Peer-Reviewed Journal Articles
- Ali Braytee, Wei Liu, Ali Anaissi, Paul J. Kennedy, “Correlated Multi-label Classification with Incomplete Label Space and Class Imbalance”, ACM Transactions on Intelligent Systems and Technology, accepted 26/6/2019.
- Chen Qiao, Lujia Lu, Lan Yang and Paul J. Kennedy, “Identifying brain abnormalities with schizophrenia based on a hybrid feature selection technology”, Applied Sciences2019, 9, 2148; doi:10.3390/app9102148.
- Ahmad A. Al-Oqaily, Siamak Tafavogh, Bronwyn L. Stark, Daniel R. Catchpoole, Paul J. Kennedy, “Feature prioritization on big genomic data for analysing gene-gene interactions”, International Journal of Bioinformatics Research and Applications, accepted 13 May 2019.
- Stephan A. Curiskis, Barry Drake, Thomas R. Osborn, Paul J. Kennedy, “An evaluation of document clustering and topic modelling in two online social networks: Twitter and Reddit”, Information Processing and Management. 2019. In press. https://doi.org/10.1016/j.ipm.2019.04.002
- Mohammad Hesam Hesamian, Wenjing Jia, Xiangjian He, Paul Kennedy, “Deep Learning Techniques for Medical Image Segmentation: Achievements and Challenges”, Journal of Digital Imaging, 2019, doi:10.1007/s10278-019-00227-x
- Soheila Gheisari, Daniel R. Catchpoole, Amanda Charlton, Zsombor Melegh, Elise Gradhand, Paul J. Kennedy, Computer Aided Classification of Neuroblastoma Histological Images using Scale Invariant Feature Transform with Feature Encoding, Diagnostics 2018, 8, 56; doi:10.3390/diagnostics8030056
- Goodswen SJ, Kennedy PJ and Ellis JT (2018) A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen. Front. Genet. 9:332. doi: 10.3389/fgene.2018.00332
- Gheisari S, Catchpoole DR, Charlton A, Kennedy PJ. Convolutional deep belief network with feature encoding for classification of neuroblastoma histological images. J Pathol Inform 2018;9:17.
- Lin Cui, Jia Wu, Dechang Pi, Peng Zhang, and Paul J. Kennedy, “Dual implicit mining-based latent friend recommendation”, in IEEE Transactions on Systems, Man, and Cybernetics: Systems. doi: 10.1109/TSMC.2017.2777889
- Qinxue Meng, Daniel Catchpoole, David Skillicorn and Paul J. Kennedy, “DBNorm: Normalizing high-density oligonucleotide microarray data based on distributions.” BMC Bioinformatics (2017) 18:527 DOI 10.1186/s12859-017-1912-5.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis, “On the application of reverse vaccinology to parasitic diseases: a perspective on feature selection and ranking of vaccine candidates”, International Journal for Parasitology, 47 (2017) 779-790, https://doi.org/10.1016/j.ijpara.2017.08.004
- Quang Vinh Nguyen, Nader Hasan Khalifa, Patricio Alzamora, Andrew Gleeson, Daniel Catchpoole, Paul J. Kennedy, Simeon Simoff, “Visual analytics of complex genomics data to guide effective treatment decisions.”, Journal of Imaging 2016, 2, 29; doi:10.3390/jimaging2040029
- Ali Anaissi, Madhu Goyal, Daniel R. Catchpoole, Ali Braytee, Paul J. Kennedy, Ensemble feature learning of genomic data using support vector machine, PLoS ONE 11(1): e0157330. doi: 10.1371/journal.pone.0157330.
- Alireza Ahadi, Samuel Brennan, Paul J. Kennedy, Gyorgy Hutvagner and Nham Tran, Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes, Sci. Rep. 6, 24922; doi: 10.1038/srep24922 (2016).
- Renhua Song, Daniel Catchpoole, Paul J. Kennedy and Jinyan Li, Identification of lung cancer miRNA-miRNA co-regulation networks through a progressive data refining approach, Journal of Theoretical Biology 380 (2015) 271-279.
- Stephen J. Goodswen, Joel L. N. Barratt, Paul J. Kennedy and John T. Ellis, Improving the gene-structure annotation of the apicomplexan parasite Neospora caninum fulfils a vital requirement towards an in silico derived vaccine, International Journal for Parasitology 45 (2015) 305-318.
