing using transform domain noise resistant local binary pattern. Multimedia Tools and Applications (in press). Refereed conference papers: 258. Wang T, Feng N, Yu J, He Y, Hu Y and Chen YPP (2021), Shot Boundary Detection through Multi-stage Deep Convolution Neural Network, MMM2021 (Accepted).
2020
Journals: 257. M Abukari and YPP Chen (2020), Ensuring privacy and security of genomic data and functionalities, Briefings in Bioinformatics, 21(2): 511–526. 256. Chaudhary C, Goyal P, Prasad DN, and Chen YPP (2020) Enhancing the quality of Image Tagging using a Visio-Textual Knowledge Base, IEEE Transactions on Multimedia,22(4):897-911. . 255. Chaudhary C, Goyal P, Goyal N, and Chen YPP (2020) Image Retrieval for Complex Queries Using Knowledge Embedding, ACM Transactions on Multimedia Computing Communications and Applications 16(1):1-23, March 2020. 254. Anees A, Chen YPP (2020), Designing secure substitution boxes based on permutation of symmetric group, Neural Computing and Applications, 32:7045–7056. 253. Liu F, Khanam S, Chen YPP (2020), A human-machine language dictionary. International Journal of Computational Intelligence Systems. 13:904-913, 2020. 252. Salem OAM, Liu F, Chen YPP, Chen X (2020) Ensemble Fuzzy Feature Selection Based on Relevancy, Redundancy, and Dependency Criteria. Entropy, An International and Interdisciplinary Journal of Entropy and Information Studies. 22, 757, 2020 251. Liu Z, Chen Q, Lan W, Liang J, Chen YPP, Chen B (2020) A Survey of Network Embedding for Drug Analysis and Prediction. Current Protein and Peptide Science. 21. 2020. 250. Feng N, Song Z, Yu J, Chen YPP, Zhao Y, He Y, Guan T (2020) SSET: a dataset for shot segmentation, event detection, player tracking in soccer videos, Multimedia Tools and Applications . 79: 28971–28992(2020). Refereed conference papers: 249. Scanlan J, Watters P, Eddy A, Fieldhouse M, Thomas T, Fung L, Tan T, Girdler S and Chen YPP, Neurodiverse knowledge, skills and ability assessment for cyber security, 31st 2020 Australasian Conference on Information Systems (ACIS 2020).
2019
Journals: 248. N Amin, A McGrath, Chen YPP (2019), Evaluation of Deep Learning in non-coding RNA Classification, Nature Machine Intelligence, 1, (May 2019), 246-256. 247. HF Yang, Chen YPP (2019) Representation Learning and Empirical Mode Decomposition for Wind Speed Forecasting Method, Artificial Intelligence, Vol 277, December 2019, 103176. 246. HF Yang, TS Dillon, E Chang, Chen YPP (2019) Optimized Configuration of Exponential Smoothing for Traffic Flow Forecasting, IEEE Transactions on Industrial Informatics, 15(1): 23-34. 245. CY Lee and Chen YPP (2019), Machine learning on adverse drug reactions for pharmacovigilance, Drug Discovery Today, 24(7): 1332-1343. 244. Anees A, Dillon T, Chen YPP (2019), A novel decision strategy for a bilateral energy contract, Applied Energy, Vol 253, 1 November 2019, 113571. 243. SA Khanam, F Liu, Chen YPP (2019) Comprehensive Structured Knowledge Base System Construction with Natural Language Presentation, Human-centric Computing and Information Sciences, December 2019, 9:23. 242. Chaudhary C, Goyal P, Tuli S, Banthia S, Goyal N, and Chen YPP (2019), A Novel Multimodal Clustering Framework for Images with Diverse Associated Text, Multimedia Tools and Applications July 2019, Vol 78, 13, 17623ï¿½17652 241. Yang HF, Chen YPP (2019), Hybrid Deep Learning and Empirical Mode Decomposition Model for Time Series Applications, Expert Systems With Applications, 120 (15 April 2019): 128-138. 240. Chen Q, Zhe Z, Lan W, Zhang R, Wang Z, Luo C, Chen YPP (2019) Identifying MiRNA-disease association based on integrating miRNA topological similarity and functional similarity, Quantitative Biology, 7, (September 2019), 202-209. 239. Wu B, Zhang H, Lin L, Wang H, Gao Y, Zhao L, Chen YPP, Chen R and Gu L* (2019) A Similarity Searching System for Biological Phenotype Images Using Deep Convolutional Encoder-decoder Architecture, Current Bioinformatics, 14(7), (September 2019), 628-639. Refereed conference papers: 238. J Cheng, Chen YPP, M Li, YG Jiang (2019), TC-GAN: Triangle Cycle-Consistent GANs for Face Frontalization with Facial Features Preserved , ACM MM2019 220-228, (Published as a full paper). 237. S Liu, Z Huang, Y Qiu, YPP Chen, W Zhang (2019), Structural Network Embedding using Multi-modal Deep Auto-encoders for Predicting Drug-drug Interactions, BIBM2019 (Published as a full paper). 236. Z Liu, F Liu, C Hong, M Gao, YPP Chen, S Liu, W Zhang (2019), Detection of Cell Types from Single-cell RNA-seq Data using Similarity via Kernel Preserving Learning Embedding, BIBM2019 (Published as a full paper). 235. Soon L, Chen YPP, Kerr D, Fraser C (2019), The use of Export Trading Knowledge, European Conference on Knowledge Management (Published as a full paper).
2018
Journals: 234. Anees A, Chen YPP (2018), Discriminative binary feature learning and quantization in biometric key generation, Pattern Recognition, 77(2018): 289-305. 233. Chiu JKH, Dillon T, Chen YPP (2018), Large-Scale Frequent Stem Pattern Mining in RNA Families, Journal of Theoretical Biology, 455, 14 October 2018, 131-139. 232. Kourfariotis L.T., Chen YPP, Stothard P, Hayes BJ (2018) Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits, BMC Genomics, (2018) 19:237. 231. Cheng Z, Zhou S, Wang Y, Liu H, Guan J, Chen YPP (2018), Effectively identifying compound-protein interactions by learning from positive and unlabeled examples, IEEE/ACM Transactions on Computational Biology and Bioinformatics , 15(6): 1832:1843. 230. Yang SX, Zhen H, Chen YPP (2018), GCOTraj: A Storage Approach for Historical Trajectory Data Sets Using Grid Cells Ordering, Information Sciences, 459 (2018): 1-19. 228. Zhu Y, Xie ZY, Li YZ, Zhu M, Chen YPP (2018), Research on folding diversity in statistical learning methods for RNA secondary structure prediction, International Journal of Biological Sciences, 14(8):872-882, 2018. Refereed conference papers: 227. Chaudhary C, Goyal P, and Chen YPP (2018), Linguistic patterns and cross modality-based image retrieval for complex queries, ACM ICMR 2018, accepted as a regular paper, ACM International Conference on Multimedia Retrieval, June 11-14, 2018, Yokohama, Japan, pp257-265.
