Kaggle-MLSP-2014

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Kaggle-MLSP-2014

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Kaggle-MLSP-2014 최신버젼 다운로드

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README
-----------------------------------------

## MLSP 2014 Schizophrenia Classification Challenge: 2nd position (solution)

*Author: Alexander V. Lebedev, MD*

*(University of Bergen, Norway)*

*Date: 26/07/2014*

### 1. Summary
The goal of the competition (https://www.kaggle.com/c/mlsp-2014-mri) was to automatically detect subjects with schizophrenia based on multimodal features derived from the magnetic resonance imaging (MRI) data.
For this challenge, I implemented so-called "feature trimming", consisting of 1) introducing a random vector into the feature set, 2) calculating feature importance, 3) removing the features with importance below the "dummy feature".
At the first step, I ran Random Forest [1] model and performed trimming based on Gini-index [2]. Then, after estimation of the inverse width parameter ("sigma"), I tuned C-parameter for my final model - Support Vector Machine with Gaussian Kernel (RBF-SVM) [3].

### 2. Feature Selection
The key step was "feature trimming". Further steps were also quite simple and none of any sophisticated approaches (like ensembling, hierarchical models) were implemented. Generally, I tried to keep the design as simple as possible due to limited number of subjects available in the training set and therefore being concerned about overfitting.

### 3. Code Description

#### 3.1 Preparatory step:

##### 3.1.1 Load the libraries:

```r
library(caret)
library(randomForest)
library(e1071)
library(kernlab)
library(doMC)
library(foreach)
library(RColorBrewer)
```

##### 3.1.2 Read the data:

```r
# Training set:
trFC <- read.csv('/YOUR-PATH/Kaggle/SCH/Train/train_FNC.csv')
trSBM <- read.csv('/YOUR-PATH/Kaggle/SCH/Train/train_SBM.csv')
tr <- merge(trFC, trSBM, by='Id')

# Test set:
tstFC <- read.csv('/YOUR-PATH/Kaggle/SCH/Test/test_FNC.csv')
tstSBM <- read.csv('/YOUR-PATH/Kaggle/SCH/Test/test_SBM.csv')
tst <- merge(tstFC, tstSBM, by='Id')

y <- read.csv('/YOUR-PATH/Kaggle/SCH/Train/train_labels.csv')
```

#### 3.2 Analysis

##### 3.2.1 "Feature Trimming"

Registering 6 cores to speed up my computations:

```r
registerDoMC(cores=6)
```

Converting a y-label vector into appropriate format:

```r
y <- as.factor(paste('X.', y[,2], sep = ''))
```

Introducing a random vector into my feature set:

```r
all <- cbind(tr, rnorm(1:dim(tr)[1]))
colnames(all)[412] <- 'rand'
```

Now I train Random Forest with this (full) feature set:

```r
rf.mod <- foreach(ntree=rep(2500, 6), .combine=combine, .multicombine=TRUE,
                  .packages='randomForest') %dopar% {
                    randomForest(all[,2:412], y, ntree=ntree)
                  }
```

Looking at the feature importances:

```r
color <- brewer.pal(n = 8, "Dark2")
imp <- as.data.frame(rf.mod$importance[order(rf.mod$importance),])
barplot(t(imp), col=color[1])
points(which(imp==imp['rand',]),0.6, col=color[2], type='h', lwd=2)
```

![plot of chunk simpleplot](https://cloud.githubusercontent.com/assets/4508892/3711386/e5b4496c-14d3-11e4-9c1d-5a94987dc4ac.png)

Everything below importance of our "dummy" feature (random vector) can likely be ignored.
So, we "cut" everything that is on the left side of the orange line.

```r
imp <- subset(imp, imp>imp['rand',])
```

Saving the data in one rda-file for further analyses:

```r
save('all', 'y', 'tst', 'imp',  file = '/YOUR-PATH/Kaggle/SCH/Train/AllData.rda')
```

Now I reduce my feature set:

```r
dat <- all[,rownames(imp)]
```

##### 3.2.2 Final Model
I usually start from SVM and then proceed with ensemble methods. However, in this competition, the use of boosted trees did not result in superior performance and I stopped.

First, I estimate "sigma" (inverse width parameter for the RBF-SVM)
(of note, sometimes I use a subset of my data, but here I used the whole training set due to its very limited size)

```r
sigDist <- sigest(y ~ as.matrix(dat), data=dat, frac = 1)
```

Creating a tune grid for further C-parameter selection):

```r
svmTuneGrid <- data.frame(.sigma = sigDist[1], .C = 2^(-20:100))
```

```
## Warning: row names were found from a short variable and have been
## discarded
```

And training the final RBF-SVM model:

```r
svmFit <- train(dat,y,
                method = "svmRadial",
                preProc = c("center", "scale"),
                tuneGrid = svmTuneGrid,
                trControl = trainControl(method = "cv", number = 86, classProbs =  TRUE))
```

Making predictions:

```r
ttst <- tst[,rownames(imp)]
predTst <- predict(svmFit, ttst, type='prob')
predTst <- predTst[,2]
```

Formatting submission:

```r
pred <- cbind(as.integer(tst$Id), as.numeric(predTst))
colnames(pred) <- c('Id', 'Probability')
```

Writing:

```r
write.table(pred, file = '/YOUR-PATH/Kaggle/SCH/submissions/submission_rbfSVM_RFtrimmed.csv', sep=',', quote=F, row.names=F, fileEncoding = 'UTF-16LE')
```

### 4. Dependencies
To execute the code the following libraries must be installed: caret [3], randomForest [4], e1071 [5], kernlab [6], doMC [7], foreach [8], RColorBrewer [9]

### 5. Additional Comments and Observations
In general, it was somewhat difficult to evaluate performance of the models, since there was a substantial mismatch between cross-validated accuracies and the feedback that I was receiving during my submissions. It was one of the reasons why I decided not to go further with feature selection and more complex modeling approaches.

### 6. References

[1] V.N. Vapnik (1995) The Nature of Statistical Learning Theory. Springer-Verlag New York, Inc. New York, NY, USA;

[2] L. Breiman (2001) Random Forests. Machine Learning Volume 45, Number 1: 5-32;

[3] M. Kuhn. Contributions from Jed Wing SW, Andre Williams, Chris Keefer and Allan Engelhardt (2012) caret: Classification and Regression Training. R package version 5.15-023. http://cran.r-project.org/packages/caret/;

[4] L. Breiman, A. Cutler, R port by Andy Liaw and Matthew Wiener (2014). randomForest: Breiman and Cutler's random forests for classification and regression. http://cran.r-project.org/web/packages/randomForest/;

[5] D. Meyer, E. Dimitriadou, K. Hornik, A. Weingessel, F. Leisch, C-C. Chang. C-C. Lin. Misc Functions of the Department of Statistics (e1071), TU Wien. http://cran.r-project.org/web/packages/e1071/;

[6] A. Karatzoglou, A. Smola, K. Hornik (2013). kernlab: Kernel-based Machine Learning Lab. http://cran.r-project.org/web/packages/kernlab/;

[7] Revolution Analytics. doMC (2014): Foreach parallel adaptor for the multicore package. http://cran.r-project.org/web/packages/doMC/;

[8] Revolution Analytics, Steve Weston (2014). foreach: Foreach looping construct for R. http://cran.r-project.org/web/packages/foreach/;

[9] Erich Neuwirth (2011). RColorBrewer: ColorBrewer palettes. http://cran.r-project.org/web/packages/RColorBrewer/.

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