- Ali Anaissi, Madhu Goyal, Daniel R. Catchpoole and Paul J. Kennedy, Case-based retrieval framework for gene expression data, Cancer Informatics 2015:14 21-31 doi: 10.4137/CIn.s22371.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis, Enhancing in silico protein-based vaccine discovery for eukaryotic pathogens using predicted peptide-MHC binding and peptide conservation scores, PLoS One, 2014; 9(12): e115745.
- Siamak Tafavogh, Daniel R. Catchpoole and Paul J. Kennedy, Cellular quantitative analysis of neuroblastoma tumor and splitting overlapping cells, BMC Bioinformatics 2014, 15:272 doi:10.1186/1471-2105-15-272.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis, Discovering a vaccine against neosporosis using computers - is it feasible?, Trends in Parasitology (2014), 30(8):401-411. doi: 10.1016/j.pt.2014.06.004.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis. Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology, Bioinformatics 2014, doi: 10.1093/bioinformatics/btu300.
- Stephen J Goodswen, Paul J Kennedy and John T Ellis, A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms, BMC Bioinformatics 2013, 14:315.
- Ali Anaissi, Paul J. Kennedy, Madhu Goyal and Daniel Catchpoole, A Balanced Iterative Random Forest For Gene Selection From Microarray Data, BMC Bioinformatics, 2013, 14:261. DOI: 10.1186/1471-2105-14-261.
- H. Ghous, P. J. Kennedy, N. Ho, and D. R. Catchpoole. Comparing functional visualisations of lists of genes using singular value decomposition. Journal of Research and Practice in IT, 2015, 14(1), 47-76.
- S. Tafavogh, K. Felix Navarro, D. R. Catchpoole, and P. J. Kennedy. Non-parametric and integrated framework for segmenting and counting neuroblastic cells within neuroblastoma tumor images. Medical and Biological Engineering and Computing, 51:645–655, 2013. SpringerLink
- P. J. Kennedy. Redesign of a data analytics major: challenges and lessons learned. Procedia-Social and Behavioral Sciences, 116 (2014) 1373-1377. ScienceDirect.
- S. J. Goodswen, P. J. Kennedy, and J. T. Ellis. Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PLoS ONE, 7(11):e50609, 2012.
- S. Goodswen, P. Kennedy, and J. Ellis. A review of the infection, genetics, and evolution of Neospora caninum: from the past to the present. Infection, Genetics and Evolution, 13:133–150, January 2013. ScienceDirect
- S. J. Goodswen, P. J. Kennedy, and J. T. Ellis. A guide to in silico vaccine discovery for eukaryotic pathogens. Briefings in Bioinformatics, (2013) 14 (6):753-774 first published online October 24, 2012.
- J. Ellis, S. Goodswen, P. J. Kennedy, and S. Bush. The core mouse response to infection by Neospora Caninum defined by gene set enrichment analyses. Bioinformatics and Biology Insights, 6:187–202, 2012.
- M. Lambert and P. Kennedy. Using artificial intelligence to build with unprocessed rock. Key Engineering Materials, 517:939–945, 2012.
- D. R. Catchpoole, P. Kennedy, D. Skillicorn, and S. Simoff. The curse of dimensionality: a blessing to personalised medicine. Journal of Clinical Oncology, 28(34):e723–e724, 1 Dec 2010.
- J. Milton and P. J. Kennedy. Static and dynamic selection thresholds governing the accumulation of information in genetic algorithms using ranked populations. Evolutionary Computation, 18(2):229–254, 2010.
- P. J. Kennedy and T. R. Osborn. A model of gene expression and regulation in an artificial cellular organism. Complex Systems, 13(1):33–59, 2001.
Peer-Reviewed Conference Papers
- Zainab Awan, Tim Kahlke, Peter Ralph, Paul Kennedy, Chemical named entity recognition with deep contextualized neural embeddings, 11thInternational Conference on Knowledge discovery and Information retrieval. 2019. Accepted 29 June 2019.
- Andrew Brunker, Daniel Catchpoole, Paul J. Kennedy, Simeon Simoff and Quang Vinh Nguyen, Two-dimensional immersive cohort analysis supporting personalized medical treatment, 23rdInternational Conference on Information Visualisation, accepted 26 May 2019. Best paper award.
- Fatemeh Mahdavi, Paul J. Kennedy, David Eager, Ageing and resulting injuries - effects on racing greyhounds, 25thCongress of the European Society of Biomechanics, July 7-10 2019, Vienna, Austria.
