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Rmd 236b909 zihao12 2020-06-05 kos_K20_ebpmf.alpha_v0.4.2.Rmd

Introduction

rm(list = ls())
library(ggplot2)
Warning: package 'ggplot2' was built under R version 3.5.2
library(pheatmap)
Warning: package 'pheatmap' was built under R version 3.5.2
library(gridExtra)
library(fastTopics)
source("code/misc.R")
source("code/util.R")

data_dir = "data/uci_BoW/"
model_initLF_name = "output/uci_BoW/v0.4.2/kos_ebpmf_wbg_initLF50_K20_maxiter2000.Rds"
model_initL_name = "output/uci_BoW/v0.4.2/kos_ebpmf_wbg_initL50_K20_maxiter2000.Rds"
model_pmf_name = "output/uci_BoW/v0.3.9/kos_pmf_initLF50_K20_maxiter2000.Rds"
dict_name = "vocab.kos.txt"
data_name = "docword.kos.txt"

Y = read_uci_bag_of_words(file= sprintf("%s/%s",
                data_dir,data_name))
model_initLF = readRDS(model_initLF_name)
model_initL = readRDS(model_initL_name)
model_pmf = readRDS(model_pmf_name)
dict = read.csv(sprintf("%s/%s", data_dir, dict_name), header = FALSE)[,1]
dict = as.vector(dict)

K = ncol(model_pmf$L)
L_pmf = model_pmf$L
F_pmf = model_pmf$F

L_initLF = model_initLF$l0 * model_initLF$qg$qls_mean
F_initLF = model_initLF$f0 * model_initLF$qg$qfs_mean

L_initL = model_initL$l0 * model_initL$qg$qls_mean
F_initL = model_initL$f0 * model_initL$qg$qfs_mean

lf_pmf = poisson2multinom(L = L_pmf,F = F_pmf)
lf_initLF = poisson2multinom(L=L_initLF,F=F_initLF)
lf_initLF = poisson2multinom(L=L_initL,F=F_initL)

## one small mistake I made: forgot to append KLs
Ks = seq(500, 2000, 500)
KL_tmp = c()
for(K in Ks){
  model_tmp = readRDS(
    sprintf("output/uci_BoW/v0.4.2/kos_ebpmf_wbg_initLF50_K20_maxiter%d.Rds", K))
  KL_tmp <- c(KL_tmp, model_tmp$KL)
}
model_initLF$KL = KL_tmp

KL_tmp = c()
for(K in Ks){
  model_tmp = readRDS(
    sprintf("output/uci_BoW/v0.4.2/kos_ebpmf_wbg_initL50_K20_maxiter%d.Rds", K))
  KL_tmp <- c(KL_tmp, model_tmp$KL)
}
model_initL$KL = KL_tmp

ELBO and KL

df <- data.frame(iter = 1:length(model_initLF$ELBO), 
                 wbg_initLF.elbo = model_initLF$ELBO,
                 wbg_initLF.kl = model_initLF$KL,
                 wbg_initLF.ell = model_initLF$ELBO + model_initLF$KL,
                 wbg_initL.elbo = model_initL$ELBO,
                 wbg_initL.kl = model_initL$KL,
                 wbg_initL.ell = model_initL$ELBO + model_initL$KL,
                 pmf.ll = model_pmf$log_liks)

## the log transformation onm y-axis does not work here!
base = 2
signed_log <- scales::trans_new("signed_log",
       transform=function(x) sign(x)*log(abs(x), base = base),
       inverse=function(x) sign(x)*(base^(abs(x))))

p1 <- ggplot(data = df) + 
  geom_point(aes(x = iter, y = wbg_initLF.elbo, color = "wbg_initLF"))+
  geom_point(aes(x = iter, y = wbg_initL.elbo, color = "wbg_initL"))+
  scale_y_continuous(trans = signed_log)+
  ylab("elbo")+
  ggtitle("ELBO")

p2 <- ggplot(data = df) + 
  geom_point(aes(x = iter, y = wbg_initLF.kl, color = "wbg_initLF"))+
  geom_point(aes(x = iter, y = wbg_initL.kl, color = "wbg_initL"))+
  scale_y_continuous(trans = signed_log)+
  ylab("kl")+
  ggtitle("KL")

p3 <- ggplot(data = df) + 
  geom_point(aes(x = iter, y = wbg_initLF.ell, color = "wbg_initLF"))+
  geom_point(aes(x = iter, y = wbg_initL.ell, color = "wbg_initL"))+
  geom_point(aes(x = iter, y = pmf.ll, color = "pmf"))+
  scale_y_continuous(trans = signed_log)+
  ylab("E(loglik)")+
  ggtitle("E(loglik)")

grid.arrange(p1, p2, p3, ncol=1)

look at priors in

\(g_L\)

get_prior_summary(model_initLF$qg$gls)

get_prior_summary(model_initL$qg$gls)

