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Given p-dimensional training data containing d groups (the design space), a classification algorithm (classifier)
predicts which group new data belongs to. Typically, the classifier is treated as a black box and the
focus is on finding classifiers with good predictive accuracy. For many problems the ability to predict new
observations accurately is sufficient, but it is very interesting to learn more about how the algorithms operate
under different conditions and inputs by looking at the boundaries between groups. Understanding the
boundaries is important for the underlying real problem because it tells us how the groups differ. Simpler,
but equally accurate, classifiers may be built with knowledge gained from visualising the boundaries, and
problems of overfitting may be intercepted.
Generally the input to these algorithms is high dimensional, and the resulting boundaries will thus be
high dimensional and perhaps curvilinear or multi-facted. This paper discusses methods for understanding
the division of space between the groups, and provides an implementation in an R package, explore, which
links R to GGobi [16, 15]. It provides a fluid environment for experimenting with classification algorithms
and their parameters and then viewing the results in the original high dimensional design space.

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Hadley Wickham, Doina Caragea, Di Cook January 20, 2006

1

Introduction

Given p-dimensional training data containing d groups (the design space), a classiﬁcation algorithm (classiﬁer) predicts which group new data belongs to. Typically, the classiﬁer is treated as a black box and the focus is on ﬁnding classiﬁers with good predictive accuracy. For many problems the ability to predict new observations accurately is suﬃcient, but it is very interesting to learn more about how the algorithms operate under diﬀerent conditions and inputs by looking at the boundaries between groups. Understanding the boundaries is important for the underlying real problem because it tells us how the groups diﬀer. Simpler, but equally accurate, classiﬁers may be built with knowledge gained from visualising the boundaries, and problems of overﬁtting may be intercepted. Generally the input to these algorithms is high dimensional, and the resulting boundaries will thus be high dimensional and perhaps curvilinear or multi-facted. This paper discusses methods for understanding the division of space between the groups, and provides an implementation in an R package, explore, which links R to GGobi [16, 15]. It provides a ﬂuid environment for experimenting with classiﬁcation algorithms and their parameters and then viewing the results in the original high dimensional design space.

2

Classiﬁcation regions

One way to think about how a classiﬁer works is to look at how it divides up the design space into the d diﬀerent groups. Each family of classiﬁers does this in a distinctive way. For example, linear discriminant analysis divides up the space with straight lines, while trees recursively split the space into boxes. Generally, most classiﬁers produce connected areas for each group, but some, e.g. k-nearest neighbours, do not. We would like a method that is ﬂexible enough to work for any type of classiﬁer. Here we present two basic approaches: we can display the boundaries between the diﬀerent regions, or display all the regions, as shown in ﬁgure 1. Typically in pedagogical 2D examples, a line is drawn between the diﬀerent classiﬁcation regions. However, in higher dimensions and with complex classiﬁcation functions determining this line is diﬃcult. Using a line implies that we know the boundary curve at every point—we can describe the boundary explicitly. However, this boundary may be diﬃcult or time consuming to calculate. We can take advantage of the fact that a line is indistinguishable from a series of closely packed points. It is easier to describe the position of a discrete number of points instead of all the twists and turns a line might make. The challenge then becomes generating a suﬃcient number of points that an illusion of a boundary is created. It is also useful to draw two boundary lines, one for each group on the boundary. This makes it easy to tell which group is on which side of the boundary, and it will make the boundary appear thicker, which is useful in higher dimensions. Finally, this is useful when we have many groups in the data or convoluted boundaries, as we may want to look at the surface of each region separately. Another approach to visualising a classiﬁer is to display the classiﬁcation region for each group. A classiﬁcation region is a high dimensional object and so in more than two dimensions, regions may obsure each other. Generally, we will have to look at one group at a time, so the other groups do not obscure our view. We can do this in ggobi by shadowing and excluding the points in groups that we are not interested in, 1

Data points are shown as large circles. The ﬁgure on the right only shows the boundary between the two regions. 2 . The ﬁgure on the left shows the classiﬁer region by shading the diﬀerent regions diﬀerent colours. Figure 2: Using shadowing to highlight the classiﬁer region for each group.Figure 1: A 2D LDA classiﬁer.

