Sequence Clustering. Spring 2011
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1 equence Cuterng COM Reerch emnr prng 20 CLUEQ The prmry tructure of mny oogc mcromoecue re etter equence depte ther 3D tructure. roten h 20 mno cd. DNA h n phet of four e {A, T, G, C} RNA h n phet {A, U, G, C} Text document Trncton og gn trem tructur mrte t the equence eve often ugget hgh kehood of eng functony/emntcy / reted. td 2
2 roem ttement Cuterng ed on tructur chrctertc cn erve powerfu too to dcrmnte equence eongng to dfferent functon ctegore. The go to crete groupng of equence uch tht equence n ech group hve mr feture. The reut cn potenty reve unknown tructur nd functon ctegore tht my ed to etter undertndng of the nture. Chenge: how to meure the tructur mrty? t 3 Meure of mrty Edt dtnce: computtony neffcent ony cpture the optm go gnment ut gnore mny other oc gnment tht often repreent mportnt feture hred dy the pr of equence. q-grm ed pproch: gnore equent retonhp e.g., orderng, correton, dependency, d etc. mong q-grm Hdden Mrkov mode: cpture ome ow order correton nd tttc vunere to noe nd erroneou prmeter ettng computtony neffcent 4
3 Meure of mrty rotc uffx Tree Effectve n cpturng gnfcnt tructur feture Ey to compute nd ncrementy mntn pre Mrkov Trnducer Aow wd crd 5 Mode of CLUEQ CLUEQ: exporng gnfcnt pttern of equence formton. equence eongng to one group/cuter my uume to the me proty dtruton of ymo condtonng on the precedng egment of certn ength, whe dfferent group/cuter my foow dfferent underyng proty dtruton. By extrctng nd mntnng gnfcnt pttern chrcterzng potent equence cuter, one cn ey determne whether equence houd eong to cuter y ccutng the kehood of reproducng the equence under the proty dtruton tht chrcterze the cuter. 6
4 M d f L E Mode of CLUEQ = 2 equence: 2 2 Cuter : q r r r r Rndom If h h d f r 2 Rndom proce: If hgh, we my conder memer of If >> r, we my conder memer of 7 M d f L E Mode of CLUEQ mrty etween nd r p p m Noe my e preent. Dfferent porton of ong equence my uume p g q y to dfferent condton proty dtruton. mx m IM 8... mx j j m IM
5 Mode of CLUEQ Gve equence = 2 nd cuter, dynmc progrmmng method cn e ued to ccute the mrty IM. V nge cn of. Let X Y Z... p mx m j... Intutvey, X, Y, nd Z cn e vewed the mrty contruted y the ymo on the th poton of.e.,, the mxmum mrty poeed y ny egment endng t the th poton, nd the mxmum mrty poeed y ny egment endng pror to or on the th poton, repectvey. mx m j 9 Mode of CLUEQ 0 Then, IM = Z, whch cn e otned y Y mx Y, X X Y Z mx Z, nd Y Z X For exmpe, IM = 2.0 f p= = 0.6 nd p = 0.4. equence X Y Z
6 rotc uffx Tree compct repreentton to orgnze the derved CD for cuter ut on the revered equence Ech node correpond to egment,, nd octed wth counter C nd proty vector. rotc uffx Tree , , , , , ,0.6 0, 0.889,0.0.97, , , , , , , , C=96 = = , root 2
7 Mode of CLUEQ Retrev of CD entry - The onget uffx j - cn e octed y trverng from the root ong the pth - 2 unt we rech ether the node eed wth or node where no further dvnce cn e mde. tke Omn{, h} where h the heght of the tree. Exmpe: 3 = , , , , , ,0.6 0, 0.889,0.0.97, , , , , , , , , root 4
8 CLUEQ equence Cuter: et of equence equence cuter f, for ech equence n, the mrty t IM etween nd greter thn or equ to ome mrty threhod t. Ojectve: utomtcy group et of equence nto et of poy overppng cuter. 5 Agorthm of CLUEQ Uncutered equence An tertve proce 6 Ech cuter repreented y protc uffx tree. The optm numer of cuter nd the numer of outer owed cn e dpted y CLUEQ utomtcy new cuter generton, cuter pt, nd cuter conodton djutment of mrty threhod mrty threhod djutment Generte new cuter equence re-cuterng Cuter pt Cuter conodton Any mprovement? No equence cuter