2017
Journals: 226. Ma CY, Chen YPP, Berger B, Liao CS (2017), Identification of Protein Complexes by Integrating Multiple Alignment of Protein Interaction Networks, Bioinformatics, 33(11):1681-1688, 2017. 225. Yang HF, Dillon T, Chen YPP (2017), Optimized Structure of the Traffic Flow Forecasting Model with a Deep Learning Approach, IEEE Transactions on Neural Networks and Learning Systems, 28(10):2371-2381, 2017. 224. Wang T, Chen YPP, Macleod IM, Pryce JE, Goddard EG, Hayes BJ (2017), Application of a Bayesian non-linear Model Hybrid Scheme to Sequence Data for Genomic Prediction and QTL Mapping, BMC Genomics, 18(618):1-23, 2017. 223. Chiu JKH, Chen YPP (2017), A Comprehensive Study of RNA Secondary Structure Alignment Algorithms, Briefings in Bioinformatics, 18(2): 291-305, 2017. 222. Chen Q, Lan C, Zhao L, Wang J, Chen B, Chen YPP (2017), Recent Advances in Sequence Assembly: Principles and Applications, Briefings in Functional Genomics, 16(6), 2017, 361-378. Refereed conference papers: 220. Chaudhary C, Goyal P, and Chen YPP (2017), Exploiting Visual and Textual Neighborhood Information to Improve Image-Tag Relevance, 2017 IEEE International Conference on Big Data (Big Data 2017), (Accepted as a regular paper), pp566-575, 18% acceptance rate, December 11-14, 2017, Boston, MA, USA.
2016
Journals: 219. Begley S, Zhen H, Chen YPP (2016), PaMeCo Join: A Parallel Main Memory Compact Hash Join, Information Systems, 58:105-125, 2016. 218. Wang T, Chen YPP, Bowman P, Goddard M, Hayes B (2016), A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping, BMC Genomics, 17(1): 1-21, 2016. 217. Yang SX, Zhen H, Chen YPP (2016), Workload-based Ordering of Multi-dimensional Data, IEEE Transactions on Knowledge and Data Engineering, 28(3):831-844, 2016. 216. Chen Q, Chen YPP, Zhang C (2016), Interval-Based Similarity for Classifying Conserved RNA Secondary Structures, IEEE Intelligent Systems, 31(3):78-85, 2016. 215. Anees A, Chen YPP (2016), True real time pricing and combined power scheduling of electric appliances in residential energy management system, Applied Energy, 165 (2016) 592-600. 214. Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky BM, Chen YPP, Gelfand MS and Khaitovich P (2016), Changes in snoRNA and snRNA abundance in the human, chimpanzee, macaque and, mouse brain, Genome Biology and Evolution, 8(3): 840-850, 2016.
2015
Journals: 212. Chiu JKH, Chen YPP (2015), Pairwise RNA Secondary Structure Alignment with Conserved Stem Pattern, Bioinformatics, 31(24):3914-3921, 2015. 211. Chiu JKH, Chen YPP (2015), Efficient conversion of RNA pseudoknots to knot-free structures using a graphical model, IEEE Transactions on Biomedical Engineering, 62(5), 1265-1271, 2015. 210. Rajasekaran R, Chen YPP (2015), Potential Therapeutic Targets and the Role of Technology in Developing Novel Antileishmanial Drugs, Drug Discovery Today, 20(8): 958-968, 2015. 209. Kourfariotis L, Chen YPP, Chamberlian A, Vanderjagt C, Hayes B (2015), A catalogue of novel bovine long noncoding RNA across 18 tissues, PLoS ONE, 10(10): e0141225. doi:10.1371/journal.pone.0141225, 2015. 208. Chen Q, Luo H, Zhang C, Chen YPP (2015), Bioinformatics in Protein Kinases Regulatory Network and Drug Discovery, Mathematical Biosciences, 262, 147-156, 2015. 207. Wang TT, Chen YPP, Goddard M, Meuwissen T, Kemper KE, Hayes B (2015), A Computationally Efficient Algorithm for Genomic Prediction Using a Bayesian Model, Genetics Selection Evolution, 47(1):34, 2015. 206. Lee H, Chen YPP (2015), Image Based Computer Aided Diagnosis System for Cancer Detection, Expert Systems with Applications, 42(12), 5356-5365, 2015. 205. Yang HF, Chen YPP (2015), Data Mining in Lung Cancer Pathologic Staging Diagnosis: Correlation between Clinical and Pathology Information, Expert Systems With Applications, 42(15-16):6168-6176, 2015. 204. Simpson A, El-Refaie A, Stephenson C, Chen YPP, Deng D, Erickson S, Tay D, Morris ME, Doube W and Caelli T (2015), Computer-Based Rehabilitation for Developing Speech and Language in Hearing-Impaired Children: A Systematic Review, Deafness & Education International, 17(2):111-119, 2015.
2014
Journals: 203. Kalyaanamoorthy S, Chen YPP (2014), A steered molecular dynamics mediated hit discovery for histone deacetylases, Physical Chemistry Chemical Physics, 16(8), 3777-3791, 2014. 202. Zhu W, Chen YPP (2014) Computational developments in microRNA-regulated protein-protein interactions, BMC Systems Biology, 2014, 8:14. 201. Liu Q, Chen YPP, Li J (2014), k-Partite Cliques of Protein Interactions: A Novel Subgraph Topology for Functional Coherence Analysis on PPI Networks, Journal of Theoretical Biology, 340:146ï¿½154, 2014. 200. Kourfariotis L., Chen YPP, Sunduimijid B, Hayes BJ (2014) Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle, BMC Genomics, 15:436, 2014. 199. Kalyaanamoorthy S, Chen YPP (2014), Modelling and enhanced molecular dynamics to steer structure-based drug discovery, Progress in Biophysics and Molecular Biology, 114(3):123ï¿½136, 2014. 198. Lee H, Chen YPP (2014) Cell Cycle Phase Detection with Cell Deformation Analysis, Expert Systems with Applications, 41(6):2644ï¿½2651, 2014. 197. Lee H, Chen YPP (2014) Skin Cancer Extraction with Optimum Fuzzy Thresholding Technique, Applied Intelligence, 40(3): 415-426, 2014. 196. Lee H, Chen YPP (2014) Cell Morphology Based Classification for Red Cells in Blood Smear Images, Pattern Recognition Letter, 49:155ï¿½161, 2014. 194. Chuang CH, Cheng SC, Chang CC, Chen YPP (2014), Model-Based Approach to Spatial-Temporal Sampling of Video Clips for Video Object Detection by Classification, Journal of Visual Communication and Image Representation, 25(5):1018ï¿½1030, 2014. 193. Chen F, Zhang Y, Chen YPP (2014) Subdividing Globally Important Zones Based on Data Distribution across Multiple Genome Fragments, Computers in Biology and Medicine, 48:109ï¿½118, 2014. 192. Chen F, Lia Z, Chen YPP (2014), Determining Common Insertion Sites Based on Retroviral Insertion Distribution across Tumors, Computational Biology and Chemistry, 51:83ï¿½92, 2014. 191. Zhu W, Hou J, Chen YPP (2014), Select Cluster Features for Better Layered Protein Function Prediction, Current Bioinformatics 9(3): 306-314, 2014.
