KPCATest.java

/*******************************************************************************
 * Copyright (c) 2010 Haifeng Li
 *   
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *  
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *******************************************************************************/
package smile.projection;

import smile.data.AttributeDataset;
import smile.data.parser.ArffParser;

import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;

import smile.math.Math;
import smile.math.kernel.GaussianKernel;
import static org.junit.Assert.*;

/**
 *
 * @author Haifeng Li
 */
@SuppressWarnings({"rawtypes", "unchecked"})
public class KPCATest {

    double[] latent = {
        0.3248377330, 0.1190608662, 0.0354473602, 0.0248222741, 0.0206817940, 0.0126434107,
        0.0086918118, 0.0049665015, 0.0038173621, 0.0036946774, 0.0033387912, 0.0027999074,
        0.0020193760, 0.0013370193, 0.0012813389, 0.0009629088, 0.0009310069, 0.0006368355,
        0.0004813594, 0.0003700926, 0.0003220757, 0.0003185161, 0.0002594431, 0.0002087690,
        0.0001859915, 0.0001488966, 0.0001421597, 0.0001217172, 0.0001156592
    };
    double[][] scores = {
        {-10.0979791656324, -0.692997265933912, 1.12969329653961, 0.649047148659402, -0.29310715534842, -0.239283255731145, -0.047274246806631, -0.077057777763598, -0.000513445947576114, 0.292868536246900, -0.0779406198264998, -0.249395416211564, -0.748843863949876, 0.374921852403731, -0.111931518607156, 0.100916844855065, 0.0708176432546577, 0.120859517180095, 0.0510705717408816, -0.160315822709653, -0.0352792239571769, -0.0724108995063577, 0.00394399131546079, -0.00466107081548298, 0.0253713395874898, 0.0346452072389977, 0.000464714413056402, -0.0347210080082545, 0.00920459078277162},
        {-9.80577882574642, -0.444228718369616, -0.00816467174850868, -2.44526015680566, 1.48913292098369, 0.0505679416815199, 0.142774139540507, 0.134688782898112, -0.109027023568503, 1.35671785459491, 0.772599876031108, -0.0441293165932329, -0.334941426958855, -0.0285096885181663, 0.091044030670192, 0.0212112796161966, -0.0134955898064987, -0.030273398065606, 0.097441964969689, -0.271926809146569, -0.0639479472913199, -0.062563156918859, 0.0106545596911825, -0.00324484166624383, -0.183307730073134, -0.120219105866759, 0.112373912405390, 0.140786799016373, 0.186217079383599},
        {-9.95221332926393, -0.859295558422995, 0.458670646883854, -2.51951509759249, 1.51710067999055, -0.236739071215125, -0.664027441812176, -0.461466282086972, 0.0582844953062473, -0.170823052045553, -0.241155764051138, 0.246085824160139, -0.459589499903796, 0.0406861401264391, -0.302706762412840, -0.00127849558167842, 0.00759439695994068, 0.057965005964771, -0.0196084022084887, 0.0228106013044832, -0.0202533469351350, 0.00647338869443356, 0.00939129276784039, 0.0228618934885304, -0.0491307434103525, -0.0294493941022816, 0.0604197168211751, 0.0632053658760128, 0.123681436555483},
        {-9.70782086681865, -0.461037945620176, -0.186299234905717, -3.193232602946, 1.80087531086424, 0.103270416387538, -0.287298170639277, 0.138955574776676, -0.0433762337840109, -0.420440926987484, -0.309729562826799, -0.100208755268945, 0.431617893559552, -0.07086667291833, 0.382588226335266, 0.0124356675260138, 0.129143740030059, 0.00252537622776539, 0.0562858489021309, 0.237323448764194, 0.211457548726782, 0.18093993242954, -0.0742220294994654, 0.123805732497819, -0.239471136069057, -0.0455022190312964, -0.0385398084099797, -0.0633850526275117, -0.0458697959629962},
