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STAT3006 Assignment 3 Classification

 STAT3006 Assignment 3, 2022 

Weighting 30% - due 18/10/2022 
This assignment involves constructing and assessing classifiers. We will first consider the 
now familiar Iris dataset, collected by Anderson (1936) and first statistically analysed by 
Fisher (1936), which requires one to solve the species problem, that is to predict which 
(known) species a given specimen belongs to. 
The second dataset to be used to train classifiers is the Modified National Institute of 
Standards and Technology (MNIST) database of handwritten digits. This contains 70,000 
images, of which 10,000 were reserved for testing. In each case you will use the given 
labelled data and attempt to construct classifiers which can accurately classify unlabelled
You should select four classifiers, with at least one classifier based on a probability model, 
and one which is not, with each preferably mentioned in this course. Classifiers discussed in 
the course which are based on a probability model include linear, quadratic, mixture and 
kernel density discriminant analysis. Classifiers discussed which are not based on a 
probability model include k nearest neighbours, classification trees and support vector 
machines. All of these are implemented via various packages in R. If you wish to use a 
different method, please check with the lecturer. You cannot use a (classifier, dataset) 
combination that you have used or are using for an assignment in another course. 
1. Assume that we will perform linear discriminant analysis for three classes in two 
dimensions. Additionally assume that we know the class proportions are equal, that common 
covariance matrix is known to be Σ = οΏ½ 𝜎𝜎1
2 𝜌𝜌 𝜎𝜎1𝜎𝜎2
𝜌𝜌 𝜎𝜎1𝜎𝜎2 𝜎𝜎2
2 οΏ½ and that the class means are also 
known to be πœ‡πœ‡π΄π΄ = οΏ½
𝐴𝐴2οΏ½, πœ‡πœ‡π΅π΅ = οΏ½
𝐡𝐡2οΏ½ and πœ‡πœ‡πΆπΆ = οΏ½
πœ‡πœ‡πΆπΆ2οΏ½, respectively, where all the mean 
scalar parameters are real-valued, the standard deviations are positive and the correlation 𝜌𝜌 ∈
(a) Prove that the decision boundaries between the pairs of classes meet at a single point
under most conditions, and state those conditions. [4 marks]
(b) Determine this point in terms of the given parameters. [1 mark]
2. Apply one probability-based and one non-probability-based classifier to the Iris dataset
(with all 4 predictor dimensions) using R, report the results and interpret them.
Results for each classifier should include the following:
(a) Characterisation of each class as modeled by the classifier. Note that, where possible, this 
should include parameter estimates for each class. Where not possible, another attempt 
should be made to characterise the class, such as via summaries of the observations which the 
classifier puts into each class. [1 mark]
(b) Cross-validation (CV)-based estimates of the overall and class-specific error rates: 
obtained by training the classifier on a large fraction of the whole dataset and then applying it 
to the remaining data and checking error rates. You may use 5-fold, 10-fold or leave-one-out 
cross-validation to estimate performance, but you should give a statistical reason for your 
choice. Also include an approximate 95% confidence interval for each error rate, along with a 
description of how this was obtained. [2 marks]
(c) Find, list and discuss any Iris observations which were misclassified in the CV checks. [1 
(d) Plots of the predicted classes as they apply to the data and the data space, including visual 
representation of the decision boundaries, covering all unique pairs of explanatory variables.
Note: you do not need to derive these boundaries – they can emerge from a plot. [1 mark]
(e) Compare and contrast the decision boundaries between classes produced by the two 
methods and try to explain their shapes. Which method do you think was best for this 
dataset? Explain. Describe some aspects of either method that you think are appropriate or 
inappropriate for this classification problem. [2 marks]
(f) You are now asked to predict the class of new observations collected from an area where 
the class proportions have changed to 0.5, 0.2 and 0.3 for setosa, virginica, and versicolor, 
Describe (with mathematical details) how you would change or refit each classifier to give it 
the lowest possible expected cost of prediction under these circumstances. Change or refit the 
classifiers as necessary to do this and report point estimates of the new classifier parameters, 
or class characterisation, as in (a). Explain the nature of the changes. [3 marks]
Note: we will not compare our classification results with those of Fisher’s 1936 paper “The 
Use of Multiple Measurements in Taxonomic Problems”. However, this paper is worth 
reading that paper for background on the dataset and some of the aims of its analysis.
3. Choose two methods of classification that you have not used on the Iris dataset and apply 
them to the MNIST dataset – see http://yann.lecun.com/exdb/mnist/ . Leave the train and test 
split as it is, but feel free to use some of the training data to help choose a model, if desired. 
Aim for best possible predictive performance, but view this as primarily a learning exercise. 
