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Articles
- Gilles Bernot and Fariza Tahi. Behaviour preservation of a biological regulatory network when
embedded into a larger network. Fundamenta Informaticae, page (to appear), 2008.
- Nicolas Brunel. Parameter estimation of ODE's via nonparametric estimators. Electronic Journal
of Statistics, p. 1242–1267, 2008.
- Cédric Auliac, Vincent Frouin, Xavier Gidrol, and Florence d' Alché-Buc. Evolutionary
approaches for the reverse-engineering of gene regulatory networks: a study on a
biologicallyrealistic dataset. BMC Bioinformatics, 9:91, 2008.
- Stefan Engelen and Fariza Tahi. Predicting rna secondary structure by the comparative approach:
how to select the homologogous sequences. BMC Bioinformatics, 8(464):Elec. Proc., 2007.
- Pierre Geurts, Nizar Touleimat, Marie Dutreix, and Florence d' Alché-Buc. Inferring biological
networks with output kernel trees. BMC Bioinformatics, (8):S4:1–12, mai 2007.
- Minh Quach, Nicolas Brunel, and Florence d' Alché-Buc. Estimating parameters and hidden
variables in non-linear state-space models based on odes for biological networks inference.
Bioinformatics, 23(23):3209–3216, 2007.
- Pierre Geurts, Damien Ernst, and Louis Wehenkel. Extremely randomized trees. Machine Learning,
36(1):3–42, 2006.
- Amel Bouzeghoub and Abdelatif Elbyed. Ontology mapping for web-based educational systems
interoperability. IBIS, 1(1):73–84, 2006.
- Géraldine Mercier, Nathalie Berthault, Nizar Touleimat, François Képès, Geneviève Fourel, Eric
Gilson, and Marie Dutreix. A haploid-specific transcriptional response to irradiationin
saccharomyces cerevisiae. Nucl. Acids Res., 33(20):6635–6643, 2005.
- Fariza Tahi, Stefan Engelen, and Mireille Régnier. P-dcfold or how to predict all kinds of
pseudoknots in rna secondary structures. International Journal on Bioinformatics Engineering
(IJBE),14(5):703–716, 2005.
- Farida Zehraoui and Younès Bennani. New self-organising maps for multivariate sequences
processing. International Journal of Computational Intelligence and Applications, 5(4):439–456,
December 2005.
Book chapters
- Florence d' Alché-Buc. Biological networks, chapter Inference of biological regulatory networks
: machine learning approaches, pages 41–83. World Scientific, 2008.
- Farida Zehraoui. Apprentissage Connexionniste, chapter 8 : Théorie de résonance adaptative
(Adaptive Resonance Theory), pages 219–247. Hermes Lavoisier, 2006.
- Farida Zehraoui and Françoise Fessant. Apprentissage Connexionniste, chapter 7 : Cartes
auto-organisatrices temporelles, pages 185–217. Hermes Lavoisier, 2006.
- Farida Zehraoui, Rushed Kanawati, and Sylvie Salotti. Raisonnement à partir de cas 2, chapter 5
: CASEP2 : Système hybride pour le traitement de séquences de navigation sur le web., pages 151–1
76. Hermes Lavoisier, 2006.
- Florence d' Alché-Buc. Bioinformatics using Computational Intelligence Paradigms, volume 176 of
Studies in Fuzziness and SOft Computing, chapter Dynamic model of gene regulatory networks based on
inertia principle, pages 93–117. Springer, 2005.
International conferences
- Cédric Auliac, Florence d'Alché-Buc, and Vincent Frouin. Learning transcriptional regulatory
networks with evolutionary algorithms enhanced with niching. In Applications of Fuzzy Sets Theory,
expanded from 7th International Workshop on Fuzzy Logic and Applications (WILF 2007), volume 4578
of Lecture Notes in Computer Science, pages 612–619, Heidelberg, 7-10 juillet 2007 Springer Berlin.
- Amel Bouzeghoub and Abdelatif Elbyed. Ontology mapping for learning objects repositories
interoperability. In Intelligent Tutoring Systems, pages 794–797, 2006.
