Research manuscripts

• Publications

  PhD thesis

  Tijl De Bie
  Semi-supervised learning based on kernel methods and graph cut algorithms
  PhD-thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2005.
  (pdf)(bib)

   

  Journal papers

  Tijl De Bie, Leon-Charles Tranchevent, Liesbeth van Oeffelen, Yves Moreau
  Kernel-based data fusion for gene prioritization
  Accepted for publication in Bioinformatics (ISMB online proceedings), 2007.
  (Bioinformatics)
   

  Margherita Bresco, Marco Turchi, Tijl De Bie, Nello Cristianini
  Modeling Sequence Evolution with Kernel Methods
  Accepted for publication in Computational Optimization and Applications, DOI: 10.1007/s10589-007-9045-9, 2007.
  (Springerlink)

   

  Jeffery Demuth, Tijl De Bie, Jason Stajich, Nello Cristianini, Matthew Hahn
  The Evolution of Mammalian Gene Families
  PLoS ONE 1(1): e85. doi:10.1371/journal.pone.0000085, 2006.
  (plosone.org)

   

  Tijl De Bie, Nello Cristianini
  Fast SDP relaxations of graph cut clustering, transduction, and other combinatorial problems
  Journal of Machine Learning Research, 7(Jul):1409-1436, 2006.
  (pdf)(bib)

   

  Karen Lemmens, Thomas D'Hollander, Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Joris Winderickx, Bart De Moor, Kathleen Marchal
  Inferring transcriptional module networks from ChIP-chip-, motif- and microarray data
  Genome Biology, 7:R37, 2006.
  (pdf)(bib)(Genome Biology website)

   

  Tijl De Bie, Nello Cristianini, Jeffery Demuth, Matthew Hahn
  CAFE: a computational tool for the study of gene family evolution
  Bioinformatics, 22: 1269-1271, 2006.
  (pdf)(bib)(CAFE, the tool!)(Bioinformatics website)

   

  John Shawe-Taylor, Tijl De Bie, Nello Cristianini
  Data mining, data fusion, and information management
  IEE Proceedings - Intelligent Transport Systems 153:3, pp. 221-229, September 2006.
  (ieeexplore)
  (This is a journal version of a Foresight Project report on Intelligent Infrastructure Systems.)

   

  Matthew Hahn*, Tijl De Bie*, Jason Stajich, Chi Nguyen, Nello Cristianini
  Estimating the tempo and mode of gene family evolution from comparative genomic data
  Genome Research 15:1153-1160, 2005.
  (bib)(GR-website)
  (*Equal contributors.)

   

  Gert Lanckriet, Tijl De Bie, Nello Cristianini, Michael Jordan, William Stafford Noble
  A Statistical Framework for Genomic Data Fusion
  Bioinformatics, 20(16):2626-2635, 2004.
  (pdf)(bib)

  
  Book chapters

  Nathalie Pochet*, Fabian Ojeda*, Frank De Smet, Tijl De Bie, Johan Suykens, Bart De Moor
  Kernel clustering for knowledge discovery in clinical microarray data analysis
  Accepted for publication in Camps-Valls G., Rojo-Alvarez J.L., and and Martinez-Ramon M. (eds.), Kernel methods in bioengineering, communications and image processing, Idea Group Inc. (Hershey, Pennsylvania (US)), 2006.
  (*Equal contributors.)

   

  Tijl De Bie, Nello Cristianini
  Semi-supervised learning using semi-definite programming
  In ``Semi-supervised learning", Chapelle O., Schoelkopf B., Zien A. (eds.), MIT Press, Cambridge Massachusetts, 2006.
  (pdf)(bib)

   

  Tijl De Bie, Nello Cristianini, Roman Rosipal
  Eigenproblems in Pattern Recognition
  In ``Handbook of Geometric Computing : Applications in Pattern Recognition, Computer Vision, Neuralcomputing, and Robotics", E. Bayro-Corrochano (editor), Springer-Verlag, Heidelberg, August, 2005.
  (pdf)(bib)
  (This book chapter contains a tutorial on eigenvalue problems in pattern recognition from a primal-dual perspective. Algorithms discussed include PCA, CCA, PLS, FDA, and spectral clustering.)

   

  Refereed conference papers published in proceedings

  Elisa Ricci, Tijl De Bie, Nello Cristianini
  Discriminative Sequence Labeling by Z-score Optimization
  Proceedings of the 18th European Conference on Machine Learning (ECML07), Warsaw, September 2007.
  (pdf)

   

  Arianna Gallo, Tijl De Bie, Nello Cristianini
  MINI: Mining Informative Non-redundant Itemsets
  Proceedings of the 11th conference on Principles and Practice of Knowledge Discovery in Databases (PKDD07), Warsaw, September 2007.
  (pdf)

   

  Elisa Ricci , Tijl De Bie, Nello Cristianini
  Learning to align: a statistical approach
  Proceedings of the7th International Symposium on Intelligent Data Analysis (IDA 2007), Ljubljana, September, 2007.
  (pdf)(bib)

   

  Tijl De Bie
  Deploying SDP for machine learning
  Proceedings of the 15th European Symposium on Artificial Neural Networks (ESANN 2007), Bruges, April 2007.
  (pdf)(bib)
  (This is a paper overviewing the applications of Semi-Definite Programming in Machine Learning.)

