Title: ??????????III (14) ?????????
1??????????III(14) ?????????
- ??? ??
- ???? ?????
- ????????????????
2????
- ?1? ????????
- ?2? ????????
- ?3? ???????????????????
- ?4? ??????????
- ?5? ?????????
- ?6? ????
- ?7? ???????
- ?8? ?????????
- ?9? ??????????
- ?10? ????
- ?11? RNA??????
- ?12? ???????????????
- ?13? ????????????????k?
- ?14? ?????????
- ?15? ???
3Color Coding
Alon et al. J. ACM 1995
4k-Path??
- ?? ????? G(V,E)??? k
- ?? G ???? k ???(???????????)
- ??(????)
- NP?? ? kn(V)?????????????
- ????????? ??? v ????????????????????????????
- ? O(nk) ????????
- ????
- V ? k ??????? (??? k ???????)
- ????????????????????????
- (?????????? ? ???????(??)??????)
5???????????
- ??????? v ????? k ?????????
- ???? v ?????????????????
- ?????????????????
- P(u,C) C ????????1??? v ?? u ???????? 1?
- ??????? 0 (C ? 1,2,,k?????)
- ??? P(v,f(v))?1, ????? 0 (f(v) ? v ??)
- ??? (C1 ?? Ck-1 ????????) u,w?E
6??????
- P(u,C) C ????????1??? v ?? u ???????? 1?
- ??????? 0 (C ? 1,2,,k?????)
- ??? P(v,f(v))?1, ????? 0 (f(v) ? v ??)
- ??? (C1 ?? Ck-1 ????????)
?? ????????????? O(2k poly(n)) ?? C ?????????
2k ?????2kn ?? P(u,C) ????????? ?????? v ???????
n ???????
7?????
- ?? P ???? G ? k-????????? k ??????????????????P
??????????????? e-k??
?? P ????????????? kk ????????????????? k!
????????????? Stirling ?????
?? ????????? ek ?????????(???????)?????1????????
1/2 ??
?? ?????????????????
?????????????????????????
8???????????(????)
k-????????? F ? V1,2,,n ?? 1,2,,k ???? f
??(??)????V ???? k ????????????????1?1?????? f?F
???????F ? k-??????????????
?? ??? n,k ????2O(k)log2n ???????? k-??????????
2O(k)nlog2n ???????
? ???????????????????????? f ? ????????
? k-Path??? 2O(k)poly(n) ??????
9Color Coding ???
- Color Coding ????????????????(??????????)?????
- ? ????????????????
- ?????????? Alon et al. Bioinformatics , 2008
- ??????????? Huffner et al. Bioinformatics 2007
-
Algorithmica 2008 - ?????????? Dao et al. Bioinformatics 2011
- ?????????????? Shlomi et al. BMC
Bioinformaics 2006
10??????
Nakano Inf. Proc. Lett. 2002
11????????
- ??????????????????????
- ?????????????????????
- ???????????????????????
- 1870??????(?????????)
- ??????????family tree ???????????
- ???????????????????????????1??????????????????????
??????? - ?????????????????
- ???1?1??????????????
12?????????
- ?? ??? n
- ?? ???? n ??????????
- (????????????????????????)
? n4
????????????????(??)????????
13Family Tree
- ???(reverse search)???????
- ???????(????????????)???
- ? ???????????
- ????????????????
- ????????????????????????
- ?????????????????????
- ?????????????????????????????(????????)??????????
?
14Family Tree??(n5)
15????????
- ????? Family Tree ????????? n ????????????
- r(T) ? T ??
- T(v,) ? T ??? v ??????????????? ?
- e ???(??????????)
?? ??? n ????????1????????????? ??
?????????(??)????????????? EnumTree???1????????(T
????????????)? Family Tree ?????????????? ????Fami
ly Tree ????(?????)?????????????
16????????
- ?????????????????????
- ??Family Tree??????????(???????)??????????????????
- ???????????????????????
- (?????)???? Nakano, Uno Proc. WG 2005
- ???????????? Zhuang, Nagamochi Proc. ISAAC
2010 - ??????? Wang, Nagamochi KUAMP Tech. Rep.
2010-007 - ?????? Makino, Uno Proc. SWAT 2004, Tomita et
al. Theoret. Comp. Sci. 2006 - ?????? Arimura, Uno Proc. ISAAC 2005
- (????????)????
- Imada et al. J. Chem.
Inf. Model., 2011
17???
- Color Coding
- ????(k-path)?????????????????
- ?????
- ???????1????????????
- ?????? Family Tree ???
- ??
- k-path ???????????????????????????????? Fomin
J. Comput. Syst. Sci. 2012 - ??k??????????????