- Mohammad Hesam Hesamian, Wenjing Jia, Xiangjian He and Paul Kennedy, Atrous convolution for binary segmentation of lung nodule, 2019 IEEE International Conference on Acoustics, Speech, and Signal Processing, pages 1015-1019.
- Naji M., Al-Ani A., Braytee A., Anaissi A., Kennedy P.(2019) Queue Formation Augmented with Particle Swarm Optimisation to Improve Waiting Time in Airport Security Screening. In: Barolli L., Takizawa M., Xhafa F., Enokido T. (eds) Web, Artificial Intelligence and Network Applications. WAINA 2019. Advances in Intelligent Systems and Computing, vol 927. Springer, Cham
- Ali Braytee, Ali Anaissi and Paul Kennedy, Sparse Feature Learning using Ensemble Model for Highly-correlated High- dimensional Data, Accepted for the 25th International Conference on Neural Information Processing (ICONIP2018). 2 August 2018.
- Fatemeh Mahdavi, Imam Hossain, Hasti Hayati, David Eager, Paul Kennedy, “Track shape, resulting dynamics and injury rates of greyhounds”, submitted to Proceedings of the ASME International Conference on Engineering Congress and Exposition. Accepted 28/6/18.
- Gheisari S., Catchpoole D.R., Charlton A., Kennedy P.J. (2018) Patched Completed Local Binary Pattern is an Effective Method for Neuroblastoma Histological Image Classification. In: Boo Y., Stirling D., Chi L., Liu L., Ong KL., Williams G. (eds) Data Mining. AusDM 2017. Communications in Computer and Information Science, vol 845. Springer, Singapore
- Aedan Roberts, Daniel R. Catchpoole, Paul J. Kennedy, Variance-based feature selection for classification of cancer subtypes using gene expression, In Proceedings of 2018 IEEE World Congress on Computational Intelligence, 8-13 July 2018, Rio de Janeiro, Brazil.
- Ali Braytee, Wei Liu, Daniel R. Catchpoole, Paul J. Kennedy. 2017. Multi-Label Feature Selection using Correlation Information. In Proceedings of CIKM’17, November 6–10, 2017, Singapore, pages 1649-1656, 8 pages.
DOI: http://dx.doi.org/10.1145/3132847.3132858. - Q. Meng, D. Catchpoole, D. Skillicorn, and P. J. Kennedy. Relational autoencoder for feature extraction. In 2017 International Joint Conference on Neural Networks (IJCNN), pages 364–371, IEEE, 2017.
- Q. Meng, J. Wu, J. Ellis, and P. J. Kennedy. Dynamic island model based on spectral clustering in genetic algorithm. In 2017 International Joint Conference on Neural Networks (IJCNN), pages 1724–1731. IEEE, 2017.
- A. Braytee, W. Liu, and P. J. Kennedy. Supervised context-aware non-negative matrix factorization to handle high-dimensional high-correlated imbalanced biomedical data. In 2017 International Joint Conference on Neural Networks (IJCNN), pages 4512–4519. IEEE, 2017.
- Ali Braytee, Daniel Catchpoole, Paul Kennedy, Wei Liu, Balanced Supervised Non-Negative Matrix Factorization for Childhood Leukaemia Patients, CIKM 2016. CIKM '16 Proceedings of the 25th ACM International on Conference on Information and Knowledge Management, Indianapolis, Indiana, pages 2405-2408. doi:10.1145/2983323.2983375.
- Shoujin Wang, Wei Liu, Longbing Cao, Qinxue Meng and Paul J. Kennedy, Training Deep Neural Networks on Imbalanced Data Sets, 2016 International Joint Conference on Neural Networks (IJCNN), pp. 4368-4374, IEEE.
- Ali Braytee, Wei Liu, Paul J. Kennedy, A Cost-Sensitive Learning Strategy for Feature Extraction from Imbalanced Data. In Neural Information Processing, pages 78-86. Springer, 2016.
- Ali Braytee, Farookh Khadeer Hussain, Ali Anaissi and Paul J. Kennedy, ABC-Sampling for balancing imbalanced datasets based on Artificial Bee Colony algorithm, 14th IEEE International Conference on Machine Learning and Applications (ICMLA), Miami, Florida, pages 594-599. DOI 10.1109/ICMLA.2015.103
- A. Braytee, A. Q. Gill, P. J. Kennedy, and F. K. Hussain. A review and comparison of service e-contract architecture metamodels. In Neural Information Processing, pages 583–595. Springer, 2015.