   

  Sandor Szedmak, Tijl De Bie, David Hardoon
  A metamorphosis of Canonical Correlation Analysis into Multivariate Maximum Margin Learning
  Proceedings of the 15th European Symposium on Artificial Neural Networks (ESANN 2007), Bruges, April 2007.
  (pdf)(bib)

   

  Alexander Dolia, Tijl De Bie, Chris Harris, John Shawe-Taylor, D.M. Titterington
  The Minimum volume covering ellipsoid estimation in kernel-defined feature spaces
  Proceedings of the 17th European Conference on Machine Learning (ECML 2006), Berlin, September 2006.
  (pdf)(bib)

   

  Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini, Kathleen Marchal
  Discovering Transcriptional Modules from Motif, ChIP-chip and Microarray Data
  Proceedings of the Pacific Symposium on biocomputing (PSB 2005), Hawaii, January 2005.
  (pdf)(bib)

   

  Tijl De Bie, Nello Cristianini
  Kernel methods for exploratory data analysis: a demonstration on text data
  In Proc. of the joint IAPR international workshops on Syntactical and Structural Pattern Recognition (SSPR 2004) and Statistical Pattern Recognition (SPR 2004), Lisbon, August 2004.
  (pdf)(bib)

   

  Tijl De Bie, Johan Suykens, Bart De Moor
  Learning from General Label Constraints
  In Proc. of the joint IAPR international workshops on Syntactical and Structural Pattern Recognition (SSPR 2004) and Statistical Pattern Recognition (SPR 2004), Lisbon, August 2004.
  (pdf)(bib)

   

  Tijl De Bie, Nello Cristianini
  Convex Methods for Transduction
  Neural Information Processing Systems (NIPS2003), Vancouver, Canada, December 2003.
  (pdf)(bib)

   

  Tijl De Bie, Michinari Momma, Nello Cristianini
  Efficiently Learning the Metric using Side-Information
  In Proc. of the 14th International Conference on Algorithmic Learning Theory (ALT2003), Sapporo, Japan, Lecture Notes in Artificial Intelligence, Vol. 2842, pp. 175-189, Springer, 2003.
  (pdf)(bib)

   

  Tijl De Bie, Bart De Moor
  On the Regularization of Canonical Correlation Analysis
  In Proceedings of the International Conference on Independent Component Analysis and Blind Source Separation (ICA2003), Nara, Japan, April 2003.
  (pdf)(bib)

   

  Other publications

  Nello Cristianini, Tijl De Bie
  Artificial Intelligence, Data Mining in Medicine, Expert Systems, Machine Learning, Support Vector Machines, and Neural Networks
  In B. S. Everitt and C. Palmer (Eds.) ``Encyclopaedic Dictionary of Medical Statistics", Hodder Arnold, May 2005.

   

  Tijl De Bie, Bart De Moor
  On two classes of alternatives to Canonical Correlation Analysis, using mutual information and oblique projections
  In Proc. of the 23rd symposium on information theory in the Benelux (ITB2002), Louvian-la-Neuve, Belgium, May 2002.

   

• Submitted for publication

... (to be updated)

 

• Technical reports

  • Tijl De Bie, John Shawe-Taylor, ``Bounding the k-family-wise error rate using resampling methods'', Presented at the PASCAL Workshop on "Type I and type II errors for multiple simultaneous hypothesis testing (MSHT)", Paris, May, 2007. (pdf)

  • Alexander Dolia, Tijl De Bie, Chris Harris, John Shawe-Taylor, Mike Titterington, ``Optimal experimental design for kernel ridge regression, and the minimum volume covering ellipsoid", 2005. (see this presentation)

  • Tijl De Bie, Nello Cristianini, ``Convex Transduction with the Normalized Cut", Internal Report 04-128, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2004. (pdf)

  • Tijl De Bie, Gert Lanckriet, Nello Cristianini, ``Convex Tuning of the Soft Margin Parameter'', Technical Report CSD-03-1289, Division of Computer Science, University of California, Berkeley, 2003. (ps)(bib)

  • Koenraad Audenaert, Frank Verstraete, Tijl De Bie, Bart De Moor, ``Negativity and Concurrence of mixed 2x2 states'', quant-ph/0012074, Internal Report 00-133, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2000. Poster Presented at QIP2001, Jan. 9-12, 2001. (ps)

  • Frank Verstraete, Koenraad Audenaert, Tijl De Bie, Bart De Moor, ``Maximally Entangled Mixed States of Two Qubits'', quant-ph/0011110, as published in Phys. Rev. A (\bf 64), 012316 (2001). (arxiv)
    

• Posters, talks, seminars & lectures

  • CIL course at the Universite Catholic de Louvain on Data fusion using kernel methods (pdf)

  • A one-week course at the University of Tartu on Pattern analysis and statistical learning theory (www)

  • Tutorial talk on Optimization approaches in kernel methods, Santa Clara, Cuba. (pdf)

  • Presentation in Eurandom on Nonlinear optimum experiment design, December 2005. (pdf)

  • Presentations at the School on the analysis of patterns, Erice, Sicily on The myriad virtues of eigenproblems and Patterns in sets of points, October-November 2005. (see www.analysis-of-patterns.net)

  • A tutorial talk on Kernel methods for machine vision, presented at the IPS symposium, VUB, Brussels, November 2004. (pdf)

  • ISIS (University of Southampton), March 2004: Convex methods for SVM-transduction. (pdf)

  • SAIL (CS department, Berkeley) group meeting: on kernels on discrete structures (convolutional kernels).

  • SALSA (EE department, Berkeley) group meeting: ICA, and what it 's not used for...

  • IUAP meeting and ICCOS meeting, Leuven, March, 2002: On two alternatives for CCA.

  • SCD seminar: spectral methods in pattern recognition.

  • Several MLRG meetings on: kernel learning & metric learning with SDP; spectral methods for clustering; kernel design based on graphical models; Generalized SVD and other SVD/eigenvalue approaches in bioi problems.

Last updated: 2 August 2007