Publications

My publications are available from the Computer Science department publications repository.

In the above list of my publications the papers are NOT available on-line.

My ON-LINE List of Publications

Research Interests

I belong to the following research groups:

• Computational Intelligence Group

I am also a member of the Centre for BioMedical Informatics

My main research interests involve the following areas:

Data Mining and Knowledge Discovery;

Bio-inspired algorithms (Evolutionary Algorithms, Swarm Inteligence, Artificial Immune Systems);

Bioinformatics;

I got my PhD in Computer Science from the University of Essex, UK, in 1997, doing research on data mining. Since then the focus of my research has been the development of new bio-inspired algorithms for data mining. In terms of data mining applications, since 2005 my research has been focusing on creating new data mining methods for bioinformatics (in particular the prediction of protein functions).

Books

A.A. Freitas and S.H. Lavington. Mining Very Large Databases with Parallel Processing. (208 pages) Kluwer, 1998. Table of Contents and Publisher's address

A.A. Freitas. Data Mining and Knowledge Discovery with Evolutionary Algorightms. (264 pages) Springer-Verlag, August 2002. Book Cover Table of Contents and Publisher's Address

Journals

I am a member of the Editorial Board of the following journals:

Intelligent Data Analysis - An International Journal

International Journal on Data Warehousing and Mining

International Journal of Natural Computation Research

International Journal of Applied Metaheuristic Computing

I was a co-editor of the Special Issue of IEEE Transactions on Evolutionary Computation on Data Mining and Knowledge Discovery with Evolutionary Algorithms. See the Table of Contents and further details

Past Research Project - A Synergistic Integration of Natural and Artificial Immunology for the Prediction of Hierarchical Protein Functions

This was an EPSRC-sponsored multi-institutional project involving 3 institutions: the University of Kent, the University of York and the Edward Jenner Institute for Vaccine Research. The project involved 3 post-doc Research Associates, one post-doc at each institution. This project started in February 2006 and finished in November 2008.
For more information about this project, see the project's website.

Main publication related to this project:

M.N. Davies, A. Secker, A.A. Freitas, M. Mendao, J. Timmis and D.R. Flower. On the hierarchical classification of G protein-coupled-receptors. Bioinformatics 2007, Vol. 23, No. 23, 1 December 2007, pp. 3113-3118. (pre-print version) (pdf)

Past Research Project - Bio-inspired Classification and Data Mining Algorithms for Bioinformatics

This was an European Union Interreg III project involving 2 institutions: the University of Kent in the UK and the University of Littoral in France. The project involved 1 post-doc Research Associate at Littoral and 1 PhD student at Kent. The project started in September 2006 and finished in August 2008.
For more information about this project, see the project's website.

Past Research Project - eXtended Particle Swarms (XPS)

This was a large EPSRC-sponsored research project, which came out from the below-mentioned research cluster in Swarm Intelligence. The project involved 5 universities (Essex, Kent, Leeds, Goldsmith and UMIST), industrial collaboration with BTExact and several international collaborators who are key figures in the field. In total (in all the 5 universities) the project involved 5 post-docs full time for two years and 4 PhD students full time for three years. At Kent the project involved one post-doc research associate and one PhD student, and the co-investigator at Kent was Colin Johnson. This project started in October 2004 and finished in September 2007.

Main publication related to this project:

N. Holden and A.A. Freitas. Hierarchical classification of protein function with ensembles of rules and particle swarm optimisation. Soft Computing journal, Vol. 13, No. 3, Feb. 2009, pp. 259-272. (pre-print version) (pdf)

Past Research Project - Research Cluster in Swarm Intelligence

I have coordinated (jointly with Colin Johnson) an EPSRC-sponsored research cluster in Swarm Intelligence in the UK, in 2003. This was a multi-institutional and interdisciplinary research cluster, involving more than 15 institutions and a good mix of computer scientists, biologists and mathematicians.

Former PhD students:

Dr. Mudassar Iqbal completed his Ph.D. in 2009. The title of his PhD Thesis was "Machine Learning and Optimization Methods for the Prediction of Protein-Protein Interactions".

Dr. Sid Ghosh completed his PhD in 2009. The title of his PhD thesis was "A Machine Learning Approach to Robust Autonomous Detection of Defective Pixels in Image Sensor Arrays".

Dr. Nicholas Holden completed his PhD in 2008. The title of his PhD thesis was "Improving the Hierarchical Classification of Protein Functions with Swarm Intelligence".

Dr. Gisele Pappa completed her Ph.D. in 2007. The title of her PhD thesis was "Automatically Evolving Rule Induction Algorithms with Grammar-Based Genetic Programming".

Dr. Andrew Secker completed his Ph.D. in 2006. The title of his PhD thesis was: "Artificial Immune Systems for Web Content Mining: focusing on the discovery of interesting information".

Dr. Deborah Carvalho completed her Ph.D. in 2005. The title of her PhD thesis was "A Decision Tree/Genetic Algorithm Method for Coping with the Problem of Small Disjuncts in Data Classification" (The thesis was written in Portuguese).

Dr. Wesley Romao completed his Ph.D. in 2002. The title of his PhD thesis was "Discovery of Relevant Knowledge in Science and Technology Databases" (The thesis was written in Portuguese).

Current PhD students:

Fernando Otero is doing his PhD in the area of "Ant Colony Optimization for the hierarchical classification of protein functions". He started in October 2006. His co-supervisor is Colin Johnson

Carlos Silla is doing his PhD in the area of "Hierarchical Classification in Data Mining". He started in September 2007.