ComputeM: Compute score matrix M
In GraphAlignment: GraphAlignment
Description
Usage
Arguments
Details
Value
Author(s)
Examples
View source: R/GraphAlignment.R
Description
Compute the score matrix M.
Usage
1
2
Arguments
A
adjacency matrix for network A
B
adjacency matrix for network B
R
node similarity matrix
P
permutation vector to be used as the initial alignment (see InitialAlignment)
linkScore
link score matrix (see ComputeLinkParameters)
selfLinkScore
self link score matrix (see ComputeLinkParameters)
nodeScore1
node score vector (s1) (see ComputeNodeParameters)
nodeScore0
node score vector for unaligned nodes (s0) (see ComputeNodeParameters)
lookupLink
link bin lookup table (see GetBinNumber)
lookupNode
node bin lookup table (see GetBinNumber)
clamp
clamp values to range when performing bin lookups
Details
This function computes the score Matrix M from the network adjacency
matrices A and B, the node similarity matrix R, an alignment P (given as a
permutation vector) and the node and link scores with their associated
binning information. The alignment P is either generated by the previous
iterative step, or, initially, by using InitialAlignment. The matrix M
is then given to the linear assignment solver to compute the new alignment.
Value
The return value is the score matrix M.
Author(s)
Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
ex<-GenerateExample(dimA=22, dimB=22, filling=.5, covariance=.6,
symmetric=TRUE, numOrths=10, correlated=seq(1,18))
pinitial<-InitialAlignment(psize=34, r=ex$r, mode="reciprocal")
lookupLink<-seq(-2,2,.5)
linkParams<-ComputeLinkParameters(ex$a, ex$b, pinitial, lookupLink)
lookupNode<-c(-.5,.5,1.5)
nodeParams<-ComputeNodeParameters(dimA=22, dimB=22, ex$r,
pinitial, lookupNode)
ComputeM(A=ex$a, B=ex$b, R=ex$r, P=pinitial,
linkScore=linkParams$ls,
selfLinkScore=linkParams$ls,
nodeScore1=nodeParams$s1, nodeScore0=nodeParams$s0,
lookupLink=lookupLink, lookupNode=lookupNode)
Example output
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 10.387629 -1.0613582 -6.5060461 -4.3980171 -4.0901323 -9.85218370
[2,] -5.338024 12.1041263 -5.1399544 -3.7599297 -2.8436390 -6.37209812
[3,] -5.022060 -4.1010097 11.6468105 -2.5134363 -2.9834400 -4.26437381
[4,] -4.786377 -0.3824488 -0.1749002 8.1916867 -1.9761384 -2.66928557
[5,] -2.689488 -4.0852614 -1.2937152 -2.0371631 9.8110199 -2.68948828
[6,] -5.545308 -2.5102640 -1.9523100 -5.0566119 -3.1657615 8.12280569
[7,] -6.326822 -4.8917372 -2.7243453 -2.2055516 -0.4783306 -1.75926445
[8,] -7.216224 -7.8324097 -2.9300787 -2.2840232 -5.3380244 -3.09049904
[9,] -5.074059 -3.5054429 -4.0555799 -1.7938168 1.0621144 -3.09049904
[10,] -5.984080 -5.6476077 -4.1451921 -7.1016129 -6.8784694 -2.34229208
[11,] -1.602203 -5.1527916 -4.8416977 -10.4071898 -6.0551493 -6.05514928
[12,] -5.430883 -5.2580403 -4.7000863 -5.4435342 -5.9135378 -0.01157354
[13,] -0.756720 -5.7768341 -3.8971242 -2.9665957 -3.4365993 -5.22835881
[14,] -2.499689 -1.9400735 -3.6189209 -0.2284475 -1.4969588 -5.01469401
[15,] -2.911536 -3.6629520 -1.5062841 -1.4813223 -3.5607639 -3.74308544
[16,] -9.261374 -6.6380650 -4.0494596 -0.1357381 -7.9709614 -9.41552467
[17,] -9.671863 -3.1678748 -3.7085331 -2.1556655 -3.3125467 -1.13401425