2013
Journals: 190. Mazin P, Xiong J, Liu X, Yan Z, Zhang X, Li M, He L, Somel M, Yuan Y, Chen YPP, Li N, Hu Y, Fu N, Ning Z, Zeng R, Yang H, Chen W, Gelfand M and Khaitovich P (2013), Widespread splicing changes in human brain development and aging, Molecular Systems Biology,9:633, 2013. 189. Li Z, Bammann H, Li M, Liang H, Yan Z, Chen YPP, Zhao M. and Khaitovich P (2013), Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains, RNA 2013 19:1693-1702. 188. Yuan Y, Yang L, Shi M, Lu D, Lou H, Chen YPP, Jin L, Xu S (2013), Identification of Well-Differentiated Gene Expressions between Han Chinese and Japanese Using Genome-Wide Microarray Data Analysis, Journal of Medical Genetics, 50(8):534-42, 2013. 187. Cheng SC, Cheng KY, Chen YPP (2013), GHT-Based Associative Memory Learning and Its Application to Human Action Detection and Classification, Pattern Recognition, 46(11):3117ï¿½3128, 2013. 186. Kalyaanamoorthy S, Chen YPP (2013), Ligand release mechanisms and channels in histone deacetylases. Journal of Computational Chemistry 34(26): 2270-2283, 2013. 185. Kalyaanamoorthy S, Chen YPP (2013), Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes, BBA - Proteins and Proteomics, 1834(1):317-328, 2013. 184. Kalyaanamoorthy S, Chen YPP (2013),Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors, Journal of Molecular Graphics and Modelling, 44:44ï¿½53, 2013. 183. Lee CC, Chen YPP, Yao TJ, Lo WC, Lyu PC, Tang CY and Ma CY (2013), GI-POP: A combinational annotation and Genomic Island prediction Pipeline for Ongoing microbial genome Projects, Gene, 518:114-123, 2013. 182. Nahar J, Imam T, Tickle K, and Chen YPP (2013), "Computational Intelligence for Heart Disease Diagnosis: A Medical Knowledge Driven Approach", Expert Systems With Applications, 40(1):96-104, 2013. 181. Nahar J, Imam T, Tickle K, and Chen YPP (2013), "Association Rule Mining to Detect Factors which contribute to Heart Disease in Males and Females", Expert Systems With Applications, 40(4):1086-1093, 2013. 180. Nguyen T, Zhen H, Chen YPP (2013), SeTPR-tree: Efficient Buffering for Spatiotemporal Indexes Via Shared Execution, The Computer Journal,* 56(1):115-137, 2013. 179. Zhu W, Hou J, Chen YPP (2013), Semantically Predicting Protein Functions Based on Protein Functional Connectivity, Computational Biology and Chemistry, 44: 9-14, 2013. 178. Song X, Wang M, Chen YPP (2013), Wang H, Han P, Sun H: Prediction of pre-miRNA with multiple stem-loops using pruning algorithm. Computers in Biology and Medicine. 43(5):409-416, 2013. 177. Hou J, Zhu W, Chen YPP (2013), Dynamically predicting protein functions from semantic associations of proteins, Network Modeling Analysis in Health Informatics and Bioinformatics, 2(4):175-183, 2013.
2012
Journals: 176. Yuan Y, Chen YPP, Boyd-Kirkup J, Khaitovich P and Somel M (2012), Accelerated aging-related transcriptome changes in the female prefrontal cortex, Aging Cell, 11(5):894-901, 2012. 175. Kalyaanamoorthy S, Chen YPP (2012), Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations, Journal of Chemical Information and Modeling, 52(2): 589ï¿½603, 2012. 174. Lee CC, Lo WC, Lai SM, Chen YPP (2012), Tang CY and Lyu PC, Metabolic classification of microbial genomes using functional probes, BMC Genomics, 13:157, 2012. 173. Chiu JKH, Chen YPP (2012), Conformational Features of Topologically Classified RNA Secondary Structures, PLoS ONE, 7(7):e39907, 2012. 172. Zhu W, Hou J, and Chen YPP (2012), Exploiting Multi-Layered Information to Iteratively Predict Protein Functions, Mathematical Biosciences, 236(2):108ï¿½116, 2012. 171. Chen Q, Chen YPP (2012), Discovering Inhibition Pathways for Protein Kinases. IEEE Intelligent Systems, 27(5):19-26, 2012. 170. Song X, Cheng L, Zhou T, Guo X, Zhang X, Chen YPP, Han P, Sha J (2012), Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features, Computers in Biology and Medicine, 42(1):1ï¿½7, 2012. 169. Nahar J, Imam T, Tickle K, Ali S and Chen YPP (2012), "Computational Intelligence for Microarray Data and Biomedical Image Analysis for the Early Diagnosis of Breast Cancer", Expert Systems With Applications, 39:12371ï¿½12377, 2012. 168. Rajasekaran R, Chen YPP (2012), Probing the structure of Leishmania major DHFR TS and structure based virtual screening of peptide library for the identification of anti-leishmanial leads, Journal of Molecular Modeling, 18(9):4089-4100, 2012. 167. Gotoh Y, Yoshihisa T, Taniguchi H, Kanazawa M, Rahayu W, and Chen YPP (2012), "A Scheduling Method to Reduce Waiting Time for Close-range Broadcasting'', Mobile Information Systems Journal (MOBIS), Vol.8, Issue.4, pp.303-314, 2012. Refereed conference papers: 166. Begley S, Zhen H, Chen YPP (2012), ï¿½MCJoin: A memory-constrained join for column-based main-memory databasesï¿½, Proceedings of the ACM SIGMOD 39th International Conference on Management of Data, SIGMOD 2012, 121-165. Scottsdale, Arizona, USA, 20-24 May 2012. 164. Gotoh Y, Yoshihisa T, Taniguchi H, Kanazawa M, Rahayu W, and Chen YPP (2012), "A Scheduling Method for Node Relay-based Webcast Considering Reconnection'' 26th IEEE International Conference on Advanced Information Networking and Applications (AINA-2012), 787-794, Fukuoka, Japan, 26-29 March 2012.