- Amel Bouzeghoub, Abdelatif Elbyed, and Fariza Tahi. OMIE: Ontology mapping within an
interactive and extensible environment. In International Workshop of Data Integration in Life
Sciences (DILS), pages 161–168, June 2008. To appear in LNCS Proceedings.
- Florence d' Alché-Buc and Vincent Schächter. Modeling of biological networks. In Proceedings of
XI International Symposium on Applied Stochastic Models and Data Analysis (AMSDA), pages 167–180.
Groupe des écoles de télécommunications de France, may 2005.
- Pierre Geurts, Nizar Touleimat, Marie Dutreix, and Florence d' Alché-Buc. Completion of
biological networks: the output kernel trees approach. In Proc. of the Workshop on Probabilistic
Modeling and Machine Learning in Structural and Systems Biology, page Elec. Proc., 2006.
- Pierre Geurts, Louis Wehenkel, and Florence d' Alché-Buc. Kernelizing the output of tree-based
methods. In Proc. of the 23rd International Conference on Machine Learning, pages 345–3 52. ACM,
2006.
- Pierre Geurts, Louis Wehenkel, and Florence d' Alché-Buc. Gradient boosting for kernelized
output spaces. In Proceedings of the 24th Annual International Conference on Machine Learning (ICML
2007), pages 289–296. Omnipress, 2007.
- Minh Quach, Pierre Geurts, and Florence d' Alché-Buc. Elucidating the structure of genetic
regulatory networks: a study of a second order dynamical model on artificial data. In Proceedings
of XIVth European Symposium on Artificial Neural Networks (ESANN 2006) Bruges, Belgium, pages 569–5
74, 2006.
- Liva Ralaivola and Florence d' Alché-Buc. Time series filtering, smoothing and learning using
the kernel kalman filter. In Proceedings of IEEE International Joint Conference on Neural Networks
2005 (IJCNN 2005), volume 3, pages 1449–1454. IEEE, 2005.
Conferences
- Cédric Auliac, Vincent Frouin, and Florence d' Alché-Buc. Approches évolutionnaires pour
l'apprentissage de réseaux de régulation transcriptionnelle. In Conférence francophone sur
l'Apprentissage automatique (CAp), volume 91, page (Elec. Proc.), 2007.
- Amel Bouzeghoub, Abdelatif Elbyed, and Fariza Tahi. Un système interactif et extensible pour le
mapping d'ontologies, July 2008.
- Stefan Engelen and Fariza Tahi. Ssca, an algorithm for selecting sequences to use in RNA
secondary structure prediction by the comparative approach, July 2008.
- Pierre Geurts, Raphaël Marée, and Louis Wehenkel. Segment and combine: a generic approach for
supervised learning of invariant classifiers from topologically structured data. In Proceedings of
the Machine Learning Conference of Belgium and The Netherlands (Benelearn), pages 15–23,
2006.
- Pierre Geurts, Louis Wehenkel, and Florence d' Alché-Buc. Ok3: Méthode d'arbres à sortie noyau
pour la prédiction de sorties structurées et l'apprentissage de noyau. In Proc. de la conférence
francophone d'apprentissage automatique (CAP'2006), page 16, 2006.
- Pierre Geurts, Louis Wehenkel, and Florence d' Alché-Buc. Okboost: boosting par gradient pour
les espaces de sortie structurés par un noyau. In Actes de la conférence CAp 2007 : Conférence
francophone sur l'Apprentissage automatique, pages 897–904. Cépaduès, 4-6 juillet 2007.
- Minh Quach, Nicolas Brunel, and Florence d' Alché-Buc. Estimation de paramètres et de variables
cachées dans un modèle non linéaire à espace d'états pour l'inférence de réseaux biologiques. In
Actes de la conférence CAp 2007 : Conférence francophone sur l'Apprentissage automatique, page 16.
Cépaduès, 4-6 juillet 2007.
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Machine Learning in Systems Biology,2009
This international workshop will take place at Ljubljana, Slovenia on September 5-6, 2009.
All details
here
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Accessible Version
Imprint