[18,] -4.972169 -7.7542361 -8.3249924 -8.0938807 -10.9842525 -10.06796174
[19,] -6.182299 -4.5240711 -2.0689971 -0.4515910 -3.7932743 -1.26754564
[20,] -7.311009 -2.7165633 0.5494409 -1.2926193 -3.5356902 -0.84633218
[21,] -4.572861 0.3279592 0.3750875 -3.1409491 -2.0015148 -3.38153957
[22,] -5.537942 -3.0042453 -3.6094422 -3.2542778 -6.0205969 -3.84206445
[23,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[24,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[25,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[26,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[27,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[28,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[29,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[30,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[31,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[32,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[33,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[34,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -7.23374565 -9.206165 -5.8331016 -7.1048221 -3.4442628 -7.71337736
[2,] -4.25500696 -11.738163 -4.5708599 -8.6841620 -4.5035637 -7.09549266
[3,] -2.14728265 -3.436033 -5.8551196 -4.3697343 -0.9512761 -4.98776835
[4,] 1.05724350 -3.400082 -1.8426070 -3.3781811 -5.2818687 -1.78324220
[5,] -4.54268903 -4.231215 -1.4085544 -8.8727531 -5.4749142 -7.38317473
[6,] 2.15151333 -3.134418 -4.4280032 -2.9520967 -6.3566526 2.90402531
[7,] 7.27063690 -3.965968 1.4613099 -5.1699406 -5.4704599 -1.97183337
[8,] -4.14519209 9.650563 -1.8785581 -2.7540268 -5.1653676 -1.00048286
[9,] -1.98240800 -3.533614 6.2018573 -7.7634169 -8.2367790 -5.66392195
[10,] -2.75889773 -5.396293 -5.7153186 11.1232970 -7.1914112 -4.50077114
[11,] -6.35842624 -7.108181 -10.1997946 -10.6635286 1.1104573 -5.10456739
[12,] 1.76459103 -2.227756 -4.8149255 -4.4376313 -6.9353752 3.99300953
[13,] -1.33820032 -6.092687 -2.3379871 -2.4715184 -9.5273409 -3.08007373
[14,] -0.02592322 -4.870022 -0.1752030 -7.3267578 -4.5919681 -2.86640892
[15,] -1.11516866 -3.334448 -4.8230056 -3.7588338 -6.1920391 -2.85704207
[16,] -2.13043840 -3.527493 -4.0006695 -5.6433027 -10.2550404 -7.26723958
[17,] -0.11553538 -3.474249 -0.4408671 0.2666298 -9.9141139 -2.95602108
[18,] -8.67218864 -5.160760 -9.5979581 -1.1717758 -7.9117452 -8.89423630
[19,] 1.52400057 -1.023783 -2.6946620 -2.3819063 -8.2745779 -0.21787285
[20,] 0.68297232 -4.225665 -3.9569037 -4.3215468 -2.1966736 0.03971119
[21,] -2.36306069 -7.207160 -4.2978303 -5.8176561 -2.9588136 -5.20354640
[22,] 0.04809405 -7.578072 -2.0503050 0.6878432 -9.2396588 -1.69377937
[23,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[24,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[25,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[26,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[27,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[28,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[29,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[30,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[31,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[32,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[33,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[34,] 0.00000000 0.000000 0.0000000 0.0000000 0.0000000 0.00000000