2011
Journals: 163. Chen Q, Chen YPP (2011), Modeling Conserved Structure Patterns for Functional Noncoding RNA. IEEE Transactions on Biomedical Engineering, 58(6):1528-1533, 2011. 162. Chen Q, Li G, Chen YPP (2011), Interval-Based Distance Function for Identifying RNA Structure Candidates, Journal of Theoretical Biology, 269(8):280-286, 2011. 161. Yang L, Zhen H, Chen YPP, Nguyen T (2011), External Sorting on Flash Memory Via Natural Page Run Generation, The Computer Journal, 54(11):1882-1990, 2011. 160. Yuan Y, Chen YPP, Ni S, Xu AG, Tang L, Vingron M, Somel M, Khaitovich P (2011), Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series, BMC Bioinformatics, 12:347, 2011. 159. Kalyaanamoorthy S, Chen YPP (2011), Structure-based drug design to augment hit discovery, Drug Discovery Today, 16(17-18):831-839, 2011. 158. Xi Y, Chen YPP, Qian C., Wang F (2011), Comparative study of computational methods to detect the correlated reaction sets in biochemical networks, Briefings in Bioinformatics 12(2):132-150, 2011. 157. Nahar J, Tickle K, Ali S. Chen YPP (2011), Significant Cancer Prevention Factor Extraction: An Association Rule Discovery Approach, Journal of Medical Systems 35(3):353-367, 2011. 156. Chen Q, Chen YPP (2011), Mining Protein Kinases Regulation using Graphical Models. IEEE Transactions on NanoBioscience, 10(1):1-8, 2011. 155. Song XF, Han P, Chen YPP (2011), Genetic variation of the hemagglutinin of Avian influenza Virus H9N2, Journal of Medical Virology, 83(5):838-46, 2011. 154. Chen Q, Chen YPP (2011), Function Annotation for Pseudoknot using Structure Similarity. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(6):1535-1544, Nov-Dec 2011. 153. Wang TT, Chen F. Chen YPP (2011), Ranking Inter-Relationships between Clusters, International Journal of Systems Science, 42(12):2071-2083, 2011. Refereed conference papers: 152. Gotoh Y, Yoshihisa T, Taniguchi H, Kanazawa M, Rahayu W, and Chen YPP (2011), "A Method to Reduce Waiting Time for Close-range Broadcasting." The 9th International Conference on Advances in Mobile Computing and Multimedia (MoMM 2011), Ho Chi Minh City, Vietnam, vol. MoMM 2011, 116-122. 151. Song XF, Wang M, Chen YPP, and Ping H (2011), "Identifying multiple stem-loops pre-miRNA using support vector machine." The 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2011), Atlanta, Georgia, USA, vol. BIBMW 2011, 446-448. 150. Wang HW, Wu WK, Pai TW, Chen YPP, and Chang MDT (2011), "Impact of complex formation on predicting conformational epitopes." The 2nd IASTED International Conference on Computational Bioscience, CompBio 2011, Cambridge, United Kingdom, vol. CompBio 2011, 284-290.
2010
Journals: 149. Chen F, Chen YPP (2010) Exploring Cross-species Related miRNAs Based on Sequence and Secondary Structure, IEEE Transactions on Biomedical Engineering 57(7)1547ï¿½1553, 2010. 148. Chen Q, Chen YPP (2010) Mining Characteristic Relations Bind to RNA Secondary Structures, IEEE Transactions on Information Technology in Biomedicine, 14(1):10-15, 2010. 147. Zhu W, Hou J, and Chen YPP (2010) Semantic and layered protein function prediction from PPI networks, Journal of Theoretical Biology, 267(2):129-136, 2010. 144. Chen F, Chen YPP (2010) Exploring the ncRNA-ncRNA patterns based on bridging rules. Journal of Biomedical Informatics 43(4):569-577, 2010. 143. Jiang D, Zhou S, Liu H, Chen YPP (2010) Inferring minimal feasible metabolic networks of Escherichia coli, Applied Biochemistry and Biotechnology, 160(1):222-231, 2010. 142. Tjondronegoro, D, Chen YPP, Knowledge-discounted Event Detection in Sports Video, IEEE Transactions on Systems Man & Cybernetics, Part A. 40(5):1009-1024, 2010. 141. An J, Choi KP, Wells CA, Chen YPP (2010), Identifying co-regulating microRNA Groups, Journal of Bioinformatics and Computational Biology. 8(1):99-115, 2010. 140. Sajjanhar A, Lu G, Zhang D, Hou J, Zhou W, Chen YPP (2010), Spectral Shape Descriptor using Spherical Harmonics, Integrated Computer-Aided Engineering 17:1ï¿½7, 2010. 139. Zhang Z, Chen YPP (2010) Guest Editors' Introduction. International Journal of Software Engineering and Knowledge Engineering 20(8):1043-1044, 2010. Book Chapter 138. Chen F, Chen YPP (2010), Pattern recognition for genomics context, Pattern Recognition and Machine Vision, Chapter 7, editor by Patrick S.P. Wang, River Publishers. 105-118, 2010. 137. Chen YPP, Ivanova E, Carloni P, Wang F (2010), Bioinformatics and its applications, in Comprehensive Natural Products II: Chemistry and Biology, Eds., Lewis N. Mander and Hung-wen (Ben) Liu, pp569-593 (Elsevier, 2010).
2009
Journals: 136. Chen Q. Chen YPP (2009), Discovery of Structural and Functional Features in RNA Pseudoknots, IEEE Transactions on Knowledge and Data Engineering, 21(7):974-984, 2009. 135. Xi Y, Chen YPP, Cao M, Wang W and Wang F (2009), Analysis on relationship between extreme pathways and correlated reaction sets. BMC Bioinformatics, 10(S1):S58, 2009. 134. Jiang D, Zhou S, Chen YPP (2009), Compensatory ability to null mutation in metabolic networks, Biotechnology and Bioengineering, 103(2):361-369, 2009. 133. Song XF, Chen WM, Chen YPP, Jiang B (2009), Candidate Working Set Strategy based SMO Algorithm in Support Vector Machine, Information Processing & Management 45(5): 584-592, 2009. 132. Rong J, Li G, Chen YPP (2009), Acoustic Feature Selection for Automatic Emotion Recognition from Speech. Information Processing & Management, 45(3):315-328, 2009. 131. An J, Chen YPP (2009), Finding Coverage Using Incremental Attribute Combinations, International Journal of Innovative Computing, Information and Control, 5(5):1419-1428, 2009. 130. An J, Chen YPP (2009), Finding rule groups to classify high dimensional gene expression datasets, Computational Biology and Chemistry 33(1):108-113, 2009. Book Chapters 129. Chen YPP, Rong J, Li G (2009), Advanced Graph Mining Methods for Protein Analysis. Biological Data Mining. Edited by Jake Y. Chen, Stefano Lonardi, Chapter 6, Chapman & Hall/CRC Press, 111-132. Lecture Notes in Computer Science/Artificial Intelligence: 128. Sajjanhar A, Lu G, Zhang D, Hou J, Chen YPP (2009), Spherical Harmonics and Distance Transform for Image Representation and Retrieval, E. Corchado and H. Yin (Eds.), Lecture Notes in Computer Science, Volume 5788, pp. 309-316, 2009. Refereed conference papers: 127. Liu Q, Chen YPP, Li J (2009), High functional coherence in k-partite protein cliques of protein interaction networks, Proceedings of 2009 IEEE International conference on Bioinfomratics and Biomedicine, page 111-117. Washington D.C., USA. 1-4 November 2009. 126. Nahar J., Tickle K, Ali S. Chen YPP (2009), Early Breast Cancer Identification: Which Way to Go? Microarray or Image Based Computer Aided Diagnosis!, 2009 Third International Conference on Network and System Security, pp456-461. 2009. 125. Hou J, Chen YPP (2009), Data Pre-Processing for More Effective Gene Clustering, The 2009 International Joint Conference on Computational Sciences and Optimization (CSO 2009), Sanya, Hainan, China, April 24-26, 2009.