- Stephan A. Curiskis, Thomas R. Osborn and Paul J. Kennedy, Link prediction and topological feature influence in social networks, Thirteenth Australasian Data Mining Conference, Sydney, Australia. Conferences in Research and Practice in Information Technology, Vol. 168. Ed. Md Zahidul Islam, Ling Chen, Kok-Leong Ong, Yanchang Zhao, Richi Nayak, Paul Kennedy, pages 39-50, ACS, 2015.
- Qinxue Meng and Paul J. Kennedy, Community detection on heterogeneous networks by multiple semantic-path clustering, In 6th International Conference on Computational Aspects of Social Networks (CASoN), Porto, Portugal, pages 7-12. IEEE, 2014.
- Siamak Tafavogh, Meng Qinxue, Daniel R. Catchpoole and Paul J. Kennedy, Automated quantitative and qualitative analysis of the whole slide images of Neuroblastoma tumour for making prognosis decision, In IASTED 11th International Conference on Biomedical Engineering (BioMed 2014), Zurich, Switzerland, pages 244-251. Acta Press, 2014.
- Q. Meng and P. J. Kennedy. Discovering influential authors in heterogeneous academic networks by a co-ranking method. In CIKM ’13 Proceedings of the 22nd ACM International Conference on Information and Knowledge Management, pages 1029–1036. ACM, 2013.
- S. Tafavogh, K. Felix Navarro, D. R. Catchpoole, and P. J. Kennedy. Segmenting neuroblastoma tumor images and splitting overlapping cells using shortest path between convex regions of cell contours. In N. Peek, R. M. Morales, and M. Peleg, editors, Artificial Intelligence in Medicine, LNCS 7885, pages 171–175. Springer, 2013.
- H. Homayounfard, P. J. Kennedy, and R. Braun. NARGES: prediction model for informed routing in a communications network. In J. Pei, V. S. Tseng, L. Cao, and H. Motoda, editors, Advances in knowledge discovery and data mining: 17th Pacific-Asia Conference, PAKDD 2013, Part I, LNAI 7818, pages 327–338. Springer, 2013.
- H. Ghous, N. Ho, D. R. Catchpoole, and P. J. Kennedy. Functional visualisation of genes using singular value decomposition. In Y. Zhao, J. Li, P. J. Kennedy, and P. Christen, editors, Proceedings of the Tenth Australasian Data Mining Conference (AusDM 12), volume 134 of Conferences in Research and Practice in IT (CRPIT), pages 53–59. Australian Computer Society, 2012.
- Q. Meng and P. J. Kennedy. Using network evolution theory and singular value decomposition method to improve accuracy of link prediction in social networks. In Y. Zhao, J. Li, P. J. Kennedy, and P. Christen, editors, Proceedings of the Tenth Australasian Data Mining Conference (AusDM 12), volume 134 of Conferences in Research and Practice in IT (CRPIT), pages 175–181. Australian Computer Society, 2012.
- Q. Meng and P. J. Kennedy. Determining the number of clusters using social network theory. In J. Liu, J. Chen, and G. Xu, editors, Proceedings of The Second International Conference on Social Computing and its Applications, pages 337–343. IEEE, 2012. IEEE Xplore
- Q. Meng and P. J. Kennedy. Using field of research codes to discover research groups from co-authorship networks. In 2012 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), pages 289–293. IEEE, 2012. ACM Digital Library.
- S. Tafavogh, P. J. Kennedy, and D. R. Catchpoole. Determining cellularity status of tumors based on histopathology using hybrid image segmentation. In 2012 International Joint Conference on Neural Networks (IJCNN), pages 1–8. IEEE, 2012. IEEE Xplore
- A. Van, V. C. Gay, P. J. Kennedy, E. Barin, and P. Leijdekkers. Understanding risk factors in cardiac rehabilitation patients with random forests and decision trees. In P. Vamplew, A. Stranieri, K.-L. Ong, P. Christen, and P. J. Kennedy, editors, Proceedings of the Ninth Australasian Data Mining Conference (AusDM 11), volume 121 of Conferences in Research and Practice in IT (CRPIT), pages 11–22. Australian Computer Society, 2011.