        {-10.0996775695659, -0.80485423875739, 1.23830408590069, 0.646123316843043, -0.339479619475624, -0.315143898053108, -0.317182827071470, -0.230584997613147, 0.075447969617991, -0.557549200451468, -0.607768407348382, -0.207182777484128, -0.590723815926886, 0.426800465254533, -0.131796155670958, 0.155693018806911, 0.0905265473003332, 0.103713604898382, 0.0368969388648281, -0.266883560273971, -0.0570587015346534, -0.0915391206939914, -0.0301975410325121, -0.0189361998759995, 0.0144996337658687, 0.0323559983318382, -0.0337309652231159, -0.0545986669855906, -0.0384280143207517},
        {-9.1221441524404, -0.128655293939811, 1.18446002948979, 3.94638809584403, -2.13776953045720, 0.216409368119366, 0.429626490176872, 0.532704087666936, -0.161491534123783, -0.448440836254916, -0.182051344708842, -0.184874877783385, 1.04003965779476, -0.56421306210317, 0.106418045181500, -0.271515429531966, -0.252454020953428, -0.351091357759978, -0.0300176640790097, 0.142254862174602, -0.330759763489132, 0.0479666063111849, 0.145944243768914, 0.0120284867887048, 0.306547181835701, 0.046725288660855, 0.0560634068710735, 0.0802058624713928, 0.244486140069951},
        {-9.91405887798145, -0.776348891090729, 0.525161590315062, -1.9625615116874, 1.09167439596730, -0.159564930568388, -0.747423605155669, -0.251060867504693, 0.0222756773865353, -1.52637549468065, -1.14884352372417, -0.106448087773225, 0.0669088795115406, 0.0817353242202505, -0.559679070213352, -0.0558313425566516, -0.332407356912822, -0.0742748280564511, -0.125965829784593, 0.192902509262711, 0.111716660337104, 0.124066430209955, -0.0177030144330519, 0.0846829786233024, -0.0606739781791931, -0.0176070344366343, -0.110962419872354, -0.0872734063701695, -0.154063886564751},
        {-10.0785508310838, -0.454345394745687, 0.726656599904068, -0.184146637137241, 0.166380629404614, -0.0212848257094857, 0.092852435314594, 0.317325855496212, -0.130500349030537, 0.198834696716121, -0.275741768589902, -0.574874446891082, -0.358972227881504, 0.336033142375354, 0.187606830837850, 0.0555331232714551, 0.126207286811980, 0.0529264282827867, 0.0668435054956571, -0.0781590808551468, -0.0194654623329028, -0.0225333527709008, -0.0167119920494690, 0.0109453993732984, -0.0343677806389803, 0.000610288263516828, 0.008467071167676, -0.0105629622572911, 0.0303659382548436},
        {-9.21203910521835, -0.66349261812197, -0.582658857671111, -4.61907060340832, 2.63335025955876, 0.0297484614178161, -0.681158899355994, -0.415440113045078, 0.132302776227917, -0.459248903410298, 0.140322084108785, 0.798245285438928, 0.881942968015786, -0.618281424564167, 0.361968402679501, -0.0851177827158627, 0.144169474574133, -0.0704639337449072, 0.0197132945519881, 0.414148410388974, 0.179293808463233, 0.247263106321442, -0.0423772195513936, 0.0901146202498355, -0.0422504738212608, 0.0448808604992123, -0.0626666768194935, -0.137035879158561, -0.101746001889252},
        {-9.87384503653197, -0.378520996328206, 0.091927533178001, -1.99421608279801, 1.22504614271717, 0.0728570313411145, 0.177535355514623, 0.324654572086644, -0.119637333530845, 0.992131637673205, 0.301252682698415, -0.377480891100445, -0.273634689929278, 0.293357659136179, 0.767947577957208, 0.112248531940932, 0.509906916146054, 0.127270055712126, 0.144626291455361, -0.0961541605403955, 0.00124473104680597, -0.0615096688788872, -0.0565285354528543, 0.0168545026885762, -0.207567402778240, -0.113716418044344, 0.0909272833322382, 0.126783723976427, 0.184137355756427},