2008
Journals: 124. Chen YPP, Chen F (2008), Using Bioinformatics Techniques for Gene Identification in Drug Discovery and Development, Current Drug Metabolism, 9(6):567-573, 2008. 123. Knapp K, Chonka A, and Chen YPP (2008), POEM, a 3-Dimensional Exon Taxonomy and Patterns in Untranslated Exons, BMC Genomics, 9:428, 2008. 122. An J, Chen YPP (2008), Finding Edging Genes From Microarray Data, Journal of Biotechnology, 135(3):233-240, 2008. 121. Chen YPP, Chen F (2008), Identifying Targets for Drug Discovery using Bioinformatics, Expert Opinion on Therapeutic Targets, 12(4):383-389, 2008. 120. Tjondronegoro D, Chen YPP, Joly A (2008), A Scalable and Extensible Segment-Event-Object based Sports Video Retrieval System, ACM Transactions on Multimedia Computing, Communications and Applications, 4(2):13:1-13:40, 2008. [PDF]. 119. Chen Q, Zhang S. Chen YPP (2008), Rule-based dependency models for security protocol analysis, Integrated Computer-Aided Engineering 15:369-380, 2008. Refereed conference papers: 116. Lukman S, Sim K, Li J and Chen YPP (2008), Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes, The Sixth Asia Pacific Bioinformatics Conference (APBC2008), 14-17 January 2008 Kyoto, Japan. 115. Sajjanhar A, Lu G, Zhang D, Zhou W and Chen YPP (2008), Image Retrieval Based On Semantics of Intra-Region Color Properties, IEEE 8th International Conference on Computer and Information Technology, 8-11 July 2008, Sydney Australia.
2007
Journals: 114. Knapp K. Chen YPP (2007), An Evaluation of Contemporary Hidden Markov Model Genefinders with a Predicted Exon Taxonomy, Nucleic Acids Research, 35: 317-324, 2007. [pdf] 113. Mann S., Li J., Chen YPP (2007), A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts, Nucleic Acids Research 35: e12 1-7, 2007. [pdf] 112. Chen Q, Chen YPP and Zhang C (2007), Detecting Inconsistency in Biological Molecular Databases using Ontology, Data Mining and Knowledge Discovery 15:275-296, 2007. [pdf] 111. An J. Yu JX, Ratanamahatana CA, Chen YPP (2007), A Dimensionality Reduction Algorithm and Its Application for Interactive Visualization, Visual Languages and Computing, Elsevier Science 18:48-70, 2007. [pdf] 110. Chen Y, Timms P and Chen YPP (2007), CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data, Biomolecular Engineering. 24(6):603-608, 2007.[pdf] 109. Nahar J., Ali S. Chen YPP (2007), Microarray Data Classification Using Automatic SVM Kernel Selection, DNA and Cell Biology, 26(10):707-712, 2007. [pdf] 108. Nahar J., Chen YPP, Ali S (2007), Kernel Based Naive Bayes Classifier for Breast Cancer Prediction, Journal of Biological Systems, 15(1):17-25, 2007. Lecture Notes in Computer Science/Artificial Intelligence: 107. Chen YPP, Qin Q, Chen Q (2007), Learning Dependency Model for AMP-activated Protein Kinase Regulation, Lecture Notes in Artificial Intelligence, 4798: 221-229, 2007. 106. Chen Q, Zhang S, Chen YPP (2007), Identifying Dependency between Secure Messages for Protocol Analysis, Lecture Notes in Artificial Intelligence: 4798: 30-38, 2007. Refereed conference papers: 105. Nahar J, Chen YPP, Ali S (2007), Microarray Classification and Rule Based Cancer Identification, Proceedings of International Conference on Information and Communication Technology (ICICT 2007) March 7-9, Dhaka, IEEE, pp 43-46, 2007. 104. Sunramaniam C, An J, Gubbi J, Chen YPP (2007), Finding Motifs in miRNA Sequences, Proceedings of The Sixth International Conference on Computer and Information Science (ICIS 2007), Melbourne, Australia. IEEE CS pp. 507-512, 11-13 July 2007. 103 Rong J, Chen YPP, Chowdhury M, Li G (2007), Acoustic Features Extraction for Emotion Recognition, Proceedings of The Sixth International Conference on Computer and Information Science (ICIS 2007), Melbourne, Australia. IEEE CS, pp. 419-424, 11-13 July 2007. 102. Chen Q, Zhang C. Chen YPP (2007), Probabilistic Reasoning of Inconsistent Belief in Protocol Analysis, Proceedings of 2007 International Conference on Intelligent Systems and Knowledge Engineering (ISKE2007), Chengdu, China, 2007. 101. Knapp K, Rahaman A, Chen YPP (2007), Non-Quantized Minimum Free Energy in Untranslated Region Exons, Proceedings of Computational Structural Bioinformatics Workshop (CSBW) is held in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) IEEE, pp. 32-37, 2007.
2006
Journals: 100. Chen Q. Chen YPP (2006), Mining Frequent Patterns for AMP-activated Protein Kinase Regulation on Skeletal Muscle, BMC Bioinformatics 7:394, 2006. [pdf] 99. Chen YPP, Prompramote S, Maire F (2006), MDSM: Microarray Database Schema Matching By Using Hungarian Method , Information Sciences, 176:2771-2790, 2006. [pdf] 98. Lopez C., Chen YPP (2006), Using Object and Trajectory Analysis to Facilitate Indexing and Retrieval of Video, Knowledge-Based Systems Journal, 19(8):639-646, 2006. [pdf] 97. Lau RYK, Tang M, Wong O, Milliner SW, Chen YPP (2006), An evolutionary learning approach for adaptive negotiation agents , International Journal of Intelligent Systems, 21(1):41-72, 2006. [pdf] 96. Chen YPP, Hwang MJ, Lee SK, Wong L (2006), Bioinformatics in Asia Pacific, Asia Pacific Biotech News, (10):24, 2006. 95. Shi W, Zhou W, Chen YPP (2006), Statistical Analysis of TATA Box and Its Extensions in the Promoters of Human Genes, Current Bioinformatics, 1(3):337-345, 2006. 94. Chen YPP and Chua TS (2006), Introduction: Multimedia Modelling . The Visual Computer, 22:1ï¿½2, 2006. Books: 93. Jiang T, Yang UC, Chen YPP, and Wong L Editors (2006) Proceedings of the 4th Asia-Pacific Bioinformatics Conference, Imperial College Press, London, February 2006. Advances in Bioinformatics & Computational Biology Vol 3 Feb 2006, by Imperial College Press. Lecture Notes in Computer Science/Artificial Intelligence: 92. An J. Chen YPP (2006), A similarity search algorithm to predict protein structures, 10th International Conference on Knowledge-Based & Intelligent Information & Engineering Systems (KES2006) , UK. Lecture Notes in Computer Science, LNCS 4252 Springer-Verlag, pp. 1305-1312, 9-11 October 2006. 91. Chen Q, Chen YPP, Zhang C and Li L.(2006), Mining Frequent Itemsets for Protein Kinase Regulation, Lecture Notes in Computer Science, LNCS4099, The 9th Pacific Rim International Conference on Artificial Intelligence, Springer-Verlag, pp222-230, 2006. 90. Chen Q, Chen YPP, Zhang C, Zhang S (2006), Detecting Collusion Attacks in Security Protocols, The Eighth Asia Pacific Web Conference January (APWeb2006) 16-18, Harbin, China. Lecture Notes in Computer Science, LNCS3841. pp297-306, 2006. Refereed conference papers: 89. An J, Chen YPP (2006), Finding Rule Groups to Classify High Dimensional Gene Expression Datasets, The 18th International Conference on Pattern Recognition 2006 (ICPR2006) 20 - 24 August 2006, Hong Kong, IEEE CS Press, pp1196-1199. (Tier A) 88. An J, Chen YPP (2006), Finding Short Patterns to Classify Text Documents, The 2006 IEEE/WIC/ACM International Conference on Web Intelligence (WI-06) 18 - 22 Dec 2006, Hong Kong, IEEE CS Press. 87. Chen YPP, Chen Q (2006), Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases, Proceedings of the fourth Asia-Pacific Bioinformatics Conference (APBC2006) Taipei Taiwan, pp197-206, 13-16 Feb 2006. 86. Tjondronegoro D, Chen YPP (2006), Using Decision-Tree to Automatically Construct Learned-Heuristics for Events Classification in Sports Video . IEEE International Conference on Multimedia & Expo (ICME2006) IEEE CS Press, Toronto, Canada, pp1465-1468, July 9-12, 2006, . 85. Tjondronegoro D, Chen YPP (2006), Towards Universal and Statistical-Driven Heuristics for Automatic Classification of Sports Video Events . the 12th International Multimedia Modelling Conference (MMM2006) IEEE Press, pp43-50, 2006. 84. Tjondronegoro D, Chen YPP, Pham B (2006), Extensible Detection and Indexing of Highlight Events in Broadcast Sports Video Towards Universal and Statistical-Driven Heuristics for Automatic Classification of Sports Video Events . The 29th Australasian Computer Science Conference-2006 (ACSC2006) Hobart, TAS, Australia, pp237-246, 2006. 83. An J, Chen YPP (2006), Depth First Rule Generation for Text Categorization , Proceedings of The Fourth International Conference on Active Media Technology (AMT 2006), Brisbane Australia, pp.302-306, June 7-9 2006. 82. Subramaniam C, An J., Chen YPP (2006), Microarray Analysis for Gene Expression that involves Trace Metals , Proceedings of The Fourth International Conference on Active Media Technology (AMT 2006), Brisbane Australia pp211-216, June 7-9 2006. 81. Morrison D, Saijanhar A, Hou J, Chen YPP (2005) Providing Real-Time Information Services for Public Bus Commuters , Proceedings of The Fourth International Conference on Active Media Technology (AMT 2006), Brisbane Australia pp384-387, June 7-9, 2006.
