The goal of this project is to predict how physical and environmental factors impact housing values in Boston using various machine learning algorithms. The Boston Housing dataset includes 13 qualitative and quantitative features that can be used to predict the median housing value (feature name: medv). This project predicts Boston housing values using machine learning. I explored the impact of physical and environmental factors by engineering features from the Boston Housing dataset and comparing the performance (RMSE) of LASSO Regression, Random Forest, and Ensemble models.
Censoring in MEDV: The median value of owner-occupied homes (MEDV) appears to be capped at $50,000. This is inferred from: 16 cases with a median price exactly $50,000. 15 cases with prices between $40,000 and $50,000.
This dataset is a fundamental resource in algorithm benchmarking, particularly in the field of housing economics and environmental studies.
Goal: To use regression method predict median value of real estate (MEDV) using social, economic, and environmental features.
Key Steps:
library(caret)
## Loading required package: ggplot2
## Loading required package: lattice
library(dplyr)
## Warning: package 'dplyr' was built under R version 4.2.3
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
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## intersect, setdiff, setequal, union
library(tidyr)
library(GGally)
## Warning: package 'GGally' was built under R version 4.2.3
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
library(glmnet)
## Loading required package: Matrix
## Warning: package 'Matrix' was built under R version 4.2.3
##
## Attaching package: 'Matrix'
## The following objects are masked from 'package:tidyr':
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## expand, pack, unpack
## Loaded glmnet 4.1-8
library(magrittr)
##
## Attaching package: 'magrittr'
## The following object is masked from 'package:tidyr':
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## extract
library(MASS)
##
## Attaching package: 'MASS'
## The following object is masked from 'package:dplyr':
##
## select
library(corrplot)
## corrplot 0.92 loaded
housing_raw <- read.csv("ML-Capstone-Housing-Data-BostonHousing.csv")
housing_raw$index <- seq_along(housing_raw[,1])
set.seed(2023) # for reproducibility
train_index <- createDataPartition(housing_raw$index, times = 1, p = 0.8, list = FALSE)
train_data <- housing_raw[train_index, ]
test_data <- housing_raw[-train_index, ]
Overview of the data set
summary(train_data)
## crim zn indus chas
## Min. : 0.00906 Min. : 0.00 Min. : 0.460 Min. :0.00000
## 1st Qu.: 0.07910 1st Qu.: 0.00 1st Qu.: 5.145 1st Qu.:0.00000
## Median : 0.22948 Median : 0.00 Median : 9.125 Median :0.00000
## Mean : 3.62858 Mean : 12.02 Mean :10.915 Mean :0.06158
## 3rd Qu.: 3.64742 3rd Qu.: 16.25 3rd Qu.:18.100 3rd Qu.:0.00000
## Max. :88.97620 Max. :100.00 Max. :27.740 Max. :1.00000
## nox rm age dis
## Min. :0.3850 Min. :3.561 Min. : 2.90 Min. : 1.137
## 1st Qu.:0.4480 1st Qu.:5.887 1st Qu.: 42.65 1st Qu.: 2.122
## Median :0.5320 Median :6.210 Median : 75.50 Median : 3.346
## Mean :0.5511 Mean :6.294 Mean : 67.73 Mean : 3.883
## 3rd Qu.:0.6240 3rd Qu.:6.629 3rd Qu.: 93.38 3rd Qu.: 5.372
## Max. :0.8710 Max. :8.725 Max. :100.00 Max. :12.127
## rad tax ptratio b
## Min. : 1.00 Min. :187.0 Min. :12.60 Min. : 2.52
## 1st Qu.: 4.00 1st Qu.:279.0 1st Qu.:17.40 