\(g_F\)

get_prior_summary(model_initLF$qg$gfs)

get_prior_summary(model_initL$qg$gfs)

look at w

get_w_scaled <- function(model){model$w * sum(model$l0) * sum(model$f0)}

plot(get_w_scaled(model_initLF), get_w_scaled(model_initL))
abline(a = 0, b = 1, col = "red")

hist(get_w_scaled(model_initLF), breaks = 100)

hist(get_w_scaled(model_initL), breaks = 100)

## average number of words for each topic
sum(Y@x)/ncol(model_pmf$L)
[1] 23385.7

look at l0, f0

plot(model_initLF$f0/sum(model_initLF$f0), model_initL$f0/sum(model_initL$f0), log = "xy")
abline(a = 0, b = 1, col = "red")

plot(model_initLF$l0/sum(model_initLF$l0), model_initL$l0/sum(model_initL$l0), log = "xy")
abline(a = 0, b = 1, col = "red")

look at top words (compared with other methods)

I use wbg_init_L together with bg, pmf and pmf2binom (which is log fold change computed from fastTopics::poisson2binom). I show their top 20 words for each topic.

top_words_df = read.csv("output/uci_BoW/v0.4.2/top_words_v0.4.2.csv")
# K = ncol(model_pmf$F)
# for(k in 1:K){
#   print(top_words_df[top_words_df$Topic == k, ])
# }
library('knitr')
Warning: package 'knitr' was built under R version 3.5.2
kable(top_words_df, format = "markdown")
bg wbg pmf2binom pmf Topic
upenn liberalrakkasan liberalrakkasan november 1
lud sunzoo rad voting 1
senategovernors bradnickel senategovernors republicans 1
jiacinto altsite nprigo vote 1
abstain boxblogroll jiacinto house 1
bald boxfeed_listing bald account 1
danielua boxrdf_feeds lud kerry 1
converted bushsux lawnorder senate 1
lawnorder calculator danielua governor 1
rad calistan converted electoral 1
bradnickel dryfly upenn poll 1
nprigo endspan egon polls 1
egon montclair bradnickel bush 1
seamus newwindow seamus election 1
peanut openhttpwwwedwardsforprezcomdailykoshtml abstain voter 1
buh racine furiousxgeorge sunzoo 1
luaptifer republicansforkerry buh general 1
furiousxgeorge startspan luaptifer experience 1
cfr var maximumken media 1
suppression lawnorder peanut planned 1
rasmussen surveyusa rasmussen bush 2
gallup rasmussen evs kerry 2
battleground gallup tipp poll 2
surveyusa evs lvs polls 2
battlegrounds tipp gallup general 2
tipp zogby oregonian states 2
gotv masondixon battlegrounds voters 2
bounce lvs cnnusa florida 2
lvs arkansas nbcwsj polling 2
evs cnnusa rasmussens election 2
arkansas zogbys gallups state 2
wisconsin leads arkansas results 2
ruy nader orlando ohio 2
kerryedwards quinnipiac rimjob nader 2
undecided susa columbus numbers 2
pollsters oregonian sampling oct 2
kerry bounce surveyusa vote 2
masondixon battleground roundup battleground 2
soto favorableunfavorable snapshot gore 2
nbcwsj ruy minnesota news 2
sharpton clark lieberman dean 3
braun braun sharpton edwards 3
clarks gephardt braun kerry 3
secondplace sharpton lieb clark 3
parenthesis kucinich secondplace primary 3
gep clarks marist democratic 3
undecided lieberman composite poll 3
lieb secondplace deanclark lieberman 3
caucuses dean kucinich gephardt 3
marist parenthesis clark iowa 3
arg lieb moseley results 3
antidean gep parenthesis polls 3
composite marist edwards numbers 3
deanclark edwards intangibles kucinich 3
moseley caucuses inching sharpton 3
zogbys composite clarks jan 3
wisconsin deanclark geps feb 3
lieberman moseley susas candidates 3
edwards thirdplace wesley state 3
matchups geps delegate latest 3
nagourney swift nagourney bush 4
boat nagourney fournier kerry 4
millers boat brooks president 4
swift sbvt sbvt john 4
fournier fournier mccains general 4
veterans cheney broder bushs 4
mccains cutter playbook campaign 4
cutter flipflopper cutter kerrys 4
kerry unfit veepstakes cheney 4
sbvt vietnam flipflopper war 4
admire vice vet debate 4
cleland debates acceptance george 4
ahnold kerrys cheney iraq 4
vietnam mccains millers speech 4
dukakis cheneys ahnold republicans 4
podium edwards unfit convention 4
broder speech advertisement presidential 4
vet acceptance dishonest time 4
miserable broder vets senator 4
chooses nixon profiles vice 4
toomey thune herseth senate 5
salazar diedrich thune house 5
diedrich salazar toomey republican 5
daschle toomey diedrich race 5
thune demint salazar democrats 5
herseth herseth beauprez elections 5
dakota dakota tenenbaum state 5
tenenbaum specter campbell seat 5
demint tenenbaum toomeys democratic 5
coors coors inez gop 5
campbell beauprez specters district 5
beauprez inez hoeffels democrat 5
inez seat jindal candidate 5
runoff daschle vitter races 5
rodney hoeffel herseths south 5
seats vitter diedrichs primary 5
breaux greenwood greenwood republicans 5
greenwood humphreys amdt rep 5
vitter specters mitakides herseth 5
indiana jindal cosen election 5
clarke rice clarke bush 6
counterterrorism clarke counterterrorism administration 6
plame counterterrorism clarkes house 6
clarkes clarkes plame white 6
adviser condoleezza pdb intelligence 6
libby intelligence condoleezza president 6
condoleezza cia rices commission 6
pdb powell berger report 6
rices rices hijackers security 6