2005
Journals: 80. An J., Chen YPP CHEN H. (2005), DDR: An Index Method for Large Time Series Datasets , Information Systems, (30)5:333-348, 2005. [pdf] 79. Zhang C, Chen YPP, Zhang S, Chen Q (2005), Mining Inconsistent Secure Messages Toward Analyzing Security Protocol, The International Journal of Intelligent Control and Systems (IJICS) 10(1):77- 85, 2005. 78. Garcia A, Chen YPP, Ragan MA (2005), Information Integration in Molecular Bioscience, Applied Bioinformatics, 4(3):157-173, 2005. 77. Chen YPP (2005), Advanced Techniques for Bioinformatics . The Journal of Bioinformatics & Computational Biology, 3(1):99-102, 2005. Books: 76. Chen YPP, Ed., Bioinformatics Technologies, Springer - Jan 2005. 75. Chen YPP, and Wong L. Editors (2005), Proceedings of the Third Asia-Pacific Bioinformatics Conference, Advances in Bioinformatics & Computational Biology Vol 1 Jan 2005, by Imperial College Press. 74. Chen YPP, Ed (2005), Multimedia Modelling, Proceedings of the 11th International Multimedia Modelling Conference, IEEE CS Press. Book Chapters 73. Chen YPP (2005), Introduction to Bioinformatics. Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 1, pages 1-14, Springer, pp1-13, 2005. 72. Prompramote S, Chen Y, Chen YPP (2005), Machine Learning in Bioinformatics , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 5, pages 117-154, Springer, pp117-153, 2005. 71. Shi W, Zhou W, Chen YPP (2005), Biological Sequence Assembly and Alignment , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN chapter 8, pages 243-262, Springer, pp241-261, 2005. 69. Tse B, Hume D, Chen YPP (2005), Pattern Matching for Motifs , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 10, pages 299-312, Springer, pp299-312, 2005. 68. Yu ZG, Anh V, Chen YPP (2005), Visualization and Fractal Analysis of Biological Sequences , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 11, pages 313-352, Springer, pp313-351, 2005. 67. Liew AWC, Yan H, Yang M, Chen YPP (2005), Microarray Data Analysis , Bioinformatics Technologies, edited by Y.-P. Phoebe CHEN Chapter 12, pages 353-388, Springer, pp353-388, 2005. Lecture Notes in Computer Science/Artificial Intelligence: 66. An J, Chen YPP, Xu Q and Zhou X (2005), A New Indexing Method for High Dimensional Dataset , Database Systems for Advanced Applications (DASFAA2005) Lecture Notes in Computer Science, LNCS3453, Springer-Verlag, pp385-397, 2005. (Tier A) 65. Tjondronegoro D , Chen YPP (2005), Multi-level Semantic Analysis for Sports Video . Knowledge-Based Intelligent Information and Engineering Systems (KES). Lecture Notes in Computer Science, LNCS3682, Springer pp24-30, 2005. 64. An J, Chen YPP (2005), Yet Another Induction Algorithm , Knowledge-Based & Intelligent Information & Engineering Systems (KES) Lecture Notes in Computer Science, LNCS3682, Springer, pp37-44, 2005. [PDF] 63. Chen Q, Chen YPP, (2005), Analyzing Security Protocols using Association Rule Mining, The 18th Australian Joint Conference on Artificial Intelligence, Sydney Australia, Lecture Notes in Artificial Intelligence LNAI3809. Springer-Verlag, pp 245-253, 5-9 December 2005. Refereed conference papers: 62. Tjondronegoro D, Chen YPP and Pham B (2005), Extraction and Classification of Self-consumable Sport Video Highlights , in Proceedings of The ACM MM2005, Singapore, 2005. (Tier A+) 61. Garcia A, Thoraval S, Garcia LJ, Chen YPP, Ragan MA, (2005), Bioinformatics workflows: G-PIPE as an implementation, Fifth workshop on Workflow Managements: new abailities for the biological information overview, Naples, Italy. pp61-64, Oct 5-7 2005. 60. Tjondronegoro D, Chen YPP and Pham B (2005), A Statistical-driven Approach for Automatic Classification of Events in AFL Video Highlights. In Proc. Twenty-Eighth Australasian Computer Science Conference (ACSC2005) Newcastle, Australia. CRPIT, 38. Estivill-Castro, V., Ed. ACS. pp209-218, 2005. 59. An J, Chen YPP (2005), Keyword Extraction for Text Categorization , Proceedings of The Third International Conference on Active Media Technology (AMT 2005), Takamatsu, Kagawa, Japan, IEEE, pp556-561, MAy 19-21, 2005. 58. Tjondronegoro D, Chen YPP and Pham B (2005), Content-based Video Indexing for Sports Applications using Integrated Multi-Modal Approach , in Proceedings of The 4th Asia Pacific International Symposium on Information Technology, Gold Coast, Australia, pp200-203, Jan. 26-27, 2005. 57. An J, Chen YPP, Subramaniam C (2005), Side Chain Conformational Preferences in Protein Structures , The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '05) Monte Carlo Resort, Las Vegas, Nevada, USA. pp48-52, June 20-23, 2005. 56. Saijanhar A, Hou J, Chen YPP (2005), Content Exploration for e-Learning Using XML Web Services , Proceedings of The Third International Conference on Active Media Technology (AMT 2005) May 19-21, 2005, Takamatsu, Kagawa, Japan, IEEE, p266. 55. Chen Q, Chen YPP, Zhang C., Zhang S (2005), A Framework for Merging Inconsistent Beliefs in Security Protocol Analysis, International Workshop on Data Engineering Issues in E-Commerce (DEEC2005) in conjunction with ICDE2005 conference Tokyo, Japan, Tokyo, Japan, IEEE, pp112-117, 9 Apr 2005. 54. Prompramote S, Chen YPP (2005), ANNODA: Tool for integrating Molecular-biological Annotation Data, in Proceedings of International Workshop on Biomedical Data Engineering (BMDE2005) in conjunction with ICDE2005, IEEE, pp113-120, April 3-4, 2005, Tokyo, Japan.