9 New Cuter Generton New cuter re generted from un-cutered equence t the egnnng of ech terton. k f new cuter numer of conodted d cuter f mx{ k' n k' k' n c,0} Uncutered equence Generte new cuter 7 numer of cuter numer of new cuter generted t the prevou terton mrty threhod djutment equence re-cuterng Cuter pt Cuter conodton Any mprovement? No equence cuter equence Re-Cuterng 8 For ech equence, cuter pr Ccute mrty T updte f necery Ony mr porton ued The updte weghted y the mrty vue ,0.594 Uncutered equence 0.47, , Generte new cuter 0.636, , ,0.55 0, 300 equence re-cuterng root 0.889, , , mrty Cuter pt threhod djutment Cuter conodton , , Any 0.25, , mprovement? ,0.789 No equence 0.25, ,0.833 cuter
10 Cuter pt Check the convergence of ech extng cuter Imprece prote re ued for ech proty entry n T pt non-convergent cuter Uncutered equence Generte new cuter equence re-cuterng mrty threhod djutment Cuter pt Cuter conodton 9 Any mprovement? No equence cuter Imprece rote Imprece prote ue two vue p, p 2 nted of one for proty. p ced ower proty nd p 2 ced upper proty. The true proty e omewhere etween p nd p 2. p 2 p ced mprecon. 20
11 Updte Imprece rote Aumng the pror knowedge of condton proty p, p 2 nd the occurrence n the new experment out of tr. p p ' p ' 2 p 2 where the ernng prmeter whch contro the weght tht ech experment crre. 2 roperte The foowng two properte re very mportnt. If the proty dtruton ty ttc, then p nd p 2 w converge to the true proty. If the experment gree wth the pror umpton, the rnge of fmprecon decree fter ppyng the new evdence, e.g., p 2 p < p 2 p. The cuterng gproce termnte when the mprecon of gnfcnt node e thn m threhod. 22
12 Cuter Conodton trtng from the met cuter Dm cuter tht hve few equence not covered y other cuter Uncutered equence Generte new cuter equence re-cuterng mrty threhod djutment Cuter pt Cuter conodton 23 Any mprovement? No equence cuter 24 count Adjutment of mrty Threhod Fnd the hrpet turn of the mrty dtruton functon t new t n 2 od tˆ 2 tˆ mx r r mrty threhod djutment Uncutered equence Generte new cuter equence re-cuterng Cuter pt Cuter conodton Any mprovement? No mrty equence cuter
13 Agorthm of CLUEQ Impementton ue Lmted memory pce rune the node wth met count tfrt. rune the node wth onget e frt. rune the node wth expected proty vector frt. roty moothng Emnte zero emprc proty Other conderton Bckground prote A pror knowedge Other tructur feture 25 Experment tudy We hve expermented wth proten dte of 8000 proten from 30 fme from WI-ROT dte. Mode CLUEQ Edt Edt Hdden Q-grm Dtnce Dtnce wth Bock Operton Mrkov Mode Accurcy 92% 23% 90% 9% 75% Repone Tme ec 26
14 Experment tudy ynthetc dt Int t Fn t Repone tme precon 8.3% 83.% 83.4% 8.9% rec 82.% 82.8% 83.6% 82.7% 27 Experment tudy ynthetc dt Int cuter numer Fn cuter numer Repone tme precon 8.3% 82.% 82.6% 8% rec 8.6% 82% 83.4% 8.7% 28
15 Experment tudy CLUEQ h ner cty wth repect to the numer of cuter, numer of equence, nd equence ength. pone tme ec re numer of cuter re pone tme ec numer of equence pone tme ec re verge equence ength ynthetc Dt 29 Remrk mrty meure owerfu n cpturng hgh order tttc nd dependence Effcent n computton ner compexty Rout to noe Cuterng gorthm Hgh ccurcy Hgh dptty Hgh cty Hgh rety 30
16 Reference CLUEQ: effcent nd effectve equence cuterng, roceedng of the 9 th IEEE Internton Conference on Dt Engneerng ICDE, A frme work towrd effcent nd effectve proten cuterng, roceedng of the t IEEE CB,
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