and if all its neighbours are of the same class.as seen in ﬁgure 2. The advantage of this method is that it is completely general and can be applied to any classiﬁcation function. which means they take up 0% of the design space. 3 Finding boundaries As mentioned above. Points that are uncertain. In this case. Here we look at each point. Figure 3: The colour and glyph panel in ggobi lets us easily choose which groups to shadow.45. ﬁgure 3. explore can use either approach. the boundaries are a p − 1 dimensional structure embedded in a p dimensional space. We can use this idea to ﬁnd the boundaries.55. This is easy to do in GGobi using the colour and glyph palette. because it computes distances between all pairs of points to ﬁnd the nearest neighbours. Ideally.000 3 . and just classify the point to the group with the highest probability. we can use a k -nearest neighbours approach. if point A is in group 1 with probability 0. then that point will be close to the boundary between the two groups. this seems to impose a limit of around 20. suggest that the points are near the boundary between the two groups. we would like this to be as small as possible so that our boundaries are accurate. i. another way to display classiﬁcation functions is to show the boundaries between the diﬀerent regions. for example. For some classiﬁers it is possible to ﬁnd a simple parametric formula that describes the boundaries between groups. An example of this in 2D is shown in ﬁgure 4. However. This approach is more useful when we have many groups or many dimensions. or it is tedious to do so. otherwise it will fall back to one of the slower numerical approaches. Linear discriminant analysis and support vector machines are two techniques for which this is possible. however. In practice. How can we ﬁnd these boundaries? There are two basic methods: explicitly from knowledge of the classiﬁcation function. it is not possible to extract an explicit functional representation of the boundary from most classiﬁcation functions. have similar classiﬁcation probabilities for two or more groups. then the point is not on the boundary and can be discarded.e. as the boundaries become more complicated to view. If an explicit technique has been programmed it will use that. The thickness of the boundary can be controlled by changing the value which determines whether two probabilities are similar or not. The disadvantage is that it is slow (O(n2 )). Most classiﬁcation functions can output the posterior probability of an observation belonging to a group. nearest neighbour classiﬁcation using only one neighbour. and group 2 in probability 0. In general. The R package. If we sample points throughout the design space we can then select only those uncertain points near boundaries. Much of the time we don’t look at these. or by treating the classiﬁer as a black box and ﬁnding the boundaries numerically. For example. Some classiﬁcation functions do not generate posterior probabilities. We will need to give the boundaries some thickness so that we can see them.

93 0.99 0. We need to ensure the number of points is suﬃcient to create the illusion of a surface. To ﬁll the design space with points.11 0. 1] prior to analysis so that variables are treated equally for classiﬁcation algorithm and graphic.99 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0. and we need an approach to ﬁll the design space with points. points for moderately fast interactive use. we need to standardise variables correctly to ensure that the boundary is sharp.99 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.72 0.99 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Figure 4: Posterior probabilty of each point belonging to the blue group.45 0.1 0. and relatively easy for three variables in a 3D plot.1 0. The grid sometimes produces distracting visual artefacts. especially when the design space is high dimensional.03 0.34 0. and by increasing the thickness of the boundary.85 0.97 0.09 0.36 0.64 0.74 0.91 0.76 0.82 0.000 points. This means the slowest part is classifying these points.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0. The random sample works better in high-D but generally needs many more points to create the illusion of solids.62 0.42 0.98 0.98 0. If we are trying to ﬁnd boundaries then both of these approaches start to break down as dimensionality increases.02 0.82 0.01 0.02 0.91 0. 4 Visualising high D structures The dimensionality of the classiﬁer is equal to the number of predictor variables. This is the “curse of dimensionality” and is because the same number of points need to spread out across more dimensions.97 0.04 0.01 0.9 0. What can we do if we 4 .22 0.67 0. and GGobi can comfortable display up to around 100.87 0.01 0.04 0.01 0. it is best to scale all variables to [0.01 0. This depends entirely on the classiﬁer used.2 0.99 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0. 1]. To control the thickness of the boundaries. Scaling is one ﬁnal important consideration. We can attack this in two ways: by increasing the number of points we use to ﬁll the design space.78 0. It is easy to view the results with two variables on a 2D plot.99 0.42 0.84 0.98 0.99 0.99 0. each variable is implicitly scaled to [0.02 0.88 0.98 0. using a uniform grid.01 0.7 0.98 0. the number of points required to make a perceivable boundary increases.5 0.95 0.93 0.24 0.07 0. there are two simple approaches.59 0. Generating the points to ﬁll the design space is rapid.48 0.96 0.01 0.02 0.01 0.08 0. There are three important considerations with these numerical approaches.94 0.92 0.07 0.01 0.39 0.29 0.18 0.01 0.02 0.06 0.78 0.98 0.89 0. When we plot the data points.97 0.99 0.8 0. As the dimensionality of the design space increases.67 0.94 0.08 0.14 0.96 0.96 0.62 0. and weeding out non-boundary points.05 0.15 0. The number of points we can use depends on the speed of the classiﬁcation algorithm and the speed of the visualisation program.03 0.26 0.01 0. as shown in previous examples.05 0.31 0.95 0.17 0.12 0.56 0.53 0. because some variables will be on a diﬀerent scale.02 0.99 0.97 0. For this reason.99 0.05 0.99 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0. or a random sample (ﬁgure 5). If we do not scale the variables explicitly.01 0. boundaries discovered by the algorithms above will not appear solid.24 0. we can adjust the number of neighbours used.03 0.2 0.04 0.36 0.