2004
Journals: 53. Tjondronegoro D, Chen YPP and Pham B (2004), Integrating Highlights for More Complete Sport Video Summarization , IEEE Multimedia, Oct-Dec, pp22-37, 2004. 52. Soon L, Chen YPP and Underwood A (2004), Knowledge Creation in Export Trading , Journal of Information & Knowledge Management (JIKM), 3(4):297-316, 2004. 51. Zhang J, Pham B and Chen YPP (2004), A Fuzzy Shape Database to Support Conceptual Design , Control and Cybernetics, 1:141-172, 2004. Books: 50. Chen YPP, Editor (2004), Bioinformatics 2004, Proceedings of the Second Asia-Pacific Bioinformatics Conference, Vol 29 in the Conferences in Research and Practice in Information Technology Series, published by the Australian Computer Society, in Association with the ACM Digital Library, Jan. 2004. 49. Chen YPP, Editor (2004), Multimedia Modelling, Proceedings of the 10th International Multimedia Modelling Conference, IEEE CS Press, 2004. Lecture Notes in Computer Science/Artificial Intelligence: 48. An J, Chen YPP and Keogh E (2004), A Grid-based Index Method for Time Warping Distance , Web-Age Information Management, Lecture Notes in Computer Science, LNCS Vol 3129, Springer-Verlag, pp65-75, 2004. 47. An J, Chen YPP and Xu Q (2004), Surface Spatial Index Structure of High-Dimensional Space , Intelligent Data Engineering and Automated Learning, Lecture Notes in Computer Science, LNCS Vol 3177, Springer-Verlag, pp272-278, 2004. Refereed conference papers: 46. Tjondronegoro D, Chen YPP and Pham B (2004), The Power of Play-Break for Automatic Detection and Browsing of Self-consumable Sport Video Highlights , 6th ACM SIGMM International Workshop on Multimedia Information Retrieval (MIR'04), New York, NY USA, in conjunction with ACM Multimedia, pp267-274, October 15-16, 2004 . (Tier A) 44. Chen Y, Chen YPP and Zhu J (2004), Real-Time Gene-Expression Extraction with Fast Classification (FC) Networks , Proceedings of The 2004 International Conference on Machine Learning, Models, Technologies and Applications (MLMTA'04), Las Vegas, Nevada, USA, pp883-889, June 21-24, 2004. 43. Tjondronegoro D, Chen YPP and Pham B (2004), Classification of Self-Consumable Highlights for Soccer Video Summaries , Proceedings of The 5th IEEE International Conference on Multimedia and Expo (ICME2004) The Grand Hotel, Taipei, Taiwan. IEEE CS Press, June 27thï¿½30th, 2004. 42. Wu ST, Li Y, Xu Y, Pham B and Chen YPP (2004), Automatic Pattern-Taxonomy Extraction for Web Mining , IEEE/WIC/ACM WI-2004, Beijing China, IEEE CS Press, pp242-248, Sep. 20-24 2004. 41. An J and Chen YPP (2004), Concept Learning of Text Documents , IEEE/WIC/ACM WI-2004, Sep 20-24 2004, Beijing China, IEEE CS Press, pp698-701, Sep. 20-24 2004. 40. Prompramote S, Chen YPP (2004), Rough Set Based Similarity Metrics for Mixed Data Set: A Case Study of Heart Disease Diagnosis , the 7th International Conference on Information Technology (CIT2004) Hyderabad, Andhra Pradesh, India, Dec. 2004. 39. Goward P and Chen YPP (2004), Redesign of a Multimedia Course to reflect process not product , international conference E-Learn 2004, Washington, DC , pp660-665, Nov. 1-5, 2004. 38. Goodman A and Chen YPP (2004), Maintaining Relevance in a Rapidly Changing Environment: Evolving a Multimedia Curriculum , Proceedings of 3rd Symposium on IT in Education, Kuala Lumpur pp9-13, Oct. 2004.
2003
Journals: 37. Chen YPP (2003), Biomedical Visualization, Visual Languages and Computing 14 (4): 295-297, 2003. 36. Chen YPP (2003), Data Mining in Bioinformatics, International Journal of Software Engineering and Knowledge Engineering, 13(6), 2003. 35. Chen YPP (2003), Bioinformatics in Asia Pacific, Asia-Pacific Biotech News, published by World Scientific,7(3), 2003. 34. Chen YPP and Colomb BM (2003), Database Technologies for L-system Simulations in Virtual Plant Applications on Bioinformatics , Knowledge and Information Systems, 5(3):288-314, 2003. [PDF] 33. Chen YPP and McLachlan G (2003), Bioinformatics Research in Australia, Asia-Pacific Biotech News, published by World Scientific, 7(3), 2003. Books: 32. Chen YPP, Editor (2003), Bioinformatics 2003, Proceedings of the First Asia-Pacific Bioinformatics Conference, Vol 19 in the Conferences in Research and Practice in Information Technology Series, published by the Australian Computer Society, in Association with the ACM Digital Library, February 2003. Book Chapters: Lecture Notes in Computer Science/Artificial Intelligence: 31. Chen YPP (2003), A Hybrid Framework Using SOM and Fuzzy Theory for Textual Classification in Data Mining , Modelling with Words, Lecture Notes in Artificial Intelligence, J. Lawry, J. Shanahan and A. Ralescu Eds, Springer-Verlag, pp153-167, 2003. 30. Tjondronegoro D, Chen YPP and Pham B (2003), Indexing of Goal Segments in Soccer Video for Semantic Retrieval , Data Mining from Multimedia and Complex Data , C. Djeraba, S. J. Simoff, and O. R. Zaiane (Eds) Springer Verlag, 2003. Refereed conference papers: 29. Chen YPP (2003), XML-based Multimedia Query Systems , Proceedings of the 9th International Multi-Media Modelling Conference (MMM'03) Taipei, Taiwan, pp.365-378. ISBN957-9078-57-2, 7-9 Jan 2003. 28. Tjondronegoro D, Chen YPP and Pham B (2003), Sports Video Summarization using Highlights and Play-Breaks, 5th ACM SIGMM International Workshop on Multimedia Information Retrieval (MIR2003), Boston, USA, in conjunction with ACM Multimedia 2003. (Tier A) 27. Prompramote S, Chen YPP and Maire F (2003), Information Management for Microarray Experimental Data , 5th IFAC Symposium on Modelling and Control in Biomedical Systems, IFAC2003, Elsevier Science, pp377-382, 2003. 26. Soon L, Chen YPP and Underwood A (2003), Explicit Knowledge in Web-based Export Trading , Proceedings of the AUSWEB 2003, The Ninth Australian World Wide Web Conference, Gold Coast Queensland Australia, 5 - 9 July 2003. 25. Lee FS and Chen YPP (2003), BioWebFinder ï¿½ Searching Biological Websites , Proceedings of the APAC'03, The APAC Conference and Exhibition on Advanced Computing, Grid Applications and eResearch, Royal Pines Resort Gold Coast, Queensland Australia, 29 Sep.- 2 Oct. 2003.