1st Qu.:374.83
## Median : 5.00 Median :330.0 Median :19.00 Median :391.31
## Mean : 9.51 Mean :406.8 Mean :18.47 Mean :356.63
## 3rd Qu.:24.00 3rd Qu.:666.0 3rd Qu.:20.20 3rd Qu.:396.21
## Max. :24.00 Max. :711.0 Max. :22.00 Max. :396.90
## lstat medv index
## Min. : 1.730 Min. : 5.00 Min. : 2.0
## 1st Qu.: 6.905 1st Qu.:16.73 1st Qu.:127.8
## Median :11.250 Median :21.20 Median :253.5
## Mean :12.524 Mean :22.51 Mean :254.7
## 3rd Qu.:16.703 3rd Qu.:24.95 3rd Qu.:379.8
## Max. :37.970 Max. :50.00 Max. :506.0
colnames(train_data)
## [1] "crim" "zn" "indus" "chas" "nox" "rm" "age"
## [8] "dis" "rad" "tax" "ptratio" "b" "lstat" "medv"
## [15] "index"
nrow(train_data)
## [1] 406
plotting distribution of median values of houses
ggplot(train_data, aes(x = medv)) +
geom_histogram(binwidth = 0.5, color = "black", fill = "grey") +
labs(title = "Histogram of Median House Values", x = "Median House Values", y = "Frequency") +
theme_minimal()
plotting scatter plot matrix for all features to view relationships
options(repr.plot.width = 60, repr.plot.height = 60)
train_data |>
#select(-c('chas', 'b')) |>
ggpairs(
mapping = ggplot2::aes(size = 0.05),
lower = list(continuous = wrap("points", alpha = 0.3, size=0.01, color = 'blue')),
diag = list(continuous = wrap("barDiag", alpha = 0.3)),
upper = list(continuous = wrap("cor", size = 1.9)),
font.label = list(size = 0.1, face = "bold"),
ggtheme = theme_minimal()
)+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, size = 3), # Rotate x-axis labels by 90 degrees and reduce font size
axis.text.y = element_text(size = 3) # Reduce y-axis label font size
)
plotting correlation matrix for all features
# correlation matrix plotting
cor_plot_matrix <-
cor(train_data[,c("crim","zn","indus", "chas", "nox","rm","age","dis","rad","tax",
"ptratio","lstat","medv")])
corrplot(cor_plot_matrix, method = 'color', type='upper',
order = 'hclust',tl.col = "black", tl.srt = 45)
#view the correlation values
cor_plot_matrix
## crim zn indus chas nox rm
## crim 1.00000000 -0.19728625 0.41272516 -0.05346437 0.4089370 -0.21640561
## zn -0.19728625 1.00000000 -0.54280468 -0.02980824 -0.5209844 0.31421177
## indus 0.41272516 -0.54280468 1.00000000 0.06768869 0.7846162 -0.41913978
## chas -0.05346437 -0.02980824 0.06768869 1.00000000 0.1203778 0.07120022
## nox 0.40893704 -0.52098440 0.78461618 0.12037778 1.0000000 -0.32988672
## rm -0.21640561 0.31421177 -0.41913978 0.07120022 -0.3298867 1.00000000
## age 0.35537384 -0.56959076 0.66514395 0.07703603 0.7339173 -0.25394150
## dis -0.37536960 0.66336359 -0.71695002 -0.09331896 -0.7678040 0.20891865
## rad 0.60679259 -0.31827343 0.62394237 -0.02567697 0.6060486 -0.23872869
## tax 0.56984326 -0.31861785 0.73735481 -0.04594003 0.6676820 -0.32894481
## ptratio 0.28158909 -0.38868901 0.35117883 -0.14927301 0.1856434 -0.37347459
## lstat 0.44976413 -0.41667183 0.63303810 -0.05117013 0.6140633 -0.62231820
## medv -0.38997005 0.37291770 -0.52103445 0.13155823 -0.4516859 0.72998473
## age dis rad tax ptratio lstat
## crim 0.35537384 -0.37536960 0.60679259 0.56984326 0.2815891 0.44976413
## zn -0.56959076 0.66336359 -0.31827343 -0.31861785 -0.3886890 -0.41667183
## indus 0.66514395 -0.71695002 0.62394237 0.73735481 0.3511788 0.63303810
## chas 0.07703603 -0.09331896 -0.02567697 -0.04594003 -0.1492730 -0.05117013
## nox 0.73391733 -0.76780403 0.60604865 0.66768196 0.1856434 0.61406326
## rm -0.25394150 