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Submitted on 16 Nov 2010
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Modelling Biological Sequences by Grammatical Inference
François Coste
To cite this version:
François Coste. Modelling Biological Sequences by Grammatical Inference. ICGI 2010 Tutorial Day,
José M. Sempere and Pedro Garcias, Sep 2010, Valencia, Spain. �inria-00531552�
▼♦❞❡❧❧✐♥❣ ❇✐♦❧♦❣✐❝❛❧ ❙❡q✉❡♥❝❡s ❜② ●r❛♠♠❛t✐❝❛❧
■♥❢❡r❡♥❝❡
❋r❛♥ç♦✐s ❈♦st❡
❙②♠❜✐♦s❡ Pr♦❥❡❝t
■❘■❙❆✴■◆❘■❆ ❘❡♥♥❡s✲❇r❡t❛❣♥❡ ❆t❧❛♥t✐q✉❡✱ ❋r❛♥❝❡
❋♦r❡✇♦r❞
❚❤✐s ❞♦❝✉♠❡♥t ✐s ❛ ❝♦♠♣❧❡♠❡♥t ♦❢ t❤❡ t✉t♦r✐❛❧ ♦♥ ✏▼♦❞❡❧❧✐♥❣ ❇✐♦❧♦❣✐❝❛❧ ❙❡✲
q✉❡♥❝❡s ❜② ●r❛♠♠❛t✐❝❛❧ ■♥❢❡r❡♥❝❡✑ ♦r❣❛♥✐③❡❞ ❢♦r t❤❡ t❡♥t❤ ❛♥♥✐✈❡rs❛r② ❡❞✐t✐♦♥
♦❢ t❤❡ ■♥t❡r♥❛t✐♦♥❛❧ ❈♦❧❧♦q✉✐✉♠ ♦♥ ●r❛♠♠❛t✐❝❛❧ ■♥❢❡r❡♥❝❡ ✭■❈●■ ✷✵✶✵✮ ❤❡❧❞ ✐♥
❱❛❧❡♥❝✐❛✱ ❙♣❛✐♥✳
❚❤❡ t✉t♦r✐❛❧ s✉r✈❡②s t❤❡ ❛♣♣r♦❛❝❤❡s r❡❧❛t❡❞ t♦ ❣r❛♠♠❛t✐❝❛❧ ✐♥❢❡r❡♥❝❡ ✇❤✐❝❤
❤❛✈❡ ❜❡❡♥ ❞❡✈❡❧♦♣❡❞ ✐♥ ❇✐♦✐♥❢♦r♠❛t✐❝s t♦ ♠♦❞❡❧ ❢❛♠✐❧② ♦❢ s❡q✉❡♥❝❡s
✶✱ ❢r♦♠ ✇❡❧❧
❡st❛❜❧✐s❤❡❞ ✇❡✐❣❤t✐♥❣ s❝❤❡♠❡s ❢♦r ♣r♦✜❧❡ ❤✐❞❞❡♥ ▼❛r❦♦✈ ♠♦❞❡❧s ❛♥❞ ❙t♦❝❤❛st✐❝
❈♦♥t❡①t✲❋r❡❡ ❣r❛♠♠❛rs ✭s❡❝t✐♦♥ ✷✮ t♦ ❛♣♣r♦❛❝❤❡s ❧❡❛r♥✐♥❣ ✭❛❧s♦✮ t❤❡ str✉❝t✉r❡
♦r t♦♣♦❧♦❣② ♦❢ t❤❡ ❣r❛♠♠❛rs ✭s❡❝t✐♦♥ ✸✮✳ ❚❤❡ ✐♥t❡♥t ♦❢ t❤✐s ❞♦❝✉♠❡♥t ✐s t♦ ❣✐✈❡