        {-9.64975811072074, -0.538520625015615, 1.37076500446408, 2.93491078540385, -1.54922168090106, -0.179147505947504, 0.345478565941435, 0.0269497595574481, 0.0338040734285699, 0.632929605398797, 0.370151293375317, -0.0578283023124318, -0.310799674952526, 0.149353397791884, 0.323939397486146, 0.0241039142619057, 0.293854100016201, 0.117291584338654, 0.0447313862314212, 0.136953223488327, -0.042315241749641, -0.00929335701665772, 0.00021775444790536, -0.0336833947698394, 0.254843456553245, 0.137905870752935, -0.0484458787988082, -0.0940843270343703, -0.0559293655050893},
        {-9.96181028732276, -0.340052886907838, 0.396806652862297, -1.00676636679852, 0.547409356387922, 0.116259276777592, -0.0577891169805184, 0.521714682866157, -0.155477355623899, -0.772162870506852, -0.924417754356474, -0.781274848725945, 0.223396929283256, 0.324529195860562, 0.49182094970943, 0.0494455656871773, 0.200874267073718, 0.0253507523255806, 0.0734965095339888, 0.0627524931182498, 0.104683220014712, 0.0507241058875918, -0.0491594790615541, 0.0563514761910233, -0.127392195694093, -0.0133477024974374, -0.0411247158120768, -0.0878470289090933, -0.091583628002881},
        {-9.770067994984, -0.579089715939744, -0.00285946338162428, -2.88971205682450, 1.74845757715816, -0.0310530263259475, -0.134603058174427, -0.056565207702839, -0.0242502295861455, 0.991730270828872, 0.510500269612099, 0.0881789582378859, -0.282145109729974, 0.0655922606915108, 0.569575211280975, 0.08252968314933, 0.436248277019921, 0.0960515570397019, 0.154167696463333, -0.155376178383803, -0.0510954422577173, -0.0741556453984683, -0.0246271548316623, 0.00485362568633991, -0.194566321307639, -0.118068911485846, 0.141475859235108, 0.144780387192344, 0.253725518572314},
        {-9.06398822335438, -1.27732194197529, 0.0140619558767589, -4.62958076432196, 2.81935256506716, -0.456980660508129, -1.69702820622754, -1.58410171364801, 0.355085954237378, -0.815198580266669, -0.252435401945989, 1.69365815181846, 0.0304584381927383, -0.625290981008267, -0.169835000178682, -0.230985854389351, 0.564693575065646, 0.122341898672551, -0.225098273643131, 0.74242417756952, -0.185153880235293, -0.00937168409103956, 0.0516298036761726, -0.179008951325401, 0.543405432983491, 0.130436911866241, 0.162203864283640, 0.157388838665561, 0.235458858582121},
        {-8.58966843562756, -1.15497167293183, 1.80323030806025, 5.02771374972929, -2.88835085047828, -0.755776055089853, 0.063119546117566, -1.45918510519665, 0.73583605086782, 0.815091858795201, 1.89246801725762, 1.90831475654699, -0.461150008003749, -0.272647297035201, -0.0413423725719265, 0.246718572949428, 0.299321744827743, 0.502427695719276, -0.00753697812953086, 0.640623246508066, 0.810340518865815, 0.220695222605374, -0.116660277307088, 0.134023323373091, -0.357453310527941, 0.0705225020337569, -0.0984174867292015, -0.300153097591612, -0.558918231400663},
        {-7.92235711731788, -0.89282024540157, 1.63442851863339, 6.03799070531467, -3.50946667237162, -0.420144317049612, -0.053121733517995, -1.11279116149088, 0.679234011127925, -1.21663910205986, 0.903133826260012, 2.00035145656098, 1.75868087636036, -1.21178926213681, 0.358126614033816, 0.0590996034909119, -0.0328533192447587, -0.324551487740051, 0.0193545814125325, 0.0260548745031830, 0.0707302386935431, 0.260201913458919, -0.0784782288307803, 0.113058067389405, -0.607883776202711, -0.383268051877139, 0.251501768683112, 0.435195911853891, 0.563224496041646},
        {-9.4345213841142, -0.9231569085643, 1.71872437499588, 3.60966981611959, -2.07800034247791, -0.480350912591558, -0.0667061262734402, -0.733496688647285, 0.325656779433361, -0.266314808225478, 0.462235189240754, 0.770728300908779, -0.287285107162735, -0.2561125432752, -0.984607844283527, 0.082132834658603, -0.671496213632517, -0.105909756255267, -0.104219265427448, -0.151925143597022, 0.14760932582776, 0.137356492394879, 0.080315724410843, 0.117552610736934, -0.225433370773909, -0.0724635063189488, -0.0469639187110009, -0.055714803809998, -0.079742726715441},
