Inria / Raweb 2004
Project-Team: MODBIO

Search in Activity Report, year 2004:



Major publications by the team in recent years

E. Althaus, A. Caprara, H.-P. Lenhof, K. Reinert.
Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics., in: "Proc. European Conference on Computational Biology", Bioinformatics, October 2002, vol. 18, no Supplement 2, p. S4–S16.
E. Althaus, K. Mehlhorn.
Traveling Salesman-Based Curve Reconstruction in Polynomial Time, in: "SIAM Journal on Computing", 2001, vol. 31, no 1, p. 27–66.
E. Balas, A. Bockmayr, N. Pisaruk, L. Wolsey.
On unions and dominants of polytopes, in: "Mathematical Programming, Ser. A", 2004, vol. 299, p. 223-239.
A. Bockmayr, A. Courtois.
Using hybrid concurrent constraint programming to model dynamic biological systems, in: "18th International Conference on Logic Programming, ICLP'02, Copenhagen", Springer, LNCS 2401, 2002, p. 85-99.
A. Bockmayr, V. Weispfenning.
Solving numerical constraints, in: "Handbook of Automated Reasoning", A. Robinson, A. Voronkov (editors)., Elsevier, 2001, vol. 1, chap. 12, p. 751-842.
Y. Guermeur, A. Elisseeff, D. Zelus.
Bound on the risk for M-SVMs, in: "Statistical Learning, Theory and Applications", 2002, p. 48–52.
Y. Guermeur, C. Geourjon, P. Gallinari, G. Deléage.
Improved performance in protein secondary structure prediction by inhomogeneous score combination, in: "Bioinformatics", 1999, vol. 15, no 5, p. 413–421.
Y. Guermeur.
Combining discriminant models with new multi-class SVMs, in: "Pattern Analysis and Applications", 2002, vol. 5, no 2, p. 168–179.
Y. Guermeur, H. Paugam-Moisy.
Théorie de l'apprentissage de Vapnik et SVM, Support Vector Machines, in: "Apprentissage Automatique", M. Sebban, G. Venturini (editors)., Hermès, 1999, p. 109–138.
V. Y. Lunin, A. Urzhumtsev, A. Bockmayr.
Direct phasing by binary integer programming, in: "Acta Crystallographica Section A", 2002, vol. 58, p. 283-291.

Doctoral dissertations and Habilitation theses

D. Eveillard.
Modélisation statistique et formelle de la régulation de l'épissage alternatif, PhD Thesis, Université Henri Poincaré, Nancy 1, May 2004.

Articles in referred journals and book chapters

A. Bockmayr, J. N. Hooker.
Constraint Programming, in: "Handbook of Discrete Optimization", K. Aardal, G. Nemhauser, R. Weismantel (editors)., Handbooks in Operations Research and Management Science, To appear, Elsevier, 2004.
P. Dupont, F. Denis, Y. Esposito.
Links between Probabilistic Automata and Hidden Markov Models: probability distributions, learning models and induction algorithms, in: "Pattern Recognition Journal", to appear, 2004.
D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr.
A multi-scale constraint programming model of alternative splicing regulation, in: "Theoretical Computer Science", 2004, vol. 325, no 1, p. 3-24.
Y. Guermeur, A. Lifchitz, R. Vert.
A kernel for protein secondary structure prediction, in: "Kernel Methods in Computational Biology", B. Schölkopf, K. Tsuda, J.-P. Vert (editors)., MIT Press, 2004, p. 193–206.

Publications in Conferences and Workshops

E. Althaus, N. Karamanis, A. Koller.
Computing Locally Coherent Discourses, in: "Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics (ACL 2004), Barcelona, Spain", 2004.
A. Bockmayr, A. Courtois, D. Eveillard, M. Vezain.
Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing, in: "Computational Methods in Systems Biology, CMSB'04, Paris", To appear, Springer, LNCS, 2004.
F. Denis, Y. Esposito.
Learning classes of Probabilistic Automata, in: "COLT 2004", LNAI, 2004, no 3120, p. 124-139.
D. Eveillard, A. Larhlimi, D. Ropers, S. Billaut, S. Peyrefitte.
KOALAB: A new method for regulatory motif search, in: "5èmes Journées Ouvertes Biologie Informatique Mathématiques, JOBIM 2004, Montreal", 10 pages, 2004.

Internal Reports

S. Bonne.
Modélisation du métabolisme des monocarbones et du cycle de la méthionine, Master thesis, Univ. Bordeaux, Sep 2004.
Y. Guermeur.
Large margin multi-category discriminant models and scale-sensitive $ \Psi$-dimensions, Research Report RR-5314, INRIA, September 2004,
A. Larhlimi.
Analyse de voies métaboliques en programmation par contraintes, Stage de DEA, Université Henri Poincaré, Nancy 1, Jun 2004.
M. Vezain.
Modélisation de la régulation de l'épissage alternatif de HIV-1, Rapport de Stage, DESS EGOISt, Rouen, Université Rouen, June 2004.