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -2.14312627 -0.1187445 -8.6078036 -5.0066091 -6.87555824 -7.161579
[2,] -6.80781059 -0.1940070 -7.6534466 -6.7400997 -4.05097022 -12.459896
[3,] -4.98776835 -1.9024239 -0.6496609 -6.2512920 -7.02162886 -7.936258
[4,] -1.11826589 0.2034899 -2.6883924 -0.8400626 -0.01965361 -7.909785
[5,] -5.61958614 1.0682347 -4.3949940 -4.6669278 -4.77228828 -8.102831
[6,] -1.79706340 -2.0847455 -0.6591397 -8.7944676 -1.62422059 -9.553664
[7,] -4.17853669 -2.8567808 -5.2378376 -4.9989456 -2.74345216 -10.044287
[8,] -5.91523638 -6.6178623 -4.8950957 -4.6355845 -1.02068557 -3.918874
[9,] -1.95442321 -0.2177235 -5.4704599 -4.5665916 -2.46524884 -8.330999
[10,] -2.73718255 -7.5829432 0.3561301 -7.5465756 -1.81292365 -2.216727
[11,] -8.40988300 -3.1178352 -6.7611337 -10.1747536 -12.20733210 -8.359431
[12,] -2.18398571 -4.8325218 -4.5055283 -9.1813899 -2.01114289 -8.464680
[13,] 6.79694150 -2.3555833 -3.6380277 -6.7044514 -1.14364232 -5.399955
[14,] -2.71225824 0.9703516 -7.3946548 -3.3785165 -2.53941543 -9.503778
[15,] 1.26740052 -0.2825233 0.2080997 -4.1205658 -2.01922295 -5.013293
[16,] -7.11308890 -5.7913331 -8.9238059 3.9678991 -4.06856646 -7.226266
[17,] -5.16272440 -6.2018226 -2.2517334 -4.2195448 2.95070224 -7.983952
[18,] -7.13064771 -9.7791838 -6.5805107 -3.8266141 -5.69556318 2.883259
[19,] -0.06372217 -2.7122582 -1.8744391 -4.1894467 0.10912064 -6.344416
[20,] -3.26560442 -2.4546742 -1.4532257 -6.2927167 -3.09276160 -8.447686
[21,] -7.41024972 -0.3451346 -3.4006464 -3.4317610 -3.26711499 -11.330090
[22,] 0.06980922 -4.9395809 -3.3503456 -4.2195448 1.34126433 -10.181177
[23,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[24,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[25,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[26,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[27,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[28,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[29,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[30,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[31,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[32,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[33,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[34,] 0.00000000 0.0000000 0.0000000 0.0000000 0.00000000 0.000000
[,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
[1,] -14.264494 -1.503377 -5.138859 -9.2914720 0 0 0 0 0
[2,] -8.711237 -3.246346 -7.692758 -8.6735873 0 0 0 0 0
[3,] -3.731833 -0.850940 -5.718565 -6.5658630 0 0 0 0 0
[4,] -3.746183 -1.586608 -3.612651 -3.3613369 0 0 0 0 0
[5,] -2.408262 -3.967664 -1.272000 -8.9612694 0 0 0 0 0
[6,] -2.815542 -3.518168 -2.777893 2.1368609 0 0 0 0 0
[7,] -3.801242 -7.007733 -3.213456 -2.1541549 0 0 0 0 0
[8,] -6.240568 -3.793311 -3.004245 -2.1085739 0 0 0 0 0
[9,] -5.266008 -4.522826 1.371512 -5.9797749 0 0 0 0 0
[10,] -7.023327 -5.432847 -9.712685 -4.1329557 0 0 0 0 0
[11,] -10.526974 -4.397107 -6.933976 -4.3218080 0 0 0 0 0
[12,] -6.661931 -3.403744 -3.579759 3.5135272 0 0 0 0 0
[13,] -9.764722 -3.634855 -3.127202 -4.6581684 0 0 0 0 0