        {-10.0732808896247, -0.61521072699972, 1.06796382941686, 0.693956136650091, -0.337292978498938, -0.163681162992408, 0.0221199354076388, 0.0231780832712060, -0.0607150087239084, 0.218392506063207, -0.0520788779195706, -0.277919356948783, -0.585796528584203, 0.168947007087005, -0.577861550054845, 0.00294874794921383, -0.381026905020934, -0.0429821591805232, -0.0202451560610824, -0.147481349983933, -0.0264918293690499, 0.00814371388165318, 0.0581696594063204, 0.0373218490430461, -0.0149106855753834, 0.00562489849282745, -0.0139592710141719, -0.0363323592590314, -0.00243588376401976},
        {-8.73066355814028, -0.0376031672308371, 1.11640348368332, 4.63602860621192, -2.29382538849912, 0.218545887212297, 0.825060122025352, 0.409688529240142, -0.145215436678046, 1.16244285152755, 0.875022749951454, 0.188241761525393, 0.766579855944553, -0.532129965552563, 0.564884129422714, -0.440886992477316, 0.322611335113969, -0.0505106979834452, -0.168271876186253, 0.974080488570548, -0.212744718646081, 0.153332591136120, 0.0758506874311181, 0.009745766202586, 0.60568632939121, 0.174247476916784, -0.0723522616005121, 0.0537684368063062, 0.142643062669328},
        {-9.82933332054077, -0.649943880730139, 1.36101428588647, 2.10179604783352, -1.22193667160137, -0.199228749924733, -0.139490459800439, -0.0169549565937940, 0.050514258031674, -1.09602034959505, -0.76915025416472, -0.249365228571389, 0.0755169723928181, 0.121158192488967, -0.193663977877977, 0.0779504033632028, -0.211424919843763, -0.143065845108707, 0.0213156213510195, -0.365522874832868, -0.143113597969002, -0.0436225831495414, 0.0234449579442854, -0.0222499023013054, 0.055015968169391, 0.0156927479016869, -0.0440364420088226, -0.0682002654645149, -0.0445805938175135},
        {-9.46907077787977, 0.19651161743955, 0.481949915441497, 1.81631524138901, -0.76799195198029, 0.360538873823016, 1.05389654315210, 0.99401840133185, -0.369703365306011, 1.76871269524432, 0.532327117503354, -0.825101730124338, -0.0228544309143142, 0.193588800266212, 0.737273122567703, -0.197513972142399, 0.452674543924165, 0.0483212663546284, -0.102479829069753, 0.424161294767149, -0.154952302737883, -0.0437083743836875, 0.0076837187901519, -0.108590762066896, 0.388527239719894, 0.0638098715547437, -0.0475633448868215, 0.106612102451432, 0.0206012178711325},
        {-9.86250815856518, -0.489459000323549, 1.15537386812605, 1.71275546964708, -0.9903586897482, -0.0499384631026385, 0.0283763662105060, 0.217401200766175, -0.0941985777788986, -0.757214666970051, -0.569168769537515, -0.396472279305096, 0.108916561884840, -0.0742433702278918, -0.70090759479659, -0.0738666013310473, -0.684089724640399, -0.276754030935372, -0.0508503979823736, -0.212983997925592, -0.0975010303802948, 0.0539838000723647, 0.0950235036841618, 0.0461367238762983, 0.00202315232845460, -0.0156299928269088, -0.0360759337553697, -0.057301644103793, -0.0167218701526062},
        {-9.66968891449916, -1.52291436102903, 1.28902514310631, -1.31226153615601, 0.825164186805184, -0.861675891671766, -1.71535404048593, -1.85167826425391, 0.50987578299151, -1.89408557054637, -1.25926347116999, 1.18112412685899, -1.33972111988223, 0.465734504396993, -1.46927923890701, 0.152477496101379, 0.0172320499607917, 0.365361944773142, -0.4668282302748, -0.108949976726149, -0.152019570358518, -0.337294183100209, -0.0200142979838099, -0.172906725310292, 0.293992952720623, 0.00852535015083424, -0.063228158804661, 0.305528854993109, 0.00141965286450673},