- H. Ghous, N. Ho, D. R. Catchpoole, and P. J. Kennedy. Comparing functional visualizations of genes. In J. Maria Pena and F. Famili, editors, 5th Workshop on Data Mining in Functional Genomics and Proteomics: Current Trends and Future Directions, ECML-PKDD 2011, pages 12–21. 5–9 September 2011.
- A. Anaissi, P. J. Kennedy, and M. Goyal. Feature selection of imbalanced gene expression microarray data. In M. Chowdhury, S. Ray, and R. Lee, editors, Proceedings 12th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing, pages 73–78. IEEE, 2011. IEEE Xplore
- H. Santosa, J. Milton, and P. J. Kennedy. HMXT–GP: an information-theoretic approach to genetic programming that maintains diversity. In Proceedings of the 26th Annual ACM Symposium on Applied Computing (SAC 2011), pages 1070–1075. ACM, New York, 2011. ACM Digital Library
- A. Anaissi, P. J. Kennedy, and M. Goyal. A framework for high dimensional data reduction in the microarray domain. In IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA 2010), pages 903–907, Changsha, September 2010. IEEE. IEEE Xplore
- J. Milton and P. J. Kennedy. Entropy profiles of ranked and random lists. In Proceedings GECCO’2010, pages 1843–1849. ACM, 2010. ACM Digital Library
- H. Homayounfard and P. J. Kennedy. HDAX: Historical symbolic modelling of delay time series in a communications network. In P. J. Kennedy, K.-L. Ong, and P. Christen, editors, Data Mining and Analytics 2009: Proceedings of the Eighth Australasian Data Mining Conference (AusDM’09), volume 101 of Conferences in Research and Practice in IT (CRPIT), pages 129–137, Sydney, 2009. Australian Computer Society.
- A. Rahman, P. J. Kennedy, A. Simmonds, and J. Edwards. Fuzzy logic based modelling and analysis of network traffic. In Computer and Information Technology, 2008. CIT 2008. 8th IEEE International Conference on, pages 652–657. IEEE, 2008. IEEE Xplore
- A. Al-Oqaily, P. J. Kennedy, D. Catchpoole, and S. Simoff. Comparison of visualization methods of genome-wide SNP profiles in childhood acute lymphoblastic leukemia. In J. F. Roddick, J. Li, P. Christen, and P. J. Kennedy, editors, Data Mining and Analytics 2008: proceedings of the Seventh Australasian Data Mining Conference (AusDM’08), volume 87 of Conferences in Research and Practice in IT (CRPIT), pages 111–121. Australian Computer Society, Sydney, 2008.
- H. Ghous, P. J. Kennedy, D. R. Catchpoole, and S. J. Simoff. Kernel-based visualisation of genes with the gene ontology. In J. F. Roddick, J. Li, P. Christen, and P. J. Kennedy, editors, Data Mining and Analytics 2008: proceedings of the Seventh Australasian Data Mining Conference (AusDM’08), volume 87 of Conferences in Research and Practice in IT (CRPIT), pages 133–140. Australian Computer Society, Sydney, 2008.
- A. Al-Oqaily and P. J. Kennedy. Using a kernel-based approach to visualize integrated chronic fatigue syndrome datasets. In P. Christen, P. J. Kennedy, J. Li, S. J. Simoff, and G. J. Williams, editors, Data Mining and Analytics 2006: proceedings of the fifth Australasian Data Mining Conference (AusDM2006), volume 61 of Conferences in Research and Practice in IT (CRPIT), pages 53–59. Australian Computer Society, Sydney, 2006.
- J. Luu and P. J. Kennedy. Investigating the size and value effect in determining performance of Australian listed companies: a neural network approach. In P. Christen, P. J. Kennedy, J. Li, S. J. Simoff, and G. J. Williams, editors, Data Mining and Analytics 2006: proceedings of the fifth Australasian Data Mining Conference (AusDM2006), volume 61 of Conferences in Research and Practice in IT (CRPIT), pages 155–161. Australian Computer Society, Sydney, 2006.
