Skip to content

Commit 1df2338

Browse files
author
Nam Pho
committed
wrapping up solution
1 parent 64e5b1e commit 1df2338

File tree

2 files changed

+184
-1
lines changed

2 files changed

+184
-1
lines changed

‎dimreduction.R

+184
Original file line numberDiff line numberDiff line change
@@ -128,3 +128,187 @@ p8 <- ggplot(ddat.tse.viz, aes(x=PC1, y=PC2, color=Class)) + geom_point() + geom
128128

129129
ggsave( "img/us-tse.png", plot=grid.arrange(p7, p8, nrow=1),
130130
width=10, height=5, units="in", device="png", dpi="retina")
131+
132+
133+
134+
### ANN
135+
ann.ctrl <- trainControl(method="cv", number=4, classProbs=T, summaryFunction=twoClassSummary, savePredictions=T)
136+
137+
nicu.ann.tune <- expand.grid(layer1=c(68), layer2=c(136), layer3=c(68),
138+
learning.rate=c(0.1), momentum=0.9,
139+
dropout=c(0.5), activation=c("sigmoid"))
140+
ddat.ann.tune <- expand.grid(layer1=c(85), layer2=c(255), layer3=c(85),
141+
learning.rate=c(0.06), momentum=0.9,
142+
dropout=c(0.5), activation=c("sigmoid"))
143+
144+
cat("[+] ann nicu testing w/NO feature selection...")
145+
start.run <- Sys.time()
146+
ann.train.nicu <- train(e_comp ~ .,
147+
dat=nicu.train,
148+
method="mxnet",
149+
metric="ROC",
150+
preProc=c("center", "scale"),
151+
trControl=ann.ctrl,
152+
tuneGrid=nicu.ann.tune
153+
)
154+
end.run <- Sys.time()
155+
cat("done!\n")
156+
cat("\tNICU control:", ann.train.nicu$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
157+
beep()
158+
159+
### ANN-control
160+
161+
cat("[+] ann ddat testing w/NO feature selection...")
162+
start.run <- Sys.time()
163+
ann.train.ddat <- train(alive ~ .,
164+
dat=ddat.train,
165+
method="mxnet",
166+
metric="ROC",
167+
preProc=c("center", "scale"),
168+
trControl=ann.ctrl,
169+
tuneGrid=ddat.ann.tune
170+
)
171+
end.run <- Sys.time()
172+
cat("done!\n")
173+
cat("\tDDAT control:", ann.train.ddat$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
174+
beep()
175+
176+
### ANN-PCA
177+
178+
nicu.pca.viz$Class <- factor(as.character(nicu.pca.viz$Class), levels=c("0", "1"), labels=c("normal", "icu"))
179+
ddat.pca.viz$Class <- factor(as.character(ddat.pca.viz$Class), levels=c("0", "1"), labels=c("death", "alive"))
180+
181+
cat("[+] ann nicu testing w/PCA feature selection...")
182+
start.run <- Sys.time()
183+
ann.train.nicu <- train(Class ~ .,
184+
dat=nicu.pca.viz,
185+
method="mxnet",
186+
metric="ROC",
187+
preProc=c("center", "scale"),
188+
trControl=ann.ctrl,
189+
tuneGrid=nicu.ann.tune
190+
)
191+
end.run <- Sys.time()
192+
cat("done!\n")
193+
cat("\tNICU PCA:", ann.train.nicu$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
194+
beep()
195+
196+
cat("[+] ann ddat testing w/PCA feature selection...")
197+
start.run <- Sys.time()
198+
ann.train.ddat <- train(Clss ~ .,
199+
dat=ddat.pca.viz,
200+
method="mxnet",
201+
metric="ROC",
202+
preProc=c("center", "scale"),
203+
trControl=ann.ctrl,
204+
tuneGrid=ddat.ann.tune
205+
)
206+
end.run <- Sys.time()
207+
cat("done!\n")
208+
cat("\tDDAT PCA:", ann.train.ddat$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
209+
beep()
210+
211+
### ANN-ICA
212+
213+
nicu.ica.viz$Class <- factor(as.character(nicu.ica.viz$Class), levels=c("0", "1"), labels=c("normal", "icu"))
214+
ddat.ica.viz$Class <- factor(as.character(ddat.ica.viz$Class), levels=c("0", "1"), labels=c("death", "alive"))
215+
216+
cat("[+] ann nicu testing w/ICA feature selection...")
217+
start.run <- Sys.time()
