Dr. Jaume Bacardit

My research interests include the development of machine learning methods for large-scale problems and their application to challenging problems, mostly involving biological data.

I have published papers on algorithmic advances to improve the scalability of machine learning methods, tackling challenges such as large dimensionality spaces, large sets of records, postprocessing operators or the use of data-intensive computing technologies such as GPUs and MapReduce.

The main focus of my applied research on biological data is knowledge discovery: i've created methods to analyse the structure of the data mining models to discover useful knowledge, such as (panels of) biomarkers or functional networks and in this way bring the data mining process closer to the domain experts. My methods have been applied to a variety of biological/biomedical domains: the proces of germination in plants, cancer in humans or osteoarthitis both in humans and model organisms and multiple data-generating biotechnologies: transcriptomics, proteomics, lipidomics, etc.

I lead the data analytics efforts in several large biological/biomedical projects:

  • D-BOARD (€6M, EU-FP7) that focused on biomarkers discovery
  • APPROACH (€15M, EU-Innovative Medicine Initiative), focusing on patient stratification
  • Synthetic Portabolomics (£4.3M EPSRC Programme Grant -EP/N031962/1) focusing on synthetic biology

My PhD thesis dealt with the Pittburgh model of Learning Classifier Systems (LCS). Specifically, the thesis had the following objectives:

  • Improving the generalization capacity of the model
  • Reducing the run-time of the system
  • Proposing rule-based representations for real-valued attributes
You can download my thesis here

From 2005 to 2007 I worked as RA applying LCSs to protein structure prediction, in an EPSRC project called Robust Prediction with Explanatory Power for Protein Structure and Related Prediction Problems

Research team and visitors:

  • Artur Sakalouski (PhD student, CRITICAL project, 2018-)
  • Paweł Widera (Postdoc, APPROACH project, 2015-)
  • Federico Angelini (Postdoc, APPROACH project. 2020-)
  • Conor Turner (PhD student, EPSRC CASE studentship. 2019-)
  • Philip Darke (PhD student, Cloud Computing for Big Data CDT. 2019-)
  • Christian Taylor (PhD student. AHDB studentship. 2019-)
  • Yiming Huang (PhD student, Portabolomics project, 2018-)
  • Jordan Connolly (PhD student, Portabolomics project, 2019-)
Previous members and visitors:
  • Ossama Alshabrawy (PhD student, 2016-2020)
  • Jake Cowton (PhD student, 2017-2021)
  • Stephen Matthews (Postdoc, CATALYST project, 2017-2019)
  • Farida Mustafazade (KTP research associate, Orchard Systems LTD., 2017-2019)
  • Wayne Smith (KTP research associate, Rain Data LTD., 2017-2019)
  • Nicola Lazzarini (PhD student, 2013-2017, D-BOARD project). Now Data Scientist at Shryne.
  • Samuel Danso (Postdoc, 2017, APPROACH project).
  • Bart Craenen (Postdoc, 2016, CRITICAL project).
  • Maria Franco (PhD student, 2009-2013). Now working at Palantir technologies.
  • Anna Swan (PhD student, 2010-2014). Now a science writer for doctors.net.uk.
  • Xiaolei (Celina) Xia (Postdoc, Computer Science, June 2010-August 2011; LCSxLCD project)
  • Jesús Alcalá-Fernández (Visiting lecturer, University of Granada, Spain, May 2010)
  • Julián Luengo-Martín (Visiting PhD student, University of Granada, Spain, May-July 2010)
  • Nuria Macià-Antolinez (PhD student visiting from the Ramon Llull University, Spain, July-October 2010)
  • Álvaro García-Piquer (PhD student visiting from the Ramon Llull University, Spain, September 2010-March 2011)
  • Dan Andrei Calian (Undergraduate student. EPSRC Vacation Bursary and final year dissertation)
  • Maria Martinez Ballesteros (PhD student visiting from the University of Seville, Spain, June 2011-September 2011)
  • Alfonso Marquez (PhD student visiting from the Pablo de Olavide University, Spain, September 2011-December 2011)
  • Gualberto Asencio (PhD student visiting from the Pablo de Olavide University, Spain, November 2011-February 2012)
  • Andreu Sancho Asensio (PhD student visiting from the Ramon Llull University, Spain, April 2012-July 2012)
  • Isaac Triguero (Visiting PhD student, University of Granada, Spain, July-September 2013)
  • Pablo Gutierrez Perez (visiting PhD student, University of Granada, Spain, April-June 2014)
  • Ismael Rodriguez Fernandez (visiting PhD student, University of Santiago de Compostela, Spain, May-July 2014)
  • Juan Carlos Gamez Granados (visiting PhD student, University of Cordoba, June-September 2016)