About me...
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My main activity is to analyse molecular biology data, such as those produced by gene expression microarray, based on machine learning (a.k.a data mining) techniques. I take part in projects centered on Cancer (Melanoma, Lung), Immunology, Allergy, Rheumatology,... Part of the job of our research team is to counsel big pharma companies and other scientific institutions since the end of 2007. Our main fields of expertise are genomic data analysis leading to robust models for diagnosis, prognosis and gene profiling. We are also interested in helping our partners to design rigorous experimental protocols to generate their valuable data potentially leading to innovative industrial and/or scientifical results.
I'm an Engineer in Computing Sciences. I studied engineering at the Université catholique de Louvain (UCL) and graduated in 2006. I then joined the Computing Sciences and Engineering Dept. (INGI) of the Polytechnical School of Louvain (EPL, previously FSA) at the UCL as a researcher and a PhD Student.
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My main interests are in Machine Learning and Bioinformatics (also known as computational biology) and more generally in Artificial Intelligence. I like to consider both fundamentals and practical aspects of science. Industrial application of my research is also a strong concern for me. As time and projects go by, basics of biology tend to become a part of my education as well. At least, biological applications of my work receive my greatest interest.
I am member of the Machine Learning Group (MLG), the Computational Intelligence and Learning doctoral school (CIL) and the Health Cluster of Wallonia: Biowin.
Apart from my main scientific topics, I'm also interested in Operational Research (Constraints Programming, Local Search,...), Web Technologies, Web Mining, Social Networks and Web2.0.
Research
My current research topic is to develop analysis techniques of high dimensional data such as those produced by gene expression microarray.
In 2005-2006, I worked with Profs. Pierre Dupont, Yves Deville, Etienne Sokal and Jean-Luc Gala on low-density microarray data to study hepatocyte cryopreservation influence on gene expressions in the context of a Liver Cell Transplantation therapy.
I started my PhD under the supervision of Prof. Pierre Dupont and Etienne Sokal on August 2006. The aim of this research project is to design robust analysis techniques for genomic data allowing medical prognosis along with the identification of relevant genes for this prognosis task. The results of this research will be applied to data produced in the context of the CRISTALL project, in which a cohort of 300 children is involved. This project is aimed at identifying allergies risk-factors among newborns. Learn more about the cristall project on www.cristall.be. This project is a collaboration between UCL (EPL/INGI, MD/PEDI, MD/LTMA), the Walloon Region and GlaxoSmithKline Biologicals.
Keywords of my research activity are classification, feature selection, transfer learning, regularized linear models, prior knowledge incorporation. See the list of my publications below.
My research is funded by a FRIA second grant obtained in the end 2008. I previously was funded by a FRIA first grant obtained in 2006.
Publications
Machine Learning Publications:
2010
- Abeel T., Helleputte T., Van de Peer Y. and Saeys Y., Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics Advance Access published on February 1, 2010, DOI 10.1093/bioinformatics/btp630. Bioinformatics 26: pp. 392-398.
Download: Paper | Supplementary Material
2009
- Helleputte T. and Dupont P., Feature Selection by Transfer Learning with Linear Regularized Models, European Conference on Machine Learning (ECML), Bled, Slovenia, September 7-11, 2009.
Download: Paper | Poster | Slides | Talk Video:
- Abeel T., Helleputte T., Van de Peer Y., Dupont P., and Saeys Y., Robust biomarker identification for cancer diagnosis using ensemble feature selection methods, Third International Workshop on Machine Learning in Systems Biology (MLSB), pp. 135, Ljubljana, Slovenia, September 5-6, 2009.
Download: Abstract | Poster
- Helleputte T. and Dupont P., Biomarker Selection by Transfer Learning with Linear Regularized Models, Third International Workshop on Machine Learning in Systems Biology (MLSB), pp. 159-160, Ljubljana, Slovenia, September 5-6, 2009.
Download: Abstract | Poster
- Helleputte T. and Dupont P., Partially Supervised Feature Selection with Regularized Linear Models, 26th International Conference on Machine Learning (ICML), Montreal, Canada, June 14-18, 2009.
Download: Paper | Poster | Slides | Talk video:
2008
- Louahed J., Gaulis S., Helleputte T., Dupont P., Gruselle O., Spatz A., Kruit Wim H J, Dreno B, Lehmann F, Brichard V, Clinical response to the MAGE-3 immunotherapeutic in metastatic melanoma patients is associated with a specific gene profile present prior to treatment, In: 33th European Society for Medical Oncology (ESMO) Congress, Stockholm, Sweden, September 12-16, 2008, 470129.
Download: Abstract
- Helleputte T., Dupont P., Feature Selection and Classification of Microarray Data: Semi-Supervised Feature Selection Improves Stability. In: CIL Third Contact Day (ECML'08), Antwerp, Belgium, September 19, 2008.
Download: Poster
2007
- Helleputte T., Dupont P., A Comparative Study of Normalization and Feature Selection Techniques for Breast Cancer Prognosis from Gene Expression. In: Benelux Bioinformatics Conference (BBC), KUL, Leuven, Belgium, November 12-13, 2007.
Download: Poster
- Helleputte T., Microarray data classification for medical prognosis: Influence of sample vs feature normalization. In: CIL Second Contact Day, KUL, Leuven, Belgium, August 29, 2007.
Download: Poster
- Helleputte T., Microarray data classification for medical prognosis. In: Fifth International Summer School of Pattern Recognition, Plymouth, UK, July 2007.
Download: Poster
Publications not related to Machine Learning:
- Helleputte T., Maroye P., Le Jour et la Nuit - Idées reçues sur le folklore néo-louvaniste. ASBO Editor, 36 pages, September 2009.
Download: Book
Reviews
I'm reviewer for the IEEE journal Transactions on Systems, Man, and Cybernetics.
Teaching Activities
GBIO2010: Bioinformatique
Web site available on iCampus here.
Lectures are given on thursday (10:45-12:45)
Practical work on tuesday (10:45-12:45)
Using R language: You can choose to use the R language for your practical assignments implementations. R is a free and open source statistical software. It is a standard language for bioinformatics applications, with hundreds of dedicated packages available. Biology-related packages can be downloaded at Bioconductor.org. Its syntax is realy close to the matlab one. R is available at least on the INGI machines. You can easily install it on your personnal laptop. Hint: for the first assignment you can use the Biostrings package to make your task easier.
Contact me
Department of Computing Science and Engineering
Place Sainte Barbe, 2 - A.158
B-1348 Louvain-la-Neuve, Belgium
Phone: (++32) 10 47 91 06
Fax: (++32) 10 45 03 45
E-mail: thibault [dot] helleputte [at] uclouvain [dot] be
If you want to send me an encrypted mail, please use my PGP Public Key. (Show / Hide)
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Links
Websites
UCL's Machine Learning Group
R language official site
Bioconductor.org (Bioinfo R packages)
Personomics (blog about personal genomics)
Less Academic Links
Cercle Industriel
OLIVIA asbl
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