        {-9.54439408160453, 0.468809054153949, -0.115608470777445, 0.132342334930891, -0.066730761317567, 0.666931187703297, 0.976758642299883, 1.35530679996433, -0.555357142924757, 0.578920615708004, 0.0820687973860217, -1.07046838691250, 0.597120084592075, -0.329815116072608, -0.74689490101665, -0.294560347199536, -0.935923652563107, -0.342202382204932, -0.113791531641548, 0.111251766952270, 0.0401241212926702, 0.105584930340303, -0.000326701524651564, -0.00549584381958488, -0.0618041640547727, -0.020904230367235, -0.0102043391648923, 0.0352359818598907, -0.0429567053274071},
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        {6.28860328239642, 0.786858340153053, 2.31876510612293, -2.24934175352176, -2.80140567155993, -1.54662060285667, -0.703086265211117, -0.171640143166909, -0.165258048980973, 0.188360826164179, 0.414463663620125, -0.532374096232042, 0.439452973340269, 0.17325153877235, -0.109743593929700, -0.158431587027186, 0.143873332170946, 0.0494304366944087, -0.40766745436179, -0.0866168797638174, -0.121290117558088, 0.162735780044557, -0.27365457477244, 0.0589598196689758, -0.0364145173305872, 0.0472455912630257, 0.0237714086487439, -0.00770749451755856, -0.0354897043733125},
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        {5.43414167917479, -6.70346558529509, -0.175984478176685, -1.04904210962611, -1.65581731219436, 2.78565715923955, 1.33559236862151, -1.03181584363056, 0.0584807682243581, 0.338836455104766, -0.933749001897226, 0.372366308333935, -0.322693501873548, -0.152393225147778, 0.440832601896841, -0.341775698978559, -0.450811402974748, 0.0418292497109614, 0.114840097121013, 0.0273462324888589, 0.0796410583712146, -0.149202331665885, 0.0742938892505292, -0.0989010143831152, -0.130208970706035, 0.25299203779704, -0.128061930560928, 0.092647939807011, 0.0285835284510502},
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        {6.53923980016782, -0.206626012507942, 2.12929726554961, -0.946736720979541, -0.309028693243593, -2.37781407543408, 1.26227779369913, -1.09202628654848, -1.14726539002825, -0.190071507907986, 0.207987920030400, -0.841604926387125, 0.335676641563983, -0.448934657892577, -0.197226379465267, 0.404240244431233, 0.165587848874020, 0.382138593448104, 0.244524203142953, -0.0241541065443781, 0.0842819353744078, 0.0230487605966779, 0.235370080713475, 0.145402732072875, 0.110180805532016, 0.0533553148495334, 0.125901893084107, 0.093038245073649, -0.0296239821062452},
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        {5.98548655694873, -3.82068766980941, 2.17307665520094, -1.84557965615825, -2.39478415311103, 3.15609083168164, -0.0165898617433295, -0.235328115653983, 0.41986344983781, 0.496150701450483, -0.296605076457486, 0.613030892763612, 0.388311864153522, 0.896080120326996, -0.089579374861701, 0.216769581003401, 0.00893465209158385, -0.864922384233197, 0.0103469168272224, 0.250913842415194, 0.329171214703867, -0.514330442859511, 0.0773617471693147, -0.176177897374323, 0.0268832456307033, 0.00478404757435427, 0.0734106688326031, -0.0453323429846474, 0.076620629715664},
        {6.47917365442517, 0.367036862729552, 2.62573418891823, -1.6305210309568, -1.90412804398726, -0.00086506406614333, -1.28426442744895, 0.762227948774155, 0.453071198659356, 0.280912176835487, 0.245326104084929, 0.008603904185405, 0.219624333398044, 0.322337018319098, -0.0343359816103188, 0.353255000257996, -0.0605949587180135, -0.256238213144213, -0.273698762168305, -0.00661091104345721, 0.0879472473410888, 0.0760490973669652, -0.376034161545947, -0.0302138828885868, 0.163805996241899, -0.207050644658436, 0.00576310137902719, -0.0814469226894047, 0.0343846233673611}
    };