2002
Journals: 24.Chen YPP, and Hanan J (2002), Partial Automation of Database Processing of Simulation Outputs from L-systems Models of Plant Morphogenesis , BioSystems. (Journal of Biological and Information Processing Sciences) 65(2-3):187-197, 2002. [pdf] 23. Tjondronegoro D and Chen YPP (2002), Content-based Indexing and Retrieval using MPEG-7 and X-Query in Video Data Management Systems, World Wide Web Journal 5(3):207-227, 2002.[pdf] Refereed conference papers: 22. Runoiang B, Chen YPP, Burrage K, Hanan J, Room P, Belward J (2002), Derivation of L-system models from measurements of biological branching structures using genetic algorithms, Proceedings of the Fifteenth International Conference on Industrial & Engineering Application of Artificial Intelligence & Expert Systems, June 17-20, 2002. Cairns, Australia, Lecture Notes in Artifical Intelligence, pp.514-524, Springer-Verlag, 2002. [PDF] 21. Tjondronegoro D and Chen YPP (2002), Content-Based Video Data Management: Key-Segment Extraction, MPEG-7 Summarisation, and XQUERY Retrieval , Proceedings of International Workshop on Knowledge Discovery in Multimedia and Complex Data (KDMCD'02) in conjunction with the Sixth Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD-02), Taipei Taiwan, pp. 39-49. May 6-8 2002. 20. Zhang J, Pham B and Chen YPP (2002), Indexing and Retrieval of Fuzzy Shapes , Fuzzy Logic: a Paradigm for the New Millennium, Studies in Fuzziness and Soft Computing Volume No. 81, V. Dimitrov and V. Korotkich, eds., Physica-Verlag, pp240-252, 2002. 19. Zhang J, Pham B and Chen YPP (2002), Modelling and Indexing of Fuzzy Complex Shapes , Proceedings of the Sixth IFIP Working Conference on Visual Database Systems, Brisbane Australia, pp.401-415, Kluwer Academic Publishers, 2002. 18. Soon L and Chen YPP (2002), Visualisation of Web-based Australian Export Trading , Proceedings of the Sixth IFIP Working Conference on Visual Database Systems (VDB6) Brisbane, Australia, pp.281-295, Kluwer Academic Publishers, 2002. 17. Zhang J, Pham B and Chen YPP (2002), A Fuzzy Genetic Algorithm for Creative Shape Design , Proceedings of the Fourth International Symposium on Tools and Methods of Competitive Engineering. pp.315-329, Wuhan, Hubei, China, 2002. 16. Li X, and Chen YPP (2002), Automatic Assessment of e-Businesses , Proceedings of the International Conference on E-Business 2002, pp. 294-299, Beijing, China, pp294-299, May 23-26 2002. 15. Soon L, Chen YPP and Underwood A (2002), A Case Study on Virtual Export Trade Community , Proceedings of the AUSWEB 2002, The Eighth Australian World Wide Web Conference, pp. 211-224, Sunshine Coast Queensland Australia, July 6-10 2002.
2001
14. Chen YPP (2001), A Practical Approach for Professional Development Portfolio . TechTrain2001, Brisbane, Australia, 5 July - 7 July, 2001, . 13. Gunther P and Chen YPP (2001), A New Approach To Hybrid SOM Implementations For Text Classification , Proceedings of the 10th International IEEE conference on Fuzzy Systems, IEEE CS Press, pp.968-972, Melbourne December 2-5 2001. (Tier A) 12. Zhang J, Pham B and Chen YPP (2001), Fuzzy Genetic Algorithms Based on Level Interval Algorithm Proceedings of the 10th International IEEE conference on Fuzzy Systems, IEEE CS Press. pp.1424-1428, Melbourne December 2-5 2001. (Tier A) 11. Zhang J, Pham B and Chen YPP (2001), Fuzzy Genetic Algorithms with Fuzzy Solutions , Australian Journal of Intelligent Information Processing Systems, Vol. 7 No. 1/2, pp. 1-10, 2001.
2000
10. Chen YPP and Colomb RM (2000), Querying Recursive Structures Without Recursive Queries , the 11th Australian Database Conference, ADC-2000, IEEE CS Press, Canberra, Australia. pp.21-27, 31 January - 2 February, 2000. 9. Chen YPP (2000), Generating Database Representations of L-systems in Virtual Plant Applications , PhD Thesis, School of Computer Science and Electrical Engineering, The University of Queensland, 2001. 8. Zhang J, Pham B and Chen YPP (2000), Indexing and Information Retrieval of Shape Databases , Fuzzy Logic: a Paradigm for the New Millennium, Studies in Fuzziness and Soft Computing, V. Dimitrov and V. Korotkich, eds., Physica-Verlag, 2001. 7. Zhang J, Pham B and Chen YPP (2000), Construction of Fuzzy Shape Database, in With Fuzzy Logic in the New Millennium, V. Dimitrov and V. Korotkich, Eds., pp. 53-54, 2001.
1999
6. Chen YPP and Colomb RM (1999) Generic Process Solution in Database Systems and L-systems for Bioinformatics Research Proc of The Second International Symposium on Cooperative Database Systems for Advanced Applications (CODAS'99), Wollongong, Australia, March 27-28, 1999. 5. Chen YPP (1999), DML: A Bridge between Database Systems and L-Systems for Biological Research , The 11th International Conference on Scientific and Statistical Database Management (SSDBM'99) ACM SIGMOD and VLDB Endowment, IEEE press, Cleveland, Ohio, USA, July 28-30 1999. (Tier A) 4. Chen YPP and Colomb RM (1999), Decision Support in Bioninformatics Research , Proc: The Fifth International Conference of The International Society for Decision Support Systems (ISDSS'99), Melbourne, Australia, 20-23 July 1999. 3. Chen YPP and Colomb RM (1999), Generic Process Solution in Database Systems and L-systems for Bioinformatics Research , in Zhang Y., Rusinkiewicz M. and Kambayashi Y. (eds) Cooperative Databases and Applicationsï¿½99, Springer-Verlag, pp.328-339.
1997-1998
2. Chen YPP and Colomb RM (1998), Design: A Visual Database Development System in B. Verma, Z. Liu, Z. Sattar, R. Surawski and J. You (eds.) 2nd IEEE International Conference on Intelligent Processing Systems (ICIPS'98) Gold Coast, Australia 4-7 August, 1998, IEEE CS Press, pp.198-202. 1. Colomb RM and Chen YPP (1997) Use of Partial Functional Dependencies to make Practical Approximate Translations Among Forms of Propositional Expert Systems in Sattar A. (ed.) Advanced Topics in Artificial Intelligence, Lecture Notes in Artificial Intelligence Vol 1342. Springer-Verlag, pp 167-176, 1997.
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