- M. Beauregard and P. J. Kennedy. Robust simulation of lamprey tracking. In T. P. Runarsson, H. Beyer, E. Burke, J. J. Morelo-Guervos, L. D. Whitley, and X. Yao, editors, Parallel Problem Solving from Nature – PPSN IX, LNCS 4193, pages 641–650. Springer, Berlin, 2006. SpringerLink
- Beauregard, M., Kennedy, P. J. and Debenham, J., (2006), Fast simulation of animal locomotion: lamprey swimming, in J. Debenham (eds.), IFIP International Federation for Information Processing, Volume 218, Professional Practice in Artificial Intelligence, pp. 247-256, Springer: Boston. SpringerLink
- Milton, J. Kennedy, P.J. and Mitchell, H., (2005), The effect of mutation on the accumulation of information in a genetic algorithm, In Zhang, S. and Jarvis, R. (eds.), AI 2005, LNAI 3809, pp360-368, Springer-Verlag: Berlin. SpringerLink
- Whitehead, D.J., Skusa, A. and Kennedy, P.J., (2004), Evaluating an evolutionary approach for reconstructing gene regulatory networks, Proc. Artificial Life IX, Boston, USA, Pollack, J., Bedau, M., Husbands, P., Ikegami, T., and Watson, R. A. (eds), pp 427-432, MIT Press. dionamago.net
- P. J. Kennedy, S. J. Simoff, D. Skillicorn, and D. Catchpoole. Extracting and explaining biological knowledge in microarray data. In H. Dai, R. R. Srikant, and C. Zhang, editors, Proc. Eighth Pacific-Asia Conference on Knowledge Discovery and Data Mining, Sydney, LNAI 3056, pages 699–703. Springer, Berlin, 2004. Link
- Skillicorn, D. B., Simoff, S., Kennedy, P. and Catchpoole, D. (2004) Strategies for Winnowing Microarray Data. Proc. SIAM Bioinformatics Workshop 2004, in conjunction with Fourth International Conference on Data Mining, Walt Disney World Resort, Florida, USA, pp 42-51.
- Kennedy, P.J. and Simoff, S.J., (2003) CONGO: Clustering on the Gene Ontology, in Proceedings Australasian Data Mining Workshop ADM03, in conjunction with Congress on Evolutionary Computation, Canberra, December 2003, pp181-198.
- Kennedy P. J. and Osborn, T. R., (2001), A Double—Stranded Encoding Scheme with Inversion Operator for Genetic Algorithms. Proceedings of the 2001 Genetic and Evolutionary Computation Conference, pp. 398–407. July 7-11, 2001, San Francisco, California. (ed.) L. Spector, E., D. Goodman et al, Morgan Kaufmann: San Francisco. Email me.
- Kennedy P. J. and Osborn, 2000, Evolution of Adaptive Behaviour in a Simulated Single–Celled Organism, in T. R. Meyer, Berthoz, Floreano, Roitblat and Wilson (Eds). SAB2000 Proceedings Supplement Book. Publication of the International Society for Adaptive Behavior, Honolulu, pp. 225–234. 6th International Conference on the Simulation of Adaptive Behaviour, Paris, France, 11–16 September 2000.
- Kennedy P. J. and Osborn, T. R., 2000, Operon Expression and Regulation with Spiders, Proceedings of the 2000 Genetic and Evolutionary Computation Conference Workshop Program, pp. 161–166. Las Vegas, Nevada, 8 July 2000. (ed.) Annie S. Wu, University of Central Florida.
- Kennedy P. J. and Osborn, T. R., 1999, A Coevolutionary Model of a Single–Celled Organism with Double–Stranded Genome and Time–Varying Phenotype, Proceedings of the 3rd Australia–Japan Joint Workshop on Intelligent and Evolutionary Systems, pp.145–152. Canberra, Australia, 23–35 November 1999.
Peer-reviewed Book Chapters
- F. A. Ubaudi, P. J. Kennedy, D. R. Catchpoole, D. Guo, and S. J. Simoff. Microarray data mining: Selecting trustworthy genes with gene feature ranking. In L. Cao, P. S. Yu, C. Zhang, and H. Zhang, editors, Data Mining for Business Applications, chapter 11, pages 159–168. Springer, 2009. Prepress
- P. Kennedy, S. J. Simoff, D. R. Catchpoole, D. B. Skillicorn, F. Ubaudi, and A. Al-Oqaily. Integrative visual data mining of biomedical data: Investigating cases in chronic fatigue syndrome and acute lymphoblastic leukaemia. In S. J. Simoff, M. H. Boehlen, and A. Mazeika, editors, Visual Data Mining: Theory, Techniques and Tools for Visual Analytics, volume 4404 of LNCS, pages 367–388. Springer, 2008.
