Background

I did my "licenciatura" (5 year degree) in Computer Engineering (2004) and a Masters degree in Artificial Intelligence (2006) both at Universidade Nova de Lisboa, Portugal. I worked as junior consultant for a major Portuguese IT consultancy company (Novabase) and did an internship, as Software Development Engineer, at Microsoft in Redmond.

I came to Imperial in October 2006 after earning a Wellcome Trust PhD scholarship. As part of the 4-year PhD programme, in the first year I did an MSc. in Bioinformatics (2007). On November 2010 I defended my PhD thesis. The examiners were Professor Peter Flach and Professor Marek Sergot. My PhD supervisor was Professor Stephen Muggleton.

My main research topic was Machine Learning, more specifically the theory, implementation and applications of Inductive Logic Programming (ILP). The application explored was a protein-ligand interaction, namely the automated identification of hexose binding sites.

Detailed curriculum vitae.

• Subsumer - A generic theta-subsumption engine implemented in Prolog.
• GILPS - Generic Inductive Logic Programming System (superseds TopLog, which is now a particular case). Implements TopLog (Top Theory), FuncLog (HOV) and ProGolem (ARMG).
• TopLog - A prototype ILP system (outdated, use GILPS instead)
• MazeTrap – An action puzzle game for Android I did in 2011. Applet version also available.
• Cypher – A simple substitution cypher program for high school students, I developed as part of the researchers in residence programme
• Addique – A game I did in 2009 to emulate an old numerical board family game. Try it!
• JSudoku – A game I did in 2006 to create and solve Sudoku puzzles.
• Many others – Link to my old webpage with some programs I did (e.g. a chess game, a expression solver,...)

• Jose Santos, Houssam Nassif, David Page, Stephen Muggleton and Mike Sternberg: Automated identification of features of protein-ligand interactions using Inductive Logic Programming: a hexose binding case study, submitted to BMC Bioinformatics (data and pdf)
• Ph.D. Thesis, Imperial College, 2010 Efficient Learning and Evaluation of Complex Concepts in Inductive Logic Programming
• Jose Santos and Stephen Muggleton: When does it payoff to use sophisticated entailment engines in ILP?, ILP2010 (data and pdf)
• Jose Santos and Stephen Muggleton: Subsumer: A Prolog theta-subsumption engine, ICLP2010 (data and pdf)
• Jose Santos, Alireza Tamaddoni-Nezhad and Stephen Muggleton: An ILP system for learning Head Output Connected predicates, EPIA 2009 (pdf)
• Stephen Muggleton, Jose Santos and Alireza Tamaddoni-Nezhad: ProGolem: a system based on relative minimal generalization, ILP 2009 (pdf) (data)
• Stephen Muggleton, Jose Santos and Alireza Tamaddoni-Nezhad: TopLog: ILP using a logic program declarative bias, ICLP 2008 (pdf)
• Jianzhong Chen, Stephen Muggleton and Jose Santos: Learning Probabilistic Logic Models from Probabilistic Examples , Journal of Machine Learning, 2008 (pdf)
• Jose Santos, Pedro Barahona and Ludwig Krippahl: Mining Protein Structure Data, EPIA 2007 (pdf)
• MSc Thesis, Universidade Nova de Lisboa, 2006 Mining Protein Structure Data