    public KPCATest() {
    }

    @BeforeClass
    public static void setUpClass() throws Exception {
    }

    @AfterClass
    public static void tearDownClass() throws Exception {
    }

    @Before
    public void setUp() {
    }

    @After
    public void tearDown() {
    }

    /**
     * Test of learn method, of class PCA.
     */
    @Test
    public void testKPCAThreshold() {
        System.out.println("learn threshold");
        ArffParser arffParser = new ArffParser();
        arffParser.setResponseIndex(4);
        try {
            AttributeDataset iris = arffParser.parse(smile.data.parser.IOUtils.getTestDataFile("weka/iris.arff"));

            double[][] x = iris.toArray(new double[iris.size()][]);
            KPCA<double[]> kpca = new KPCA(x, new GaussianKernel(Math.sqrt(2.5)), 1E-4);
            assertTrue(Math.equals(latent, kpca.getVariances(), 1E-3));
            double[][] points = kpca.project(x);
            points[0] = kpca.project(x[0]);
            assertTrue(Math.equals(points, kpca.getCoordinates(), 1E-7));
/*
            for (int j = 0; j < points[0].length; j++) {
                double sign = Math.signum(points[0][j] / scores[0][j]);
                for (int i = 0; i < points.length; i++) {
                    points[i][j] *= sign;
                }
            }

            assertTrue(Math.equals(scores, points, 1E-1));
 */
        } catch (Exception ex) {
            System.err.println(ex);
        }
    }

    /**
     * Test of learn method, of class PCA.
     */
    @Test
    public void testKPCAK() {
        System.out.println("learn k");
        ArffParser arffParser = new ArffParser();
        arffParser.setResponseIndex(4);
        try {
            AttributeDataset iris = arffParser.parse(smile.data.parser.IOUtils.getTestDataFile("weka/iris.arff"));

            double[][] x = iris.toArray(new double[iris.size()][]);
            KPCA<double[]> kpca = new KPCA(x, new GaussianKernel(Math.sqrt(2.5)), 29);
            assertTrue(Math.equals(latent, kpca.getVariances(), 1E-3));
            double[][] points = kpca.project(x);
            points[0] = kpca.project(x[0]);
            assertTrue(Math.equals(points, kpca.getCoordinates(), 1E-7));
/*
            for (int j = 0; j < points[0].length; j++) {
                double sign = Math.signum(points[0][j] / scores[0][j]);
                for (int i = 0; i < points.length; i++) {
                    points[i][j] *= sign;
                }
            }

            assertTrue(Math.equals(scores, points, 1E-1));
 */
        } catch (Exception ex) {
            System.err.println(ex);
        }
    }
}