[14,] -9.551057 -5.030628 -4.108031 -4.4445036 0 0 0 0 0
[15,] -3.210545 0.211272 -5.197277 -4.4351367 0 0 0 0 0
[16,] -4.912692 -7.234235 -8.508862 -5.9736546 0 0 0 0 0
[17,] -3.309524 -7.991920 -3.003149 -4.5341157 0 0 0 0 0
[18,] -9.247739 -5.989552 -11.745297 -9.2100892 0 0 0 0 0
[19,] -2.932229 -3.480705 -5.429787 -0.6973552 0 0 0 0 0
[20,] -2.511016 -3.059491 -5.172203 -2.6369958 0 0 0 0 0
[21,] -5.557049 -5.170541 -5.934343 -6.7816411 0 0 0 0 0
[22,] -8.378428 -7.317465 -7.657110 -3.2718740 0 0 0 0 0
[23,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[24,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[25,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[26,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[27,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[28,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[29,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[30,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[31,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[32,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[33,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[34,] 0.000000 0.000000 0.000000 0.0000000 0 0 0 0 0
[,28] [,29] [,30] [,31] [,32] [,33] [,34]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
[10,] 0 0 0 0 0 0 0
[11,] 0 0 0 0 0 0 0
[12,] 0 0 0 0 0 0 0
[13,] 0 0 0 0 0 0 0
[14,] 0 0 0 0 0 0 0
[15,] 0 0 0 0 0 0 0
[16,] 0 0 0 0 0 0 0
[17,] 0 0 0 0 0 0 0
[18,] 0 0 0 0 0 0 0
[19,] 0 0 0 0 0 0 0
[20,] 0 0 0 0 0 0 0
[21,] 0 0 0 0 0 0 0
[22,] 0 0 0 0 0 0 0
[23,] 0 0 0 0 0 0 0
[24,] 0 0 0 0 0 0 0
[25,] 0 0 0 0 0 0 0
[26,] 0 0 0 0 0 0 0
[27,] 0 0 0 0 0 0 0
[28,] 0 0 0 0 0 0 0
[29,] 0 0 0 0 0 0 0
[30,] 0 0 0 0 0 0 0
[31,] 0 0 0 0 0 0 0
[32,] 0 0 0 0 0 0 0
[33,] 0 0 0 0 0 0 0
[34,] 0 0 0 0 0 0 0
GraphAlignment documentation built on Nov. 8, 2020, 6:56 p.m.
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Description Usage Arguments Details Value Author(s) Examples
View source: R/GraphAlignment.R
Description
Compute the score matrix M.
Usage
1 2 |
Arguments
A |
adjacency matrix for network A |
B |
adjacency matrix for network B |
R |
node similarity matrix |
P |
permutation vector to be used as the initial alignment (see InitialAlignment) |
linkScore |
link score matrix (see ComputeLinkParameters) |
selfLinkScore |
self link score matrix (see ComputeLinkParameters) |
nodeScore1 |
node score vector (s1) (see ComputeNodeParameters) |
nodeScore0 |
node score vector for unaligned nodes (s0) (see ComputeNodeParameters) |
lookupLink |
link bin lookup table (see GetBinNumber) |
lookupNode |
node bin lookup table (see GetBinNumber) |
clamp |
clamp values to range when performing bin lookups |
Details
This function computes the score Matrix M from the network adjacency matrices A and B, the node similarity matrix R, an alignment P (given as a permutation vector) and the node and link scores with their associated binning information. The alignment P is either generated by the previous iterative step, or, initially, by using InitialAlignment. The matrix M is then given to the linear assignment solver to compute the new alignment.
Value
The return value is the score matrix M.