- A. S. Sidhu, P. J. Kennedy, S. Simoff, T. S. Dillon, and E. Chang. Knowledge discovery in biomedical data facilitated by domain ontologies. In X. Zhu and I. Davidson, editors, Knowledge Discovery and Data Mining: Challenges and Realities, pages 189–201. IGI Global, Hershey, New York, 2007. Google
Edited Conference Proceedings
- P. Christen, P. J. Kennedy, L. Liu, K.-L. Ong, A. Stranieri and Y. Zhao, editors. Proceedings of the Eleventh Australasian Data Mining Conference (AusDM 13), volume 146 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Sydney, 2013.
- Y. Zhao, J. Li, P. J. Kennedy, and P. Christen, editors. Proceedings of the Tenth Australasian Data Mining Conference (AusDM 12), volume 134 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Sydney, 2012.
- P. Vamplew, A. Stranieri, K.-L. Ong, P. Christen, and P. J. Kennedy, editors. Proceedings of the Ninth Australasian Data Mining Conference (AusDM 11), volume 121 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Ballarat, 2011.
- P. J. Kennedy, K.-L. Ong, and P. Christen, editors. Data Mining and Analytics 2009: Proceedings of the Eighth Australasian Data Mining Conference (AusDM’09), volume 101 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Sydney, 2009.
- J. F. Roddick, J. Li, P. Christen, and P. J. Kennedy, editors. Data Mining and Analytics 2008: Proceedings of the Seventh Australasian Data Mining Conference (AusDM’08), volume 87 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Sydney, 2008.
- P. Christen, P. J. Kennedy, J. Li, I. Kolyshkina, and G. J. Williams, editors. Data Mining and Analytics 2007: Proceedings of the Sixth Australasian Data Mining Conference (AusDM2007), volume 70 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Sydney, 2007.
- P. Christen, P. J. Kennedy, J. Li, S. J. Simoff, and G. J. Williams, editors. Data Mining and Analytics 2006: Proceedings of the Fifth Australasian Data Mining Conference (AusDM2006), volume 61 of Conferences in Research and Practice in IT (CRPIT). Australian Computer Society, Sydney, 2006.
Non-HERDC Publications
- Siamak Tafavogh, Daniel Catchpoole, Paul J. Kennedy, Generating Actionable Knowledge from Complex Genomic Data for Personalised Clinical Decisions, Australasian Genomic Technologies Association (AGTA). Accepted 2 September 2014. Poster presentation by Siamak Tafavogh.
- Daniel R. Catchpoole, Nicholas Ho, Siamak Tafavogh, Patricio J. Alzamora, Quang Vinh Nguyen, David Skillicorn, Paul J. Kennedy, Generating actionable knowledge from complex genomic data for personalised clinical decisions in childhood cancer, ANZCHOG 2014. Accepted 17 April 2014. Oral presentation by D. Catchpoole.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis, A proposed in silico vaccine discovery pipeline for Neospora caninum, WAAVP 2013: 24th International Conference of the World Association for the Advancement of Veterinary Parasitology, 25-29 August 2013, Perth, Australia. Oral presentation by S. J. Goodswen.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis, A proposed in silico vaccine discovery pipeline for Neospora caninum, Cold Spring Harbor Asia: Vaccine Design, The Suzhou Dushu Lake Conference Center, Dushu Lake, Cold Spring Harbor Asia, 3-7 June 2013. Poster presentation by S. J. Goodswen.
- Daniel R. Catchpoole, Nicholas Ho, Guy Nelmes, Patricio J. Alzamora, Ahmad Aloqaily, Quang Vinh Nguyen, David Skillicorn, Paul J. Kennedy, Constructing a “similarity space” from complex genomics data to aid personalized treatment decisions for childhood cancer patients, Ninth AACR-Japanese Cancer Association Joint Conference: Breakthroughs in Basic and Translational Cancer Research, February 21-25, 2013, Maui, Hawaii. Poster presentation by D. R. Catchpoole.
- Paul J. Kennedy, Redesign of a data analytics major: challenges and lessons learned, World Conference on Educational Sciences, 5-8 Feb 2013. Rome, Italy. Oral presentation.
- Stephen J. Goodswen, Paul J. Kennedy and John T. Ellis, First step in an in silico vaccine discovery pipeline for eukaryotic pathogens, EMBO / EMBL Symposium: New Perspectives on Immunity to Infection, 19-22 May 2012, Heidelberg Germany. Poster presentation by S. J. Goodswen.