colin plame scooter officials 6
leak pdb rkan cia 6
intelligence documents airplane national 6
commissioners fbi declassified adviser 6
hijackers testimony ddel terrorism 6
withheld hijackers valerie rice 6
biden alqaida stonewalling powell 6
berger leak undercover attacks 6
qaeda colin aristide richard 6
rkan libby ashcrofts news 6
alqaida berger withheld secretary 6
wink server hecht people 7
hecht traffic rude time 7
johns hecht walks ive 7
amazon servers wink meteor 7
wood surgery observation blades 7
dad baseball surgery ill 7
wiki wink fatherinlaw oct 7
rude sox internets life 7
baseball sports bypass live 7
walks dad baseball lot 7
jenna bugs traffic youre 7
sox dkos driver general 7
equipment wiki amazon night 7
realitybased park dad years 7
sisters jenna sox country 7
bypass bypass gobbell put 7
strange beer taught love 7
observation karen jenna community 7
wheels youll sports guys 7
gear amazon johns war 7
deficit cuts tax bush 8
taxes tax cuts tax 8
cuts income deficit health 8
fiscal deficit prescription administration 8
prescription vaccine vaccine billion 8
flu tuition tuition budget 8
deficits prescription vaccines year 8
vaccine taxes middleclass cuts 8
tuition flu budget care 8
reagans fiscal income reagan 8
income medicare deficits president 8
middleclass middleclass incomes federal 8
medicare vaccines fiscal government 8
vaccines incomes overtime spending 8
incomes overtime taxes years 8
overtime budget cato taxes 8
wages burden grover deficit 8
package insurance tobacco bushs 8
revenues billion reagans economy 8
social deficits colmes plan 8
ethics ethics ethics delay 9
jury rowland jury republicans 9
judicial judicial judicial house 9
judiciary jury judiciary court 9
earle earle earle committee 9
justices redistricting lindauer law 9
prosecutors indicted violations republican 9
rowland janklow scalia federal 9
lawsuit lawsuit schwarz texas 9
complaint judiciary lawsuit bill 9
violations investigation justices ethics 9
redistricting mcgreevey travis investigation 9
scalia prosecutors censure senate 9
supreme complaint aarp supreme 9
indicted courts caci democrats 9
mcgreevey schwarz matrix majority 9
janklow lindauer ronnie leader 9
schwarz enron license political 9
bell kuhl obligations legal 9
kuhl subpoenas drake criminal 9
prices oil prices jobs 10
cells prices emissions bush 10
companies tariffs vance years 10
oil epa walmart administration 10
species scientists species oil 10
walmart emissions cells science 10
emissions steel china energy 10
china species treaty space 10
halliburton vance stagflation economic 10
vance gwb kyoto research 10
epa walmart wildlife economy 10
treaty cells amphibians blades 10
economists stagflation carbon meteor 10
stagflation researchers landmines policy 10
kyoto environmental petroleum states 10
tariffs industries arctic year 10
warming sea greenhouse environmental 10
wildlife pollution zimbabwe report 10
fishing wildlife tariffs labor 10
landmines economists epa united 10
marriage marriage samesex party 11
gay amendment catholics democratic 11
amendment gay cats marriage 11
abortion samesex couples rights 11
samesex abortion paige gay 11
catholic catholics bishops republican 11
couples catholic equality political 11
catholics couples marriages democrats 11
womens constitutional marriage vote 11
cats marriages marry conservative 11
religious dreier abortion amendment 11
outsiders cats communion issue 11
marriages bishops gay republicans 11
marry rosenberg discrimination state 11
abortions discrimination catholic people 11
bishops devos racial women 11
paige constitution rosenberg support 11
fma paige antigay white 11
communion communion outsiders states 11
sahni antigay womens american 11
mich duderino parecommend november 12
allegory parecommend duderino poll 12
kingelection bloomfield hotshotxi house 12
countdown virginiadem barbero polls 12
gatana idetestthispres virginiadem account 12
juppon barbero tradesports electoral 12
punkmonk hotshotxi misterajc republicans 12
sappy misterajc idetestthispres senate 12
katerina katerina vaantirepublican governor 12
chedrcheez gatana juppon ground 12
wclathe juppon countdown trouble 12
hoodies allegory gatana turnout 12
vaantirepublican kingelection punkmonk contact 12
releasing tradesports katerina duderino 12
misterajc punkmonk bloomfield parecommend 12
crooks chedrcheez sappy exit 12
tradesports wclathe allegory bush 12
barbero crooks wclathe vote 12
hotshotxi hoodies chedrcheez primary 12
idetestthispres vaantirepublican kingelection general 12
ads kerr kerr campaign 13
kerr mcauliffe oxley million 13
mcauliffe fundraising soros money 13
dccc pacs pacs party 13
oxley dccc blitz democratic 13
regula chandler dnc ads 13
pacs donations begging candidates 13
konop dnc frost dnc 13
soros blitz loophole raised 13
fund expenditures epatriots bush 13
frost oxley buys campaigns 13
blitz schrader mcauliffe fundraising 13
parity soros axelrod democrats 13
loophole frost sessions election 13
fec cash soft media 13
transfers transfers receipts house 13