0.20891865 -0.23872869 -0.32894481 -0.3734746 -0.62231820
## age 1.00000000 -0.75112439 0.46884925 0.51613062 0.2590609 0.61375808
## dis -0.75112439 1.00000000 -0.49763701 -0.53667711 -0.2224566 -0.51093880
## rad 0.46884925 -0.49763701 1.00000000 0.91630699 0.4683878 0.50205415
## tax 0.51613062 -0.53667711 0.91630699 1.00000000 0.4475885 0.56650032
## ptratio 0.25906091 -0.22245659 0.46838783 0.44758846 1.0000000 0.37529424
## lstat 0.61375808 -0.51093880 0.50205415 0.56650032 0.3752942 1.00000000
## medv -0.40482320 0.27327762 -0.41793510 -0.51025090 -0.5342755 -0.75353341
## medv
## crim -0.3899700
## zn 0.3729177
## indus -0.5210344
## chas 0.1315582
## nox -0.4516859
## rm 0.7299847
## age -0.4048232
## dis 0.2732776
## rad -0.4179351
## tax -0.5102509
## ptratio -0.5342755
## lstat -0.7535334
## medv 1.0000000
Here are the key insights I got from the scatter plot matrix and correlation matrix, which demonstrates the relationships between the all the selected features.
Notably, features “rm” (average number of rooms per dwelling) and “lstat” (% lower status of the population) showed significant correlations (0.72998473 and -0.75353341) with “medv” (median value of owner-occupied homes).
Intuitively, this result makes sense. Housing value is dependent on the size of the unit, more rooms equals to larger area usually. Lower status of the population also can indicate that the housing is more affordable or at a cheaper price comparing to other units.
RMSE function
RMSE <- function(true, predict) {
differences <- true - predict
differences <- differences[!is.na(differences)]
sqrt(mean(differences^2))
}
R^2 function * proportion of the variance for the dependent variable that’s explained by the independent variables in a regression model.
R2 <- function(true, predict){
#Total Sum of Squares (TSS)
tss <- sum((true - mean(true))^2)
#Residual Sum of Squares (RSS)
rss <- sum((true - predict)^2)
1 - (rss / tss)
}
#create model "cv_model_base" with all original features
train_data_base <- data.frame(scale(train_data[c("crim","zn","indus", "chas", "nox","rm",
"age","dis","rad","tax","ptratio","lstat")]))
train_data_base$medv <- train_data$medv
#prepare a matrix for glmnet
x_train_base <- model.matrix(medv ~ crim + zn + indus + chas + nox + rm + age + dis +
rad + tax + ptratio + lstat - 1, train_data_base)
y_train_base <- train_data$medv
#use cross validation to find the optimal lambda
cv_model_base <- cv.glmnet(x_train_base, y_train_base, alpha=1)
lambda_base <- cv_model_base$lambda.min
testing base model on the test set
test_data_base <- data.frame(scale(test_data[c("crim","zn","indus", "chas", "nox","rm",
"age","dis","rad","tax","ptratio","lstat")]))
test_data_base$medv <- test_data$medv
x_test_base <- model.matrix(medv ~ crim + zn + indus + chas + nox + rm + age + dis +
rad + tax + ptratio + lstat -1, test_data_base)
predict_base <- predict(cv_model_base, s=lambda_base, newx = x_test_base)
y_test <- test_data$medv
RMSE(y_test, predict_base)
## [1] 5.818608
R2(y_test, predict_base)
## [1] 0.5712238
first, look at which variable is more closely related to medv, and start transforming the feature by the order
library(dplyr)
cor_plot_ranked <- data.frame(cor_plot_matrix)
cor_plot_ranked['medv']|>
arrange(desc(abs(medv)))
transformations <- list(
og = function(x) x,
log = function(x) {ifelse(x > 0, log(x+1), x)},
sqrt = function(x) sqrt(x),
square = function(x) x^2