You ﬁt your classiﬁer. 5 Examples The following examples use the explore R package to demonstrate the techniques described above. We can use manual controls to explore the space intricately [3]. the guided tour picks “interesting” views that are local maxima of a projection pursuit function. as the number of dimensions is much smaller. Depending on the number of dimensions and the complexity of the classiﬁer this may happen quickly or take a long time. n=100000) Here we ﬁt a QDA classiﬁer to the iris data. We use two datasets: the Fisher’s iris data. have more than 3 dimensions? How do we understand how the classiﬁer divides up the space? In this section we describe the use of tour methods—the grand tour. and then call the explore function. To use the grand tour. 4. we simply watch it for a while waiting to see an illuminating view. thus controlling the rotation of the projection plane. on the right a random sample. The explore package is very simple to use. 5]—for viewing projections of high-dimensional spaces and thus classiﬁcation boundaries.Width + Petal. One useful approach is to use the grand or guided tour to ﬁnd a view that does a fairly good job of displaying the separation and then use manual controls on each variable to ﬁnd the best view. 1]. We can also supply 5 . Manual controls allow the user to control the projection coeﬃcient for a particular variable. The guided tour is an extension of the grand tour. a uniform grid. It does this by interpolating between randomly chosen projections. as follows: iris_qda <. iris) explore(iris_qda. 2.qda(Species ~ Sepal. three groups in four dimensions. and part of the olive oils data with two groups in eight dimensions.Width. and the number of points to generate while searching for boundaries. Instead of choosing new projections randomly. This process is illustrated in ﬁgure 6. This also helps you to understand how the classiﬁer uses the diﬀerent variables. The variables in both data sets were scaled to range [0. The grand tour continuously and smoothly changes the projection plane so we see a movie of diﬀerent projections of the data.Figure 5: Two approaches to ﬁlling the space with points. Understanding the classiﬁcation boundaries will be much easier in the iris data. the original dataset. We can use manual controls to explore how the diﬀerent variables aﬀect the classiﬁcation region.Length + Sepal. the guided tour and manual controls [1.Length + Petal. iris. On the left. and then call explore with the classiﬁer function.

as shown in ﬁgure 7. First we use the grand tour to ﬁnd a promising initial view where the groups are well separated. QDA. rpart and neural network classiﬁers. arguments to determine the method used for ﬁlling the design space with points (a grid by default). 10. LDA classiﬁers are always easy to understand. 5. 12]. Then we tweak each variable individually. svm. and whether only boundary points should be returned (true by default). This results in a linear hyperplane that separates the two regions. random forests [13] and logistic regression. the package can deal with classiﬁers generated by LDA [19]. The remainder of this section demonstrates results from LDA. This makes it easy to ﬁnd a view that illustrates how the classiﬁer works even in high dimensions. Currently. The second graph shows progress after tweaking each variable once in order. Figure 7: LDA discriminant function. and the third after a further series of tweakings. QDA [19]. 6 . neural networks [19].Figure 6: Finding a revealing projection of an LDA boundary. trees [17]. SVM [7].1 Linear discriminant analysis (LDA) LDA is based on the assumption that the data from each group comes from a multivariate normal distribution with common variance-covariance matrix across all groups [9.