❜✐❜❧✐♦❣r❛♣❤✐❝ r❡❢❡r❡♥❝❡s ♦❢ ♦r✐❣✐♥❛❧ st✉❞✐❡s ♣r❡s❡♥t❡❞ ❞✉r✐♥❣ t❤❡ t✉t♦r✐❛❧ ❛♥❞ t♦
♣r♦✈✐❞❡ ❤❡❧♣❢✉❧ ♣♦✐♥t❡rs t♦ st❛rt ❛ ❞❡❡♣❡r ✐♥✈❡st✐❣❛t✐♦♥ ✐♥t♦ t❤✐s ✜❡❧❞✳ ❚❤✐s ✐s ❛❧s♦
t❤❡ ♦♣♣♦rt✉♥✐t② t♦ ❣❛t❤❡r ❛ ❧✐st ♦❢ ♣✉❜❧✐s❤❡❞ ✇♦r❦ r❡❧❛t❡❞ t♦ t❤✐s t♦♣✐❝✳ ❚❤❡ ❧✐st
✐s ♦❜✈✐♦✉s❧② ♥♦t ❡①❤❛✉st✐✈❡ ❜✉t ❝❛♥ ❜❡ t❤❡ st❛rt✐♥❣ ♣♦✐♥t ♦❢ ❛ ♠♦r❡ ❡①❤❛✉st✐✈❡
♦♥❡✿ ❧❡t ♠❡ ❦♥♦✇ t❤❡ r❡❢❡r❡♥❝❡s t❤❛t ②♦✉ ❦♥♦✇ ♦♥ t❤❡ s✉❜❥❡❝t✱ ✇❤✐❝❤ ❛r❡ ♥❡✐t❤❡r
❝✐t❡❞ ✐♥ t❤✐s ❞♦❝✉♠❡♥t ♥♦r ✐♥ t❤❡ ❝✐t❡❞ ♣❛♣❡rs✱ ❛♥❞ ■ ✇✐❧❧ ❜❡ ♣❧❡❛s❡❞ t♦ ❝♦♠♣❧❡t❡
t❤✐s ❜✐❜❧✐♦❣r❛♣❤② ❛♥❞ t♦ ♠❛✐♥t❛✐♥ ❛♥ ✉♣❞❛t❡❞ ✈❡rs✐♦♥ ✇❤✐❝❤ ✇✐❧❧ ❜❡ ❛✈❛✐❧❛❜❧❡
❢r♦♠ ♠② ❤♦♠❡♣❛❣❡ ✭❤tt♣✿✴✴✇✇✇✳✐r✐s❛✳❢r✴s②♠❜✐♦s❡✴❢r❛♥❝♦✐s❴❝♦st❡✮✳
✶ ▲✐♥❣✉✐st✐❝ ♠♦❞❡❧❧✐♥❣ ♦❢ ❜✐♦❧♦❣✐❝❛❧ s❡q✉❡♥❝❡s
❘❡❝❡♥t s❡q✉❡♥❝✐♥❣ ♣r♦❥❡❝ts ❛♥❞ t❡❝❤♥♦❧♦❣✐❝❛❧ ♣r♦❣r❡ss ✐♥ t❤❡ ✜❡❧❞ ❛r❡ ❣✐✈✐♥❣ ❛❝✲
❝❡ss t♦ ❛♥ ❡✈❡r ✐♥❝r❡❛s✐♥❣ ❛♠♦✉♥t ♦❢ ❉◆❆✱ ❘◆❆ ❛♥❞ ♣r♦t❡✐♥ ♠❛❝r♦♠♦❧❡❝✉❧❛r s❡q✉❡♥❝❡s✳ ❚❤❡ ❝❤❛❧❧❡♥❣❡ ✐♥ t❤❡ ♣♦st✲❣❡♥♦♠✐❝ ❡r❛ ✐s ♥♦✇ t♦ ❞❡❝✐♣❤❡r ✇❤❛t ❤❛s
❜❡❡♥ ♣♦♣✉❧❛r❧② ♥❛♠❡❞ ✏t❤❡ ❧❛♥❣✉❛❣❡ ♦❢ ❧✐❢❡✑ ❬✷❪✳ ❚❤❡ ❧✐♥❣✉✐st✐❝ ♠❡t❛♣❤♦r ❤❛s ❜❡❡♥
✉s❡❞ ✐♥❞❡❡❞ ❢♦r ❛ ❧♦♥❣ t✐♠❡ ✐♥ ♠♦❧❡❝✉❧❛r ❜✐♦❧♦❣②✱ ❛♥❞ ❛♣♣❧②✐♥❣ ❝♦♠♣✉t❛t✐♦♥❛❧
❧✐♥❣✉✐st✐❝s t♦♦❧s t♦ r❡♣r❡s❡♥t✱ ✉♥❞❡rst❛♥❞ ❛♥❞ ❤❛♥❞❧❡ ❜✐♦❧♦❣✐❝❛❧ s❡q✉❡♥❝❡s ✐s ❛
♥❛t✉r❛❧ ❝♦♥t✐♥✉❛t✐♦♥ ♦❢ t❤✐s ♠❡t❛♣❤♦r✳ ❯s✐♥❣ ❢♦r♠❛❧ ❣r❛♠♠❛rs✱ s✉❝❤ ❛s t❤❡ ♦♥❡s
✶