E. Althaus, A. Caprara, H.-P. Lenhof, K. Reinert.
Aligning Multiple Sequences by Cutting Planes, Submitted, 2004.
Y. Guermeur, M. Maumy, F. Sur.
Model Selection for Multi-class SVMs, Submitted to ASMDA'05, 2004.

Bibliography in notes

E. Althaus, A. Bockmayr, M. Elf, T. Kasper, M. Jünger, K. Mehlhorn.
SCIL - Symbolic Constraints in Integer Linear Programming, in: "10th European Symposium on Algorithms, ESA'02, Rome", Springer, LNCS 2461, 2002, p. 75-87.
Y. Bartal.
Probabilistic approximation of metric spaces and its algorithmic applications, in: "Proceedings IEEE Symposium on Foundations of Computer Science", 1996, p. 184–193.
Y. Bartal.
On approximating arbitrary metrics by tree metrics, in: "Proceedings 30th Annual ACM Symposium on Theory of Computing", 1998, p. 161–168.
C. Burges.
A tutorial on support vector machines for pattern recognition, in: "Data Mining and Knowledge Discovery", June 1998, vol. 2, no 2, p. 121–167.
L. Cartegni, J. Wang, Z. Zhu, M. Q. Zhang, A. R. Krainer.
ESEfinder: a web resource to identify exonic splicing enhancers, in: "Nucleic Acid Research", 2003, vol. 31, no 13, p. 3568-3571.
W. J. Cook, W. H. Cunningham, W. R. Pulleyblank, A. Schrijver.
Combinatorial Optimization, Wiley, 1998.
C. Cortes, V. Vapnik.
Support-Vector Networks, in: "Machine Learning", 1995, vol. 20, p. 273–297.
F. Denis, Y. Esposito.
Residual languages and probabilistic automata, in: "Automata, Languages and Programming, 30th International Colloquium, ICALP 2003", Springer, LNCS 2719, 2003, p. 452-463.
Y. Esposito, A. Lemay, F. Denis, P. Dupont.
Learning probabilistic residual finite state automata, in: "Grammatical Inference: Algorithms and Applications, 6th International Colloquium, ICGI 2002", Springer, LNCS 2484, 2002.
J. Fakcharoenphol, S. Rao, K. Talwar.
A tight bound on approximating arbitrary metrics by tree metrics, in: "Proceedings ACM Symposium on Theory of Computing", 2003, p. 448–455.
K. Fukuda, A. Prodon.
Double Description Method Revisited., in: "Combinatorics and Computer Science", Springer, LNCS 1120, 1995, p. 91-111.
E. Gothié, Y. Guermeur, S. Muller, C. Branlant, A. Bockmayr.
Recherche des gènes de petits ARN non codants, Research Report RR-5057, INRIA, December 2003.
V. Gupta, R. Jagadeesan, V. Saraswat.
Computing with Continuous Change, in: "Science of computer programming", 1998, vol. 30, no 1-2, p. 3-49.
B. J. Hammond.
Quantitative Study of the Control of HIV-1 Gene Expression, in: "J. Theor. Biol", 1993, vol. 163, p. 199–221.
T. Kin, K. Tsuda, K. Asai.
Marginalized kernels for RNA sequence data analysis, in: "Genome Informatics 2002", Universal Academic Press, 2002, p. 112-122.
J. A. Papin, J. Stelling, N. D. Price, S. Klamt, S. Schuster, B. O. Palsson.
Comparison of Network-Based Pathway Analysis Methods, in: "Trends in Biotechnology", 2004, vol. 22, no 8, p. 400-405.
A. Patterson.
A Fourier Series Method for the Determination of the Components of Interatomic Distances in Crystals, in: "Phys. Rev.", 1934, vol. 46, p. 372–376.
M. C. Reed, H. F. Nijhout, R. Sparks, C. M. Ulrich.
A mathematical model of the methionine cycle, in: "Journal of Theoretical Biology", 2004, vol. 226, p. 33-43.
V. A. Saraswat.
Concurrent constraint programming, ACM Doctoral Dissertation Awards, MIT Press, 1993.
J. Thompson, F. Plewniak, O. Poch.
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs, in: "Bioinformatics", 1999, vol. 15, no 1, p. 87-88.
C. Tuerk, L. Gold.
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, in: "Science", 1990, vol. 249, p. 505-510.
V. Vapnik.
Estimation of Dependences Based on Empirical Data., Springer-Verlag, N.Y., 1982.
V. Vapnik.
Statistical learning theory, John Wiley & Sons, Inc., N.Y., 1998.
E. O. Voit.
Metabolic modeling: a tool of drug discovery in the post-genomic area, in: "Drug Discovery Today", 2002, vol. 7, no 11, p. 621-628.
P. van Hentenryck, V. Saraswat.
Strategic directions in constraint programming, in: "ACM Computing Surveys", 1996, vol. 28, no 4, p. 701 – 726.