blogpac axelrod expenditures national 13
fundraising sessions konop political 13
soft committees shakeup cash 13
axelrod ginny mccainfeingold republicans 13
ghraib ghraib ghraib war 14
prisoners abu torture iraq 14
abu torture prisoners military 14
torture prison detainees soldiers 14
civilian detainees prisoner american 14
detainees prisoners civilian abu 14
prison interrogation interrogation iraqi 14
rumsfeld prisoner detention people 14
soldiers fallujah petraeus rumsfeld 14
prisoner petraeus armys ghraib 14
fallujah rumsfeld battalion general 14
fatalities detention atrocities army 14
marines battalion airborne pentagon 14
interrogation saleh maj defense 14
pentagon soldiers gehlen troops 14
petraeus pentagon gharib prisoners 14
battalion armys fatalities men 14
detention iraqi mercenaries killed 14
armys geneva blackwater fallujah 14
guatemala fatalities saleh prison 14
shiite iraqi sunni iraq 15
chalabi shiite shiite war 15
occupation iraqis sadr iraqi 15
explosives baghdad shiites bush 15
sunni sunni sistani troops 15
sadr sadr kurds saddam 15
iraqis occupation spain american 15
resistance laden kurdish forces 15
baghdad bin cleric attacks 15
spain najaf uprising baghdad 15
shiites chalabi muqtada united 15
laden spain ayatollah killed 15
bin shiites zarqawi country 15
najaf sistani sadrs military 15
osama cleric militiamen government 15
taliban insurgents alhusainy iraqis 15
saddam osama dearborn officials 15
islamic saddams kufa weapons 15
sistani kurds fubar people 15
cleric kurdish imam bin 15
signatures signatures signatures nader 16
naders naders naders ballot 16
guard thurlow petition bush 16
petition petitions thurlow general 16
medals nader sproul party 16
thurlow guard petitions state 16
sproul sproul secretaries election 16
petitions volleyball applications republican 16
secretaries martinez volleyball voter 16
applications discharge boats national 16
volleyball bronze mel guard 16
martinez drills drills service 16
absentee secretaries indymedia records 16
mel allday allday voters 16
boat verified verified campaign 16
verified petition medals bushs 16
honorable registrations absentee people 16
drills mel bronze texas 16
boats applications discharge vote 16
vietnam camejo ramsey republicans 16
coburn coburn disapprove percent 17
disapprove disapprove unfavorable poll 17
unfavorable unfavorable statistically voters 17
approval favorability percent vote 17
surveys carson registrants polls 17
latino registrants coburn numbers 17
respondents knowles approve lead 17
carson coburns favorability results 17
percent murkowski tulsa race 17
favorability rating coburns coburn 17
registrants tulsa rating carson 17
tulsa respondents latinos democratic 17
coburns statistically hispanics republican 17
murkowski polled countylevel polling 17
hispanics rotated rell support 17
statewide latinos oksen registered 17
approve registrations adults democrats 17
rating cuban twoparty election 17
survey countylevel murkowskis republicans 17
ratings favorable favorable people 17
mongiardo mongiardo murphy senate 18
keyes matsunaka keyes race 18
murphy keyes nag elections 18
nag bunning matsunaka dkos 18
matsunaka stork mongiardo campaign 18
stork seemann stork candidates 18
donors farmer seemann dozen 18
farmer romero lois obama 18
seemann crane nagging house 18
obama burt bunnings illinois 18
lois knowles samara jim 18
ilsen ditka crane donors 18
romero bunnings ditka candidate 18
samara obama hyde bunning 18
cohen lois burt jun 18
bunnings morrison actblue races 18
crane mosen barend farmer 18
nagging barend cegelis knowles 18
burt cegelis storks state 18
barend ilsen mosen mongiardo 18
blogs oreilly oreilly media 19
oreilly fox luntz news 19
bloggers luntz theaters bloggers 19
limbaugh bloggers oceana internet 19
luntz theaters debunking political 19
fox film splice blog 19
oceana moores janeane fox 19
theaters fahrenheit deceits book 19
advertisers sinclair limbaugh people 19
moores franken moores blogs 19
tnr splice bloggers radio 19
coulter janeane publications press 19
splice blogs franken conservative 19
debunking debunking brokaw read 19
janeane tnr journalism tom 19
kurtz documentary fahrenheit america 19
rationing deceits dncc liberal 19
dncc dncc programming coverage 19
deceits journalists publishing times 19
publications limbaugh documentary air 19
afscme afscme afscme dean 20
seiu gephardt seiu iowa 20
moines moines mcdonalds democratic 20
des des mcentee campaign 20
trippi seiu mcmahon primary 20
unions deans stella gephardt 20
harkin mcentee dubuque people 20
mcentee dean liebeck deans 20
mcdonalds trippi weber endorsement 20
mcmahon caucuses harts howard 20
deans unions teamsters unions 20
vermont caucus uaw candidate 20
gephardts dubuque davenport union 20
caucuses iowans aft labor 20
stella iowa des tom 20
endorsements precinct precinct candidates 20
davenport uaw moines schaller 20
organizational mcmahon harkin state 20
liebeck harts ethic edwards 20
aflcio teamsters iowans jan 20 

