User Tools

Site Tools


neuroimagen:bioface_atn

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
neuroimagen:bioface_atn [2021/09/09 09:16]
osotolongo [What we got so far]
neuroimagen:bioface_atn [2021/09/12 10:23]
osotolongo [Métodos no lineales]
Line 183: Line 183:
 library("ADNIMERGE") library("ADNIMERGE")
 pop <- adnimerge[adnimerge$VISCODE=="bl" & (adnimerge$DX=="Dementia" | adnimerge$DX=="CN"),]; pop <- adnimerge[adnimerge$VISCODE=="bl" & (adnimerge$DX=="Dementia" | adnimerge$DX=="CN"),];
-pop$ND = ifelse(pop$DX == "Dementia", 1, 0)+pop$ND = as.factor(ifelse(pop$DX == "Dementia", 1, 0))
 xt <- pop[, c("Hippocampus", "Entorhinal", "Ventricles", "MidTemp", "AGE", "ICV", "ND")] xt <- pop[, c("Hippocampus", "Entorhinal", "Ventricles", "MidTemp", "AGE", "ICV", "ND")]
 </code> </code>
Line 206: Line 206:
  
 <code> <code>
 +setwd("/home/data/bioface")
 base <- read.csv("bf_data.csv") base <- read.csv("bf_data.csv")
 base$Hippocampus = base$Left.Hippocampus + base$Right.Hippocampus base$Hippocampus = base$Left.Hippocampus + base$Right.Hippocampus
Line 223: Line 224:
  
 <code> <code>
-base$post <- predict(classifier_cl, newdata = base, type="raw)+base$post <- predict(classifier_cl, newdata = base, type="raw")
 </code> </code>
  
  
 +^ Clasificación ^ Probabilidades de N+ ^
 +| {{ :neuroimagen:bioface_nplus_classifier.png?600 | my pretty cool neurodegeneration classifier output }} | {{ :neuroimagen:nplus_probabilities_histogram.png?600 | how the probabilities are distributed? }} |
  
 +Y esto voy a hacerlo para FACEHBI también para compararlo,
  
 +<code>
 +setwd("/home/data/facehbi")
 +read.csv("face_data.csv") -> face
 +face$Hippocampus = face$Left.Hippocampus + face$Right.Hippocampus
 +face$Entorhinal = face$lh.entorhinal.GrayVol + face$rh.entorhinal.GrayVol
 +face$Ventricles <- face$Left.Inf.Lat.Vent + face$Right.Inf.Lat.Vent + face$Left.Lateral.Ventricle + face$Right.Lateral.Ventricle
 +face$MidTemp = face$lh.middletemporal.GrayVol + face$rh.middletemporal.GrayVol
 +face$ICV = face$eTIV
 +face$ND <- predict(classifier_cl, newdata = face)
 +face$post <- predict(classifier_cl, newdata = face, type="raw")
 +</code>
 +
 +^ Clasificación ^ Probabilidades de N+ ^
 +| {{ :neuroimagen:facehbi_nbayes_classifier.png?600 | my pretty cool neurodegeneration classifier output (FACEHBI)}} | {{ :neuroimagen:facehbi_nplus_prob_histogram.png?600 |how the probabilities are distributed?}} |
 +
 +==== Métodos no lineales ====
 +
 +Vamos a intentar con métodos no lineales. Ojo, estos  métodos no tienen interpretación probabilistica. Son construcciones matemáticas que funcionan.
 +
 +=== random Forest ===
 +
 +** BIOFACE **
 +<code>
 +rf_cl <- randomForest(ND ~ ., data = xt, na.action = na.omit)
 +base$ND <- predict(rf_cl, newdata = base)
 +base$post <- predict(rf_cl, newdata = base, type="prob")
 +plot(base$AGE, base$Hippocampus, main = "Hippocampus Volume versus Age", xlab="Age", ylab="HV", pch=19, col=ifelse(base$ND==1,"red","green"))
 +hist(base$post[,2], col="red", density = 50, probability=TRUE, breaks = 10, main="Probabilities profile", xlab = "Probability of N+")
 +</code>
 +
 +^ Clasificación ^ Probabilidades de N+ ^
 +| {{ :neuroimagen:rf_classifier_bioface.png?600 |}} | {{ :neuroimagen:rf_prob_profile_bioface.png?600 |}} |
 +
 +**FACEHBI** 
 +
 +<code>
 +face$ND <- predict(rf_cl, newdata = face)
 +face$post <- predict(rf_cl, newdata = face, type = "prob")
 +plot(face$AGE, face$Hippocampus, main = "Hippocampus Volume versus Age", xlab="Age", ylab="HV", pch=19, col=ifelse(face$ND==1,"red","green"))
 +hist(face$post[,2], col="red", density = 50, probability=TRUE, breaks = 10, main="Probabilities profile", xlab = "Probability of N+")
 +</code>
 +
 +^ Clasificación ^ Probabilidades de N+ ^
 +| {{ :neuroimagen:rf_classifier_facehbi.png?600 |}} | {{ :neuroimagen:rf_prob_profile_facehbi.png?600 |}} |
 +
 +=== support-vector machine ===
 +
 +**BIOFACE**
 +
 +<code>
 +svm_cl <- svm(ND ~ ., data = xt, na.action = na.omit)
 +base$ND <- predict(svm_cl, newdata = base)
 +plot(base$AGE, base$Hippocampus, main = "Hippocampus Volume versus Age", xlab="Age", ylab="HV", pch=19, col=ifelse(base$ND==1,"red","green"))
 +</code>
 +
 +{{ :neuroimagen:svm_classifier_bioface.png?600 |}}
 +
 +** FACEHBI **
 +
 +<code>
 +face$ND <- predict(svm_cl, newdata = face)
 +plot(face$AGE, face$Hippocampus, main = "Hippocampus Volume versus Age", xlab="Age", ylab="HV", pch=19, col=ifelse(face$ND==1,"red","green"))
 +</code>
 +
 +{{ :neuroimagen:svm_classifier_facehbi.png?600 |}}
neuroimagen/bioface_atn.txt · Last modified: 2022/06/14 08:22 by osotolongo