I.e. you do not need to choose methods with the best performance. However, you should aim 
to get reasonable performance out of any method chosen, e.g. with reasonable choice of any 
hyperparameters (say 20% error rate or less). You should not pre-process the data in a way 
which makes use of any knowledge you have of the digit recognition problem. I.e. don’t try 
to produce new explanatory variables which represent image features, even though this would 
likely help performance. You can use dimension reduction if you wish (e.g. PCA). 
(a) Give a brief introduction to the dataset, including quantitative aspects. [1 mark] 
(b) Give a summary of the predictive performance on the test set for each classifier. Make 
sure you do not use the test set at all before doing this. Include at least estimated overall error 
rate and class-specific error rates, along with approximate 95% confidence intervals for these. 
[2 marks]
(c) For each classifier, also report error rates as estimated using the training set. Attempt to 
explain any differences between the error rates estimated from the training and test sets. Note 
that reference to training and test sets here are to the labelling of the original data, not to how 
you may have used them. [2 marks]
(d) Explain why you chose each classifier type and describe some of their apparent strengths 
and weaknesses for this problem. [2 marks]
(e) For each classifier, show 1 example per possible digit (i.e. 20 in total) of handwritten 
digits which were classified into the correct class with the most certainty, and quantify what 
you mean by certainty. Explain why you think the classifiers were particularly successful at 
classifying these correctly and with certainty. Note: defining and implementing “certainty” 
may take some thought, creativity, maths and coding. [3 marks]
(f) For each classifier, show 1 example per digit (i.e. 20 in total) of the worst errors made by 
your classifier and quantify what you mean by worst. Explain why you think some of these 
errors may have been made by your classifier and been among the worst seen. [2 marks]
(g) What is the difference between a handwritten 7 and a 1 according to each classifier? Try 
to explain what each classifier is doing in this case, i.e. what are the main things the classifier 
considers to make this decision and how are they used? [3 marks]
(i) Some R commands you might find useful: 
objects() – gives the current list of objects in memory. 
attributes(x) – gives the set of attributes of an object x. 
(ii) For the Iris dataset, we will assume that each species was collected from an environment 
where all three are equally likely to be selected in a random sample. We can view the sample 
as representative and the prevalence of each species is similar in some environments. (See 
section VI of Fisher, 1936 for some details on how the observations were collected.) 
(iii) Make it a habit to give reasons or justifications for decisions or statements. 
(iv) Please put all the R commands in a separate file or files and submit these separately via a 
single text file or a zip file. You should not give any R commands in your main report and 
should not include any raw output – i.e. just include figures from R (each with a title, axis 
labels and caption below) and put any relevant numerical output in a table or within the text.
(v) Please name your files something like student_number_STAT3006_A3.pdf to assist with 
(vi) As per http://www.uq.edu.au/myadvisor/academic-integrity-and-plagiarism, what you 
submit should be your own work. Even where working from sources, you should endeavour 
to write in your own words. Use consistent notation throughout your assignment and define 
all of it.
(vii) Some references
Maindonald, J. and Braun, J. Data Analysis and Graphics Using R - An Example-Based 
Approach, 3rd edition, Cambridge University Press, 2010. 
Venables, W.N. and Ripley, B.D., Modern Applied Statistics with S, Fourth Edition, Springer, 
Wickham, H. and Grolemund, G. R for Data Science, O'Reilly, 2017. 
Classification and Clustering: 
Bishop, C. Pattern Recognition & Machine Learning, Springer, 2006. 
Devroye, L., Gyorfi, L. and Lugosi, G., A Probabilistic Theory of Pattern Recognition, 
Springer, 1996. 
Duda, R.O., Hart, P.E. and Stork, D.G., Pattern Classification, Wiley, 2001. 
Goodfellow, I., Bengio, Y. & Courville, A. (2016), Deep Learning, MIT Press
Hardle, W.K. and Simar, L., Applied Multivariate Statistical Analysis, 4th ed., Springer, 
Hastie, T. and Tibshirani, R. Discriminant analyses by Gaussian mixtures, Journal of the 
Royal Statistical Society B, 8, 155-176. (MDA paper), 1996. 
Hastie, T. and Tibshirani, R. and Friedman, J. The Elements of Statistical Learning: Data 
Mining, Inference, and Prediction, 2nd edition, Springer, 2009. 
McLachlan, G.J. and Peel, D. Finite Mixture Models, Wiley, 2000. 
McLachlan, G.J. Discriminant Analysis and Statistical Pattern Recognition, Wiley, 1992. 
Scholkopf, B. and Smola, A. J. Learning with Kernels, MIT Press, 2001. 
Data Sources: 
Anderson, E. The species problem in Iris, Annals of the Missouri Botanical Garden 23 (3): 
457–509, 1936. 
Fisher, R.A. The use of multiple measurements in taxonomic problems, Annals of Eugenics 7 
(2): 179–188, 1936. 
LeCun, Y., Bottou, L., Bengio, Y. and Haffner, P. Gradient-Based Learning Applied to 
Document Recognition, Proceedings of the IEEE, 86, 2278-2324, 1998. 
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