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Dr Jonathan Clark


Visiting Lecturer
BSc. Botany (Reading 1981), MSc Pure & Applied Plant Taxonomy (Reading 1984), PhD Cybernetics (Reading 2001)

Academic and research departments

Department of Computer Science.

Biography

Research interests

My main interest is bioinformatics in the broad sense, the interface between computing and biology, with emphasis on classification and pattern recognition, especially with regard to botanical taxonomy and systematics. This is a natural consequence of my BSc (Botany), MSc (Plant Taxonomy) and PhD (Cybernetics) studies. I am particularly interested in biological identification and classification techniques, especially those involving the use of artificial neural networks. My current teaching areas are Intelligent Information Systems, Information Systems Development and Computer Logic.

Research collaborations

  • Royal Botanic Gardens, Kew
  • University of York
  • University of Reading
  • Cardiff University
  • Kingston University

My publications

Publications

2012

Clark, J. Y., Corney, D., & Tang, H.L. (2012, accepted). Automated Plant Identification using  Artificial Neural Networks. In 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. San Diego, USA.

Cope, J. S., Corney, D. P. A., Clark, J. Y., Remagnino, P., & Wilkin, P. (2012). Plant Species Identification using Digital Morphometrics: a Review. Expert Systems with Applications 39(8), pp. 7562-7573.

Corney, D. P. A., Clark, J. Y., Tang, H. L., & Wilkin, P. (2012). Automatic Extraction of Leaf Characters from Herbarium Specimens. Taxon 61(1), 231-244.

2009

Clark, J. Y. (2009, February). Neural networks and cluster analysis for unsupervised classification of cultivated species of Tilia (Malvaceae). Botanical Journal of the Linnaean Society, 159(2), 300-314.

Athanasiou, M., & Clark, J. Y. (2009). A Bayesian network model for the diagnosis of the caring procedure for wheelchair users with spinal injury. Computer Methods and Programs in Biomedicine Vol. 95, pp. S44-S54. Maribor, Slovenia: Elsevier Ireland Ltd.

2007

Athanasiou, M. & Clark, J.Y. (2007). A Bayesian Network Model for the Diagnosis of the Caring Procedure for Wheelchair Users with Spinal Injury. Twentieth IEEE International Symposium on Computer-Based Medical Systems (CBMS), Slovenia, IEEE Conference Publication Services, pp. 433-438.

Clark, J. Y. (2007). Plant Identification from Characters and Measurements using Artificial Neural Networks. In MacLeod, N. (Ed.) Automated Taxon Identification in Systematics (Systematics Association Special Volume), Natural History Museum, London, CRC Press, Taylor & Francis Group, pp. 207-224.

2006

Athanasiou, M. & Clark, J.Y. (2006). DIMITRA- an online expert system for carers of paraplegics and quadriplegics. International Journal of Healthcare Technology and Management 7(5), 440-451.

2005

Heather, J., & Clark, J. Y. (2005). Family secrets. In T. Dimitrakos, & F. Martinelli (Eds.), Formal Aspects in Security and Trust Vol. 173, pp. 99-114. Springer, Toulouse, France.

2004

Clark, J.Y. (2004). Identification of botanical specimens using artificial neural networks. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 87-94, IEEE: La Jolla, California, USA

2003

Clark, J.Y. (2003). Computer-aided Taxonomy of Lithops. MSG Bulletin, vol. 18((1)), pp. 10-12.

Clark, J.Y. (2003). Artificial Neural Networks for Species Identification by Taxonomists. Biosystems, Special Issue on Computational Intelligence in Bioinformatics (Elsevier Press), vol. 72(1-2), pp. 131-147.

2000

Clark, J.Y. (2000). Botanical Identification and Classification using Artificial Neural Networks, . Unpublished doctoral thesis.

1999

Clark, J.Y. (1999). A key to Lithops N.E.Br. Lithops – Treasures of the Veld (Observations on the Genus Lithops N.E.Br.), BCSSHammer, S.A., pp. 135-141.

1998

Clark, J.Y. & Warwick, K. (1998). Artificial Keys for Botanical Identification using a Multilayer Perceptron Neural Network (MLP). Artificial Intelligence Review - Special Issue on Applications in Biology and Agriculture, vol. 12(1-3), pp. 105-115.

1997

Clark, J.Y. & Warwick, K. (1997). Machine fault diagnosis using an artificial neural network with data preprocessing. Proceedings of the 12th International Conference on Systems Engineering, ICSE'97, pp. 133-136.

1996

Clark, J.Y. & Warwick, K. (1996). Fault detection and diagnosis in high speed packaging machinery using a modular multi-layer perceptron approach. Proceedings of the International ICSC Symposium on Intelligent Industrial Automation (IAA'96), pp. A96-A101.