Professor of Computational Intelligence
School of Computing
University of Kent,
School of Computing, University of Kent
My publications are available from the
University of Kent's Academic Repository.
In the above list of my publications the papers are NOT available on-line.
My ON-LINE List of Publications
My publications' citations in Google Scholar
I am currently teaching Data Mining and Knowledge Discovery (a master-level module) and Natural Computation (evolutionary algorithms and swarm intelligence).
I belong to the following research groups:
My main research interests involve the following areas:
Data Mining (or Machine Learning) and Knowledge Discovery, focusing on developing new classification methods that produce interpretable models (e.g., decision trees, if-then rules and Bayesian network classifiers);
Applications of classification methods in the Life Sciences, mainly in the Biology of Ageing, but also in Pharmaceutical Sciences;
Biologically-inspired algorithms: mainly Evolutionary Algorithms and Ant Colony Optimisation;
I got my PhD in Computer Science from the University of Essex, UK, in 1997, doing research on data mining, and I have continued to do research on data mining up to the present. In terms of data mining applications, since 2005 my research has been focusing on creating new data mining methods for bioinformatics; initially focusing on the prediction of protein functions, and more recently focusing on classificaton methods for analysing data about ageing-related genes and proteins. In the academic year 2009-10 I did a research-oriented master's degree (MPhil) in Biological Sciences at the University of Liverpool, UK. My MPhil thesis was entitlted: "A Data Mining-Based Approach for Investigating the Relationship Between DNA Repair Genes and Ageing " (pdf)
R.C. Barros, A.C.P.L.F. de Carvalho, A.A. Freitas. Automatic Design of Decision-Tree Induction Algorithms. Springer, 2015. xii + 176 pages. Publisher's webpage about the book
G.L.Pappa and A.A. Freitas. Automating the Design of Data Mining Algorithms: an Evolutionary Computation Approach. Springer, 2010. xiii + 187 pages. Publisher's webpage about the book
A.A. Freitas. Data Mining and Knowledge Discovery with Evolutionary Algorightms. (264 pages) Springer, 2002. Book Cover Table of Contents and Publisher's Address
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
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
Current Research Grant - Data-Driven Discovery of Correlations between Genes and Ageing-Related Changes
This is a three-year research project funded by The Leverhulme Trust. This is a joint project with the University of Liverpool, Institute of Ageing and Chronic Diseases, where the Principal Investigator is Dr. Joao Pedro de Magalhaes. Each site (Liverpool and Kent) has one post-doctoral researcher working for 3 years. In essence, the post-doc at Kent is responsible for the data mining (or machine learning) part of the project, whilst the post-doc at Liverpool is responsible for data collection and preparation, and validation of the data mining results from a biological perspective. At Kent the project started in Feb. 2017, and will finish in Feb. 2020.
As part of this project, we maintain a bibliography of papers on applying supervised machine learning (classification or regression) algorithms to research on the biology of ageing.
(Webpage for this bibliography)
Past Research Grant - Predicting the volume of distribution of drugs and toxicants with data mining.
This was a two-year EPSRC-funded project carried out at the Medway School of Pharmacy, Universities of Kent and Greenwich. This project was funded by an EPSRC "discipline hopping" grant, which allowed me to spend half of my time doing research on applying data mining to the pharmaceutical sciences, in the areas of chemoinformatics and pharmacokinetics. The project started in January 2013 and finished in January 2015.
Past Research Grant - Refactoring and Neutrality in Genetic Programming
This was a 3-year EPSRC-funded project being carried out at the School of Computing, University of Kent. The principal investigator for this project was Dr. Colin Johnson, and the project involved one post-doc research associate. Broadly speaking, the goal of the project was to extend genetic programming methods with concepts and principles from refactoring techniques in software engineering and the theory of neutrality in natural evolution. The project started in February 2010 and finished in January 2013.
Past Research Grant - A Synergistic Integration of Natural and Artificial Immunology for the Prediction of Hierarchical Protein Functions
This was an EPSRC-funded 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.
Past Research Grant - 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 Grant - 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.
Past Research Grant - 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.
Current PhD students:
Caio Ribeiro is doing his PhD on classification methods for analysing longitudinal datasets of human ageing. He started in Oct. 2017.