Author(s)
Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ex<-GenerateExample(dimA=22, dimB=22, filling=.5, covariance=.6,
symmetric=TRUE, numOrths=10, correlated=seq(1,18))
pinitial<-InitialAlignment(psize=34, r=ex$r, mode="reciprocal")
lookupLink<-seq(-2,2,.5)
linkParams<-ComputeLinkParameters(ex$a, ex$b, pinitial, lookupLink)
lookupNode<-c(-.5,.5,1.5)
nodeParams<-ComputeNodeParameters(dimA=22, dimB=22, ex$r,
pinitial, lookupNode)
ComputeM(A=ex$a, B=ex$b, R=ex$r, P=pinitial,
linkScore=linkParams$ls,
selfLinkScore=linkParams$ls,
nodeScore1=nodeParams$s1, nodeScore0=nodeParams$s0,
lookupLink=lookupLink, lookupNode=lookupNode)
|
Example output
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 10.387629 -1.0613582 -6.5060461 -4.3980171 -4.0901323 -9.85218370
[2,] -5.338024 12.1041263 -5.1399544 -3.7599297 -2.8436390 -6.37209812
[3,] -5.022060 -4.1010097 11.6468105 -2.5134363 -2.9834400 -4.26437381
[4,] -4.786377 -0.3824488 -0.1749002 8.1916867 -1.9761384 -2.66928557
[5,] -2.689488 -4.0852614 -1.2937152 -2.0371631 9.8110199 -2.68948828
[6,] -5.545308 -2.5102640 -1.9523100 -5.0566119 -3.1657615 8.12280569
[7,] -6.326822 -4.8917372 -2.7243453 -2.2055516 -0.4783306 -1.75926445
[8,] -7.216224 -7.8324097 -2.9300787 -2.2840232 -5.3380244 -3.09049904
[9,] -5.074059 -3.5054429 -4.0555799 -1.7938168 1.0621144 -3.09049904
[10,] -5.984080 -5.6476077 -4.1451921 -7.1016129 -6.8784694 -2.34229208
[11,] -1.602203 -5.1527916 -4.8416977 -10.4071898 -6.0551493 -6.05514928
[12,] -5.430883 -5.2580403 -4.7000863 -5.4435342 -5.9135378 -0.01157354
[13,] -0.756720 -5.7768341 -3.8971242 -2.9665957 -3.4365993 -5.22835881
[14,] -2.499689 -1.9400735 -3.6189209 -0.2284475 -1.4969588 -5.01469401
[15,] -2.911536 -3.6629520 -1.5062841 -1.4813223 -3.5607639 -3.74308544
[16,] -9.261374 -6.6380650 -4.0494596 -0.1357381 -7.9709614 -9.41552467
[17,] -9.671863 -3.1678748 -3.7085331 -2.1556655 -3.3125467 -1.13401425
[18,] -4.972169 -7.7542361 -8.3249924 -8.0938807 -10.9842525 -10.06796174
[19,] -6.182299 -4.5240711 -2.0689971 -0.4515910 -3.7932743 -1.26754564
[20,] -7.311009 -2.7165633 0.5494409 -1.2926193 -3.5356902 -0.84633218
[21,] -4.572861 0.3279592 0.3750875 -3.1409491 -2.0015148 -3.38153957
[22,] -5.537942 -3.0042453 -3.6094422 -3.2542778 -6.0205969 -3.84206445
[23,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[24,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[25,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[26,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[27,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[28,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[29,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[30,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[31,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[32,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[33,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[34,] 0.000000 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -7.23374565 -9.206165 -5.8331016 -7.1048221 -3.4442628 -7.71337736
[2,] -4.25500696 -11.738163 -4.5708599 -8.6841620 -4.5035637 -7.09549266
[3,] -2.14728265 -3.436033 -5.8551196 -4.3697343 -0.9512761 -4.98776835
[4,] 1.05724350 -3.400082 -1.8426070 -3.3781811 -5.2818687 -1.78324220
[5,] -4.54268903 -4.231215 -1.4085544 -8.8727531 -5.4749142 -7.38317473
[6,] 2.15151333 -3.134418 -4.4280032 -2.9520967 -6.3566526 2.90402531
[7,] 7.27063690 -3.965968 1.4613099 -5.1699406 -5.4704599 -1.97183337
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