)
library(glmnet)
test_transformation <- function(data, feature, transformations, response = "medv") {
results <- list()
for (trans_name in names(transformations)) {
# apply transformation for feature
data[[paste0(feature, "_", trans_name)]] <-
transformations[[trans_name]](data[[feature]])
# prepare data for LASSO
x <- model.matrix(reformulate(termlabels = paste0(feature, "_", trans_name),
response = response), data)
y <- data[[response]]
# fit LASSO model
cv_model <- cv.glmnet(x, y, alpha = 1)
# store results
results[[trans_name]] <- min(cv_model$cvm) # store min. cross-validation error
}
return(results)
}
features <- c("crim", "zn", "indus", "nox", "rm", "age", "dis", "rad", "tax", "ptratio",
"lstat") #"chas" is removed
all_results <- list()
for (feature in features) {
all_results[[feature]] <- test_transformation(train_data, feature, transformations)
}
all_results
## $crim
## $crim$og
## [1] 73.94864
##
## $crim$log
## [1] 65.07591
##
## $crim$sqrt
## [1] 66.02352
##
## $crim$square
## [1] 83.44711
##
##
## $zn
## $zn$og
## [1] 74.97155
##
## $zn$log
## [1] 73.32584
##
## $zn$sqrt
## [1] 72.94894
##
## $zn$square
## [1] 76.76166
##
##
## $indus
## $indus$og
## [1] 63.32572
##
## $indus$log
## [1] 60.55059
##
## $indus$sqrt
## [1] 61.20971
##
## $indus$square
## [1] 67.96439
##
##
## $nox
## $nox$og
## [1] 68.6618
##
## $nox$log
## [1] 68.88375
##
## $nox$sqrt
## [1] 68.57813
##
## $nox$square
## [1] 69.84305
##
##
## $rm
## $rm$og
## [1] 40.81376
##
## $rm$log
## [1] 45.55186
##
## $rm$sqrt
## [1] 43.66835
##
## $rm$square
## [1] 36.86515
##
##
## $age
## $age$og
## [1] 72.27145
##
## $age$log
## [1] 76.14704
##
## $age$sqrt
## [1] 73.88289
##
## $age$square
## [1] 71.21946
##
##
## $dis
## $dis$og
## [1] 79.69296
##
## $dis$log
## [1] 77.75665
##
## $dis$sqrt
## [1] 78.61167
##
## $dis$square
## [1] 82.45873
##
##
## $rad
## $rad$og
## [1] 71.2702
##
## $rad$log
## [1] 73.61563
##
## $rad$sqrt
## [1] 72.28383
##
## $rad$square
## [1] 70.49924
##
##
## $tax
## $tax$og
## [1] 63.95556
##
## $tax$log
## [1] 63.41417
##
## $tax$sqrt
## [1] 64.49838
##
## $tax$square
## [1] 65.14206
##
##
## $ptratio
## $ptratio$og
## [1] 62.26636
##
## $ptratio$log
## [1] 62.0783
##
## $ptratio$sqrt
## [1] 62.20056
##
## $ptratio$square
## [1] 61.58558
##
##
## $lstat
## $lstat$og
## [1] 37.38989
##
## $lstat$log
## [1] 25.74093
##
## $lstat$sqrt
## [1] 30.35599
##
## $lstat$square
## [1] 53.28978
Result from running codes above, here are the transformation for each feature that has the lowest cross-validation error. * crim -> log * zn -> log * indus -> log * nox -> sqrt - differences are too small, may ignore * rm -> square * age -> square * dis -> log * rad -> square - differences are too small, may ignore * tax -> log - differences are too small, may ignore * ptratio -> square - differences are too small, may ignore * lstat -> log
transforming_train <- train_data |>
mutate(log_crim = log(crim + 1),
log_zn = log(zn + 1),
log_indus = log(indus + 1),
sq_rm = rm^2,
sq_age = age^2,
log_dis = log(dis+1),
log_lstat = log(lstat + 1))
transformed_train_data <- transforming_train[c('log_crim','log_zn','log_indus','sq_rm',
'sq_age','log_dis','log_lstat','chas',
'tax','ptratio','nox','rad')] |>
scale() |>
data.frame()
transformed_train_data$medv = train_data$medv
head(transformed_train_data)
testing transformed model on the test set
#prepare a matrix for glmnet