- Stephen Goodswen, Paul Kennedy and John Ellis, Evaluation of high-throughput ab initio gene finding in apicomplexan genomes, 10th Asia Pacific Bioinformatics Conference, 17-19 Jan 2012, Melbourne, Australia. Poster presentation by S. J. Goodswen.
- Malcolm Lambert and Paul Kennedy, Using Artificial Intelligence to Build with Unprocessed Rock, 13th International Conference on Non-conventional Materials and Technologies, 22-24 September 2011, Changsha, China. Oral presentation by M. Lambert.
- Nicholas Ho, Guy Nelmes, Dachuan Guo, Paul J. Kennedy and Daniel Catchpoole, Using Random Forest to identify genes that separate a cohort of Acute Lymphoblastic Leukaemia, Australian Society for Medical Research, National Scientific Conference 2011, Poster by N. Ho. Catchpoole D.R., Ho N., Morton G., Kennedy P., Simoff S., Skillicorn D., "Using decomposition methods and visualization of global gene expression and SNP data to identify leukaemia patients at risk of treatment failure.", 2nd Worldwide Innovative Networking in Personalized Cancer Medicine, Paris, July 2010.
- Nicholas Ho, Geoff Morton, David Skillicorn, Paul Kennedy and Daniel Catchpoole, Data-mining gene expression and genomic microarray datasets of Acute Lymphoblastic Leukaemia, Poster, Lowy symposium, Sydney, May 2010
- Longbing Cao, Richard Raban, Paul Kennedy, Gordon Lingard, Andrew Litchfield and Tich Phuoc Tran (2010), Educational data mining for higher education learning and teaching performance improvements. Confidential report.
- Kennedy P. J., 2009, “Making sense of Biomedical Data”, Talk at Oncology Research Unit, The Children’s Hospital at Westmead. 1 April 2009.
- Dachuan Guo, Sara Diaz, Ellie Smith, Ahmad Aloqaily, Paul Kennedy, Simeon Simoff, Daniel R Catchpoole, “Integrative Data Mining and Visualization of Genome-wide SNP Data: A Window into the Genetic Background of Childhood Acute Lymphoblastic Leukaemia (ALL) Patients”, Australian Society for Medical Research (NSW Branch), 2008, (poster)
- Dachuan Guo, Sara Diaz, Ellie Smith, Ahmad Aloqaily, Paul Kennedy, Simeon Simoff, Daniel R Catchpoole, “Integrative Data Mining and Visualization of Genome-wide SNP Data: A Window into the Genetic Background of Childhood Acute Lymphoblastic Leukaemia (ALL) Patients”, Sydney Cancer Conference, 2008, (poster)
- Kennedy P. J., (2007), Rocksolver Step 1 / Stage 1 Review of Algorithms, comissioned by Intresto Pty. Ltd.
- Kennedy P.J., Ubaudi F., Al-Oquaily A., Simoff S.J. and Catchpoole D.R., “A constructionist approach to data mining: investigating cases in Chronic Fatigue Syndrome”, Bioinformatics Australia, Sydney, 2006. (contributed talk, peer review of extended abstract)
- Al-Oquaily A. and Kennedy P.J., “Application of clustering genes using kernel methods”, Bioinformatics Australia, Sydney, 2006. (poster, peer review of extended abstract)
- Kennedy P.J., Simoff S.J., Catchpoole D.R., Ubaudi F., Al-Oquaily A., Yildiz S., Du Y. and Skillicorn D.B., “Does CFS have a biological basis? – A constructionist approach.”, Critical Assessment of Microarray Data Analysis, Duke University, North Carolina, USA, 2006. (http://www.camda.duke.edu/camda06/papers/days/posters/catchpoole/paper.doc)
- Kennedy P. J., (2005), Social networking analysis of company directorships for Proxy Australia.
- Kennedy P. J., (2005), Loyalty prediction model for Ford, commissioned by Wunderman.
- Kennedy P. J., (2005), RFM modelling for Samsung distributors paper 1.
- Kennedy P. J., (2005), RFM modelling for Samsung distributors paper 2.
- P. J. Kennedy. Simulation of the evolution of single celled organisms with genome, metabolism and time–varying phenotype. PhD thesis, University of Technology, Sydney, 1999.