SVM do not natively output posterior probabilities. This also makes it easier to see these more complicated boundaries. and with non-linear boundaries. It looks like the red group is the “default”. However. all components of the quadratic function are positive or negative) but high-dimensional saddles are tricky to visualise. Figure 9 shows two views. It can readily be extended to deal with multiple groups.2 Quadratic discriminant analysis (QDA) QDA is an extension of LDA that relaxes the assumption of a shared variance-covariance matrix and gives each group its own variance matrix. 7 .3 Support vector machines (SVM) SVM is a binary classiﬁcation method that ﬁnds a hyperplane with the greatest separation between the two groups. We need several views to understand the shape of the classiﬁer. by changing the distance measure [6. the ﬁgures below display the full regions rather than the boundaries. These are easy to understand if they are convex (i.While it is easy understand. but we can see it essentially a convex quadratic around the blue group with the red and green groups on either side. not just the boundaries. This leads to quadratic boundaries between the regions. and 13 show the results of the SVM classiﬁcation with linear. Figures 11. LDA often produces sub-optimal classiﬁers. shown in ﬁgure 10. even though it contains fewer points. quadratic and polynomial boundaries respectively. but have not yet been implemented in R. A more subtle problem is produced by how the variance-covariance matrix of each group aﬀects the classiﬁcation boundary—the boundary will be too close to groups with smaller variances. Why didn’t QDA ﬁnd this boundary? These ﬁgures show all points. 12. because it is currently prohibitively expensive to ﬁnd dense boundaries in high dimensions. Techniques are available to compute them [8.e. Figure 8 shows the boundaries of the QDA of the iris data. by separating out each group sequentially. there is a nice quadratic boundary between the two groups. Figure 8: Two views illustrating how QDA separates the three groups of the iris data set The quadratic classiﬁer of the olive oils data is much harder to understand and it is very diﬃcult to ﬁnd illuminating views. 18]. 5. There is a quadratic needle wrapped around the blue group and everything outside it is classiﬁed as red. 5. Clearly it can not ﬁnd non-linear separations (as in this example). For this reason. 11. 14].

it is simply a matter of ﬁnding a projection that projects hyperplane to a line. The right view shows points that are classiﬁed into the red group. 8 . or just the boundary. These two views show good separations and together give the impression that the blue region is needle shaped. Figure 10: The left view shows a nice quadratic boundary between the two groups of points. Linear boundaries. Figure 11: SVM with linear boundaries. are always easy to understand. like those from SVM or LDA.Figure 9: The QDA classiﬁer of the olive oils data is much harder to understand as there is overlap between the groups in almost every projection. These are easy to ﬁnd whether we have points ﬁlling the region.

This classiﬁer picks out the quadratic boundary that looked so good in the QDA examples. ﬁgure 10.Figure 12: SVM with quadratic boundaries. On the left only the red region is shown. Figure 13: SVM with polynomial boundaries. 9 . and on the right both red and blue regions are shown. This helps us to see both the extent of the smaller red region and how the blue region wraps around it.

and Hadley Wickham. Obtaining calibrated probability estimates from support vector machines. Cook. Stork. and P. but these techniques have yet to bear fruit.html. tree and neural net classiﬁers. This clearly has much pedagogical promise—as well as learning the classiﬁcation algorithm. projection pursuit guided tours and manual controls. Buja. Drish. SVM. [10] R. Wiley. [2] A. Friedrich Leisch. Pattern Classiﬁcation. [7] Evgenia Dimitriadou. D. 20(3):273–297. Additional interactivity could be added to allow the investigation of changing aspects of the data set. Asimov. 2005. Grand tour and projection pursuit. Eun-Kyung Lee.5-11. These techniques allow us to work with any classiﬁer.iastate. Support-vector networks. Florham Park. and is an avenue for future research. A. Hurley. imagine being able to select a point in GGobi. projections.6 Conclusion These techniques provide a useful toolkit for interactively exploring the results of a classiﬁcation algorithm. Andreas Buja. 1997.public.A Fisher. Buja. NJ. the major limitation is the time it takes to ﬁnd clear boundaries in high dimensions. 1936. 4(3):155–172. or parameters of the algorithm. To appear. Manual controls for high-dimensional data Journal of Computational and Graphical Statistics. TU Wien. Journal of Computational and Graphical Statistics. 2001. R package version 1. New York. [6] Corinna Cortes and Vladimir Vapnik. 1985. Cook. For example. SIAM Journal of Scientiﬁc and Statistical Computing. Also see