x_train_transformed <- model.matrix(medv ~ log_crim + log_zn + log_indus + sq_rm +
sq_age + log_dis + log_lstat + rad + chas +
tax + ptratio + nox- 1,
transformed_train_data)
y_train <- train_data$medv
#use cross validation to find the optimal lambda
cv_model_transformed <- cv.glmnet(x_train_transformed, y_train, alpha=1)
lambda_transformed <- cv_model_transformed$lambda.min
#prepare test set for prediction
transforming_test <- test_data |>
mutate(log_crim = log(crim + 1),
log_zn = log(zn + 1),
log_indus = log(indus + 1),
sq_rm = rm^2,
sq_age = age^2,
log_dis = log(dis+1),
log_lstat = log(lstat + 1))
transformed_test_data <- transforming_test[c('log_crim','log_zn','log_indus','sq_rm','sq_age','log_dis','log_lstat','chas','tax',
'ptratio','nox','rad')] |>
scale() |>
data.frame()
transformed_test_data$medv <- test_data$medv
x_test_transformed <- model.matrix(medv ~ log_crim + log_zn + log_indus + sq_rm + sq_age + log_dis +
log_lstat + rad + chas + tax + ptratio + nox - 1,
transformed_test_data)
predict_LASSO_transformed <- predict(cv_model_transformed,
newx = x_test_transformed)
y_test <- test_data$medv
RMSE(y_test, predict_LASSO_transformed)
## [1] 5.968521
R2(y_test, predict_LASSO_transformed)
## [1] 0.5488448
base model: RMSE: ~5.8 R-squared ~0.57
with transformed model RMSE: ~5.6 R-squared: ~0.60
library(randomForest)
## randomForest 4.7-1.1
## Type rfNews() to see new features/changes/bug fixes.
##
## Attaching package: 'randomForest'
## The following object is masked from 'package:dplyr':
##
## combine
## The following object is masked from 'package:ggplot2':
##
## margin
select_features_rf <- c("crim","zn","indus", "chas", "nox","rm","age","dis","rad","tax",
"ptratio","lstat", "medv")
train_data_rf <- train_data[select_features_rf]
# create cross validation parameter / train control
train_control <- trainControl(method = 'cv', number = 5)
# create tuning grid
tune_grid <- expand.grid(mtry = c(2, 3, 4, 5, 6))
# train Random Forest model with tuned parameters
rf_model_tuned <- train(medv ~ .,
data = train_data_rf,
method = 'rf',
trControl = train_control,
tuneGrid = tune_grid)
rf_model_tuned$bestTune$mtry
## [1] 5
mtry <- rf_model_tuned$bestTune$mtry
# build Random Forest model with original data
rf_model <- randomForest(medv ~ .,
data = train_data_rf,
ntree = 500,
mtry = mtry)
# view model information
print(rf_model)
##
## Call:
## randomForest(formula = medv ~ ., data = train_data_rf, ntree = 500, mtry = mtry)
## Type of random forest: regression
## Number of trees: 500
## No. of variables tried at each split: 5
##
## Mean of squared residuals: 8.599402
## % Var explained: 89.97
importance(rf_model)
## IncNodePurity
## crim 1774.53142
## zn 148.45776
## indus 1684.98412
## chas 59.13755
## nox 1240.12170
## rm 12668.15217
## age 706.98150
## dis 1426.18937
## rad 184.90533
## tax 928.32232
## ptratio 2207.30600
## lstat 11464.53382
# plotting feature importance
varImpPlot(rf_model)
# test Random Forest model by predicting test set
test_data_rf <- test_data[select_features_rf]
predictions_rf <- predict(rf_model, test_data_rf)
# get RMSE of the Random Forest model
rf_result <- data.frame(medv_actual = test_data_rf$medv,
medv_predicted = predictions_rf
)
RMSE(rf_result$medv_actual, rf_result$medv_predicted)
## [1] 5.043901
R2(rf_result$medv_actual, rf_result$medv_predicted)
## [1] 0.6778
The RMSE is around 5.0 with the tuned Random Forest model.