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] knitr_1.28        fastTopics_0.3-64 gridExtra_2.3     pheatmap_1.0.12  
[5] ggplot2_3.3.0     workflowr_1.6.2  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6       highr_0.8          RColorBrewer_1.1-2 compiler_3.5.1    
 [5] pillar_1.4.4       later_0.8.0        git2r_0.26.1       prettyunits_1.1.1 
 [9] progress_1.2.2     tools_3.5.1        digest_0.6.25      Rtsne_0.15        
[13] lattice_0.20-38    evaluate_0.14      lifecycle_0.2.0    tibble_3.0.1      
[17] gtable_0.3.0       pkgconfig_2.0.3    rlang_0.4.6        Matrix_1.2-17     
[21] yaml_2.2.0         xfun_0.8           withr_2.2.0        stringr_1.4.0     
[25] dplyr_0.8.1        hms_0.4.2          fs_1.3.1           vctrs_0.3.0       
[29] cowplot_0.9.4      rprojroot_1.3-2    grid_3.5.1         tidyselect_0.2.5  
[33] glue_1.4.1         R6_2.4.1           rmarkdown_2.1      irlba_2.3.3       
[37] farver_2.0.3       purrr_0.3.4        magrittr_1.5       whisker_0.3-2     
[41] backports_1.1.7    scales_1.1.1       promises_1.0.1     htmltools_0.3.6   
[45] ellipsis_0.3.1     assertthat_0.2.1   colorspace_1.4-1   httpuv_1.5.1      
[49] labeling_0.3       quadprog_1.5-8     stringi_1.4.3      RcppParallel_4.4.3
[53] munsell_0.5.0      crayon_1.3.4