James Brookhouse is doing his PhD in the areas of ant colony optimization and data mining. I am his co-supervisor. His main supervisor is Dr. Fernando Otero (at the Medway campus). He started in Oct. 2014.
Natalia Aniceto is doing her PhD at the Medway School of Pharmacy, Universities of Kent and Greenwich. Her research involves applying data mining to pharmaceutical science data.
Natalia started in Oct. 2014.
Former PhD students:
Dr. Sam Cramer completed his PhD in 2017. I was his co-supervisor (his main supervisor was Dr. Michael Kampouridis). The title of his PhD Thesis was "New Genetic Programming Methods for Rainfall Prediction and Rainfall Derivatives Pricing."
Dr. Fabio Fabris completed his PhD in 2017. The title of his PhD Thesis was "New Probabilistic Graphic Models and Meta-Learning Approaches for Hierarchical Classification, with Applications in Bioinformatics and Ageing." After his PhD, he became a post-doctoral research associate in our School of Computing, under my supervision, in a research project funded by the Leverhulme Trust.
Dr. Suwimol Jungjit completed her PhD in 2016. The title of her PhD Thesis was "New Multi-Label Correlation-Based Feature Selection Methods for Multi-Label Classification and Application in Bioinformatics."
Dr. Cen Wan completed his PhD in 2016. The title of his PhD Thesis was "Novel Hierarchical Feature Selection Methods for Classification and Their Application to Datasets of Ageing-Related Genes".
Dr. Eduardo Correa Goncalves completed his PhD in 2015, at the Universidade Federal Fluminense, in Brazil. I was his co-supervisor (at a distance). The title of his PhD Thesis was "Novel Classifier Chain Methods for Multi-Label Classification Based on Genetic Algorithms".
Dr. Danielle Newby completed her PhD at the Medway School of Pharmacy, Universities of Kent and Greenwich, in 2014. Her principal supervisor was Dr. Taravat Ghafourian, a Lecturer at the School of Pharmacy. The title of her PhD Thesis was: "Data Mining Methods for the Prediction of Intestinal Absorption Using QSAR".
Dr. Khalid Salama completed his PhD in 2014. The title of his PhD Thesis was "Ant Colony Optimization Algorithms for Learning Bayesian Network Classifiers".
Dr. Rodrigo Barros completed his PhD in 2013, at the University of Sao Paulo, Brazil. I was his co-supervisor. The title of his PhD Thesis was "On the Automatic Design of Decision Tree Induction Algorithms".
Dr. Carlos Silla Jr. completed his PhD in 2012. The title of his PhD Thesis was "Novel Approaches for Hierarchical Classification with Case Studies in Protein Function Prediction".
Dr. Jean Metz completed his PhD in 2011, at the University of Sao Paulo, Brazil. I was his co-supervisor. The title of his PhD thesis (written in Portuguese) was: "Approaches for Semi-supervised Multi-Label and Hierarchical Learning".
Dr. Fernando Otero completed his PhD in 2010. The title of his PhD Thesis was "New Ant Colony Optimisation Algorithms for Hierarchical Classification of Protein Functions". After his PhD, Fernando worked as a post-doc research associate at Kent, and he is now a Lecturer at the School of Computing, University of Kent (Medway campus)."
Dr. Marcio Basgalupp completed his PhD in 2010, at the University of Sao Paulo, Brazil. I was his co-supervisor. The title of his PhD thesis (written in Portuguese) was: "LEGAL-Tree: A Lexicographic Multi-Objective Genetic Algorithm for Decision Tree Induction".
Dr. Roberto Teixeira Alves completed his PhD in 2010, at the UTFPR (Federal Technological University at Parana), Brazil. I was his co-supervisor. The title of his PhD thesis (written in Portuguese) was: "An Artificial Immune System for Hierarchical Multi-Label Classification of Protein Functions".
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. Siddartha 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 (written in Portuguese) was: "A Decision Tree/Genetic Algorithm Method for Coping with the Problem of Small Disjuncts in Data Classification".
Dr. Wesley Romao completed his Ph.D. in 2002. The title of his PhD thesis (written in Portuguese) was: "Discovery of Relevant Knowledge in Science and Technology Databases".