I’ve tried standardizing all the features except for medv using scale() before training Random Forest model, and the RMSE is ~5.3, so I am using original features
| # Ensemble |
| ```r ensemble_predictions <- (predictions_rf + predict_LASSO_transformed) / 2 |
| RMSE(test_data_rf$medv, ensemble_predictions) ``` |
## [1] 5.350186 |
r R2(test_data_rf$medv, ensemble_predictions) |
## [1] 0.6374814 The RMSE for the ensemble
model is around 5.1, higher than the Random Forest model alone |
-> presents the modeling results and discusses the model performance; and.
Base Model: The base LASSO model uses original features without any transformations, and the RMSE of the model is approximately 5.8 with R-squared value around 0.57.
Transformed Model: After applying feature transformations, the RMSE of the updated model improved to about 5.6 with R-squared value increased to approximately 0.60, showing some effectiveness of feature transformations for model outcome improvement.
Random Forest model with tuned feature (mtry) using cross validation yield RMSE of around 5.0 and R-squared around 0.68, much better prediction than the LASSO models.
Feature importance analysis indicated that ‘rm’, ‘lstat’, and ‘ptratio’ were the most influential features, which is similar to the EDA finding.
When testing Random Forest model with standardization of features, I found that using original features gives better results, so that is the model I kept in this report.
The ensemble model that combined the LASSO and Random Forest models, resulted in an RMSE of approximately 5.13 and R-squared value around 0.67. Hence the model did not outperform the Random Forest model.
The aim of this project is to predict median housing values in Boston using various machine learning algorithms.
With the Boston Housing Dataset, I selected the following features to
predict MEDV (Median value of owner-occupied homes in $1000’s.): 1. CRIM
per capita crime rate by town
2. ZN proportion of residential land zoned for lots over 25,000 sq.ft.
3. INDUS proportion of non-retail business acres per town. 4. CHAS
Charles River dummy variable (= 1 if tract bounds river; 0 otherwise).
5. NOX nitric oxides concentration (parts per 10 million). 6. RM average
number of rooms per dwelling. 7. AGE proportion of owner-occupied units
built prior to 1940. 8. DIS weighted distances to five Boston employment
centres. 9. RAD index of accessibility to radial highways. 10. TAX
full-value property-tax rate per $10,000. 11. PTRATIO pupil-teacher
ratio by town. 12. LSTAT % lower status of the population.
After building 2 LASSO models, 1 Random Forest model, and 1 Ensemble Model, Random Forest model stood out as having most predicting power in this machine learning project, with ‘rm’, ‘lstat’, and ‘ptratio’ as the most influential features. The LASSO model’s performance improvement with feature transformations underscores the importance of feature engineering in predictive modeling.
Predicting housing prices is complex. There are many other features that could have been included in the training model, such as areas of the unit, the floor numbers, most recent renovation date, transportation access, number of parks nearby, noise levels, proximity to schools, neighborhood characteristics, land’s environmental attributes etc. With those features, the predicting power of the ml model shall increase. Also, this dataset is relatively old, published in the late 90s, and small in size, so the result is perhaps less relevant to the current housing market.
source: https://www.cs.toronto.edu/~delve/data/boston/bostonDetail.html
#library(knitr)
# Replace "your_file.Rmd" with the path to your Rmd file
#rmd_file <- "ML-Capstone-Housing.Rmd"
#r_script <- "ML-Capstone-Housing.R" # Output R script filename
# Extract R code from the Rmd file and write to an R script
#purl(rmd_file, output = r_script)