Accès à l'intranet
Français
François Coste
Document Actions
CR INRIA
This page is deprecated, see http://www.irisa.fr/symbiose/francois_coste for the new version
| | François Coste | |  |
NEW !
- ICGI will take place in St Malo September 22 - 24, 2008
- Protomata Learner (inference of automata on protein sequences) is available on Genouest Bioinformatics platform server.
Here are the slides (4.4M) of the presentation at Gen2bio 2008.
Main research topic
Inductive learning of grammars
and characterization of biological sequences.
Some keywords related to my research: Grammatical
Inference, Machine Learning, Protein
Structures and Functions, DNA...
PhD Students
- Matthias Gallé, Modélisation de séquences génomiques par apprentissage de grammaires.
- Goulven Kerbellec, Apprentissage de motifs structuraux.
Former PhD Students :
- Marie Lahaye, Apprentissage de signatures topologiques de protéines. Marie is gone too soon, but we are not forgetting her...
- Daniel Fredouille, Inférence d'automates finis
non déterministes par gestion de l'ambiguïté, en vue d'applications en
bioinformatique. oct. 2003
summary - résumé - manuscrit.ps.gz - manuscrit.pdf
Projects
I am currently involved in the following projects:
- ANR Proteus "Reconnaissance de pli et repliement inverse : vers une prédiction à grande échelle des structures de protéines"
- ANR Modulome "Deciphering and modelling the structural organization of genomes"
Teaching
Grammatical Inference Benchmarks and Competitions
| |  |
| I am making up a grammatical inference benchmarks repository (GIB): don't hesitate to contribute
with your own data sets, especially real world ones !. I am maintaining the Gowachin server, a continuation of the Abbadingo One DFA learning competition, allowing to generate parametrized problems. I have also co-organized Omphalos, the competition on learning context-free languages, which is now over but the data sets are still available... |
Publications
In English:
- Learning Automata on Protein Sequences, François Coste and Goulven Kerbellec, JOBIM 2006.
abstract, paper, slides (.pdf) - A Similar Fragments Merging Approach to Learn Automata on Proteins
, François Coste and Goulven Kerbellec, ECML 2005.
abstract, paper, extended version, data sets
Some recent slides presenting this work and more at a grammatical inference workshop: slides, 4 per pages for printing - Progressing
the State-of-the art in Grammatical Inference by Competition, Brad Starkie, François Coste and Menno van Zaanen, AI
Communications, vol. 18, no. 2, 2005, pp. 93-115.
abstract, paper - The Omphalos
Context-free Grammar Learning Competition. Brad Starkie, François Coste
and Menno van Zaanen. Invited
Paper, ICGI 2004.
abstract, paper, slides (.ppt)
- Introducing Domain and Typing Bias in Automata Inference,
François Coste, Daniel Fredouille, Christopher Kermorvant and Colin de la Higuera. ICGI 2004.
abstract, paper, slides (.ppt, 2.2MB)
- Mutually compatible and incompatible merges
for the search of the smallest consistent DFA, John Abela, François Coste
and
Sandro Spina. ICGI 2004.
abstract, paper, slides (.ppt)
- Unambiguous automata inference
by
means of state-merging methods. François Coste, Daniel
Fredouille, ECML'03
paper (.ps.gz), complementary experiments (.ps.gz), benchmarks (.tar.gz), slides (.ppt).
Parsing ambiguity!
- What is the Search Space for the Inference of Non Deterministic, Unambiguous and Deterministic Automata ? François Coste, Daniel Fredouille, Techn. Report, RR-4907, 2003
- Efficient ambiguity detection in C-NFA, a step toward
inference of non
deterministic automata , François Coste, Daniel
Fredouille,
ICGI 2000, Grammatical inference: algorithms and applications, Lisbonne
, 25-38 , september , 2000
paper (ps.gz) benchmark (.tar.gz).
Classification ambiguity!
- State merging inference of finite state classifiers, François Coste,
technical report 3695, INRIA/IRISA, May 1999
abstract, paper (.ps.gz) - How considering incompatible state mergings may
reduce the DFA
induction
search tree, François Coste, Jacques Nicolas, Fourth International Colloquium on
Grammatical Inference (ICGI'98),
Ames Iowa, USA, 1998.
abstract, paper (.ps.gz) - Inference of finite automata: reducing the
search space with
an ordering
of pairs of states, F.Coste, Jacques Nicolas, 10th European Conference on
Machine Learning (ECML'98),
Chemnitz, Germany, 1998.
abstract, paper (.ps.gz) - Regular Inference as a graph coloring problem,
François Coste,
Jacques Nicolas, ICML97,
Grammatical Inference Workshop, Nashville TN, USA, 1997.
postcript, paper (.ps.gz)
In
French:
Problème d'optimisation de recherche de cliques pour caractériser des familles de protéines, François Coste and Goulven Kerbellec, ROADEF 2007
paper (.pdf)- Apprentissage d'automates par
fusions de paires de fragments significativement similaires et
premières expérimentations sur les protéines MIP,
François Coste, Goulven Kerbellec, Boris Idmont, Daniel Fredouille and Christian Delamarche, JOBIM'04
paper (.pdf), techn. report (.pdf)
- Introduction de connaissances
structurelles et langagières pour l'apprentissage d'automates.
François Coste, Daniel
Fredouille, CAp'03
paper (.ps.gz, .pdf).
- Inférence d'AFNs: restriction de l'espace de recherche
aux automates
non ambigus, François Coste, Daniel
Fredouille, CAp'01.
paper (.ps.gz, .pdf) Parsing ambiguity!
- De l'inférence régulière
à
l'apprentissage
d'automates classifieurs pour la discrimination de séquences ,
François Coste, CAp 2000, june , 2000
paper (.ps.gz)
- L'inférence grammaticale
régulière vue
comme un
problème de coloriage et propagation de contraintes sur un graphe,
François Coste, Jacques Nicolas, IIIèmes Journées Nationales sur la
Résolution Pratique de Problèmes NP-Complets, Rennes,
France,
1997.
paper (.ps, .ps.gz) - Inférence de grammaires
régulières:
caractérisation
de l'ensemble des solutions canoniques, François Coste, Jacques Nicolas, JFA97,
Roscoff, France, 1997.
(.ps, .ps.gz)
- Coévolution et émergence de stratégies de coopération, François Coste, 1994, techn. report, Laboratoire d'Intelligence Artificielle et Systèmes Cognitifs, France Télécom, Brest, France.
See all publications references
Ph.D. Thesis:
François Coste