François COSTE   Research scientist (CR1), Symbiose team INRIA Rennes-Bretagne Atlantique Address   : Symbiose, IRISA,             Campus de Beaulieu,             35042 Rennes Cedex,             France Phone     : (33|0) 2 99-84-74-91 Secretary : (33|0) 2 99-84-73-34 Fax       : (33|0) 2 99-84-71-71     This e-mail address is being protected from spam bots, you need JavaScript enabled to view it

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News

• This page is no longer updated. The Symbiose team has given birth to 2 teams. My new page is now on the Dyliss team's website at  http://www.irisa.fr/dyliss/francois.coste

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    jump to: Research , Software , GI Benchmarks , PhD Students , Projects , Teaching , Publications 

 

Research

Main research topic:

Learning grammars and application to linguistic modelling of biological sequences

Keywords: Grammatical Inference, Machine Learning, Protein Structures and Functions, DNA...

 

I gave a tutorial on this subject at the tutorial day organized for the 10th anniversary of ICGI (ICGI'10). Here are the slides (6.3M)  and the related bibliography.

Software

• Protomata Learner infers automata to model families of protein sequences. You can use it through a web interface on the Genouest Bioinformatics platform server. Here are some slides (4.4M) of its presentation at Gen2bio 2008.
  
  We are working on a new version which will be soon available: stay tuned!

Grammatical Inference Benchmarks and Competitions

I am making up a grammatical inference benchmarks repository (GIB): don't hesitate to This e-mail address is being protected from spam bots, you need JavaScript enabled to view it 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... If you are interested in grammatical inference competitions, you should have a look at the 2010 competitions: Zulu and Stamina

 

PhD Students

• Gaelle Garet, Discovery of enzymatic functions in the framework of formal languages (with Jacques Nicolas).

Former PhD Students:

• Matthias Gallé, Searching for Compact Hierarchical Structures in DNA by means of the Smallest Grammar Proble january 2011
  
• Goulven Kerbellec, Apprentissage d'automates modélisant des familles de séquences protéiques, june 2008
• Marie Lahaye, Apprentissage de signatures topologiques de protéines. Marie is gone too soon, but we are not forgetting her...
• Aurélien Leroux, Inférence grammaticale sur des alphabets ordonnés, june 2005 (main supervisor: Jacques Nicolas).
• Daniel Fredouille, Inférence d'automates finis non déterministes par gestion de l'ambiguïté, en vue d'applications en bioinformatique, oct 2003

Projects

I am currently involved in the following projects:

• ANR LepidOLF: Microgénomique de la sensille phéromonale d’un lépidoptère : une approche novatrice pour comprendre les mécanismes olfactifs et leur modulation
• ANR Pelican : Competing for light in the ocean: An integrative genomic approach of the ecology, diversity and evolution of cyanobacterial pigment types in the marine environment
• Collaboration MINCyT (ex SECyT) - INRIA with the  "Grupo de Procesamiento de Lenguaje Natural " of Gabriel Infante-Lopez: Modélisation linguistique de séquences génomiques par apprentissage de grammaires

Previous 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

• Apprentissage à partir de données séquencielles symboliques (DSS)
• Formation continue: recherche et découverte de motifs

 

 

 

Selected publications

(A more exhaustive list is available here )

• 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!

• Regular Inference as a graph coloring problem, François Coste, Jacques Nicolas, ICML97, Grammatical Inference Workshop, Nashville TN, USA, 1997.
  postcript, paper (.ps.gz)

Ph.D. Thesis

Apprentissage d'automates classifieurs en inférence grammaticale, IRISA/Université de Rennes 1, 27 janvier 2000.
Advisor: Jacques Nicolas.
abstract (English and French) , thesis (.ps.gz, .pdf, errata), slides ( .ps.gz, .pdf).

 

This page is updated on an irregular basis... browse HAL for new publications

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