218+
ann.train.nicu <- train(Class ~ .,
219+
dat=nicu.ica.viz,
220+
method="mxnet",
221+
metric="ROC",
222+
preProc=c("center", "scale"),
223+
trControl=ann.ctrl,
224+
tuneGrid=nicu.ann.tune
225+
)
226+
end.run <- Sys.time()
227+
cat("done!\n")
228+
cat("\tNICU ICA:", ann.train.nicu$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
229+
beep()
230+
231+
cat("[+] ann ddat testing w/ICA feature selection...")
232+
start.run <- Sys.time()
233+
ann.train.ddat <- train(Clss ~ .,
234+
dat=ddat.ica.viz,
235+
method="mxnet",
236+
metric="ROC",
237+
preProc=c("center", "scale"),
238+
trControl=ann.ctrl,
239+
tuneGrid=ddat.ann.tune
240+
)
241+
end.run <- Sys.time()
242+
cat("done!\n")
243+
cat("\tDDAT ICA:", ann.train.ddat$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
244+
beep()
245+
246+
### ANN-RPJ
247+
248+
nicu.rpj.viz$Class <- factor(as.character(nicu.rpj.viz$Class), levels=c("0", "1"), labels=c("normal", "icu"))
249+
ddat.rpj.viz$Class <- factor(as.character(ddat.rpj.viz$Class), levels=c("0", "1"), labels=c("death", "alive"))
250+
251+
cat("[+] ann nicu testing w/RandPro feature selection...")
252+
start.run <- Sys.time()
253+
ann.train.nicu <- train(Class ~ .,
254+
dat=nicu.rpj.viz,
255+
method="mxnet",
256+
metric="ROC",
257+
preProc=c("center", "scale"),
258+
trControl=ann.ctrl,
259+
tuneGrid=nicu.ann.tune
260+
)
261+
end.run <- Sys.time()
262+
cat("done!\n")
263+
cat("\tNICU RandPro:", ann.train.nicu$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
264+
beep()
265+
266+
cat("[+] ann ddat testing w/RandPro feature selection...")
267+
start.run <- Sys.time()
268+
ann.train.ddat <- train(Clss ~ .,
269+
dat=ddat.rpj.viz,
270+
method="mxnet",
271+
metric="ROC",
272+
preProc=c("center", "scale"),
273+
trControl=ann.ctrl,
274+
tuneGrid=ddat.ann.tune
275+
)
276+
end.run <- Sys.time()
277+
cat("done!\n")
278+
cat("\tDDAT RandPro:", ann.train.ddat$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
279+
beep()
280+
281+
### ANN-TSE
282+
283+
nicu.tse.viz$Class <- factor(as.character(nicu.tse.viz$Class), levels=c("0", "1"), labels=c("normal", "icu"))
284+
ddat.tse.viz$Class <- factor(as.character(ddat.tse.viz$Class), levels=c("0", "1"), labels=c("death", "alive"))
285+
286+
cat("[+] ann nicu testing w/t-SNE feature selection...")
287+
start.run <- Sys.time()
288+
ann.train.nicu <- train(Class ~ .,
289+
dat=nicu.tse.viz,
290+
method="mxnet",
291+
metric="ROC",
292+
preProc=c("center", "scale"),
293+
trControl=ann.ctrl,
294+
tuneGrid=nicu.ann.tune
295+
)
296+
end.run <- Sys.time()
297+
cat("done!\n")
298+
cat("\tNICU t-SNE:", ann.train.nicu$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
299+
beep()
300+
301+
cat("[+] ann ddat testing w/t-SNE feature selection...")
302+
start.run <- Sys.time()
303+
ann.train.ddat <- train(Clss ~ .,
304+
dat=ddat.tse.viz,
305+
method="mxnet",
306+
metric="ROC",
307+
preProc=c("center", "scale"),
308+
trControl=ann.ctrl,
309+
tuneGrid=ddat.ann.tune
310+
)
311+
end.run <- Sys.time()
312+
cat("done!\n")
313+
cat("\tDDAT t-SNE:", ann.train.ddat$results$ROC, "AUC,", difftime(end.run, start.run, units="sec"), "seconds\n")
314+
beep()

‎em.R

-1
Original file line numberDiff line numberDiff line change
@@ -44,4 +44,3 @@ par(mfrow=c(1,2)) # 1 row, 2 col
4444
plot(nicu.bic, xlab="Clusters", ylab="BIC (Natality Data)")
4545
plot(ddat.bic, xlab="Clusters", ylab="BIC (Mortality Data)")
4646
dev.off()
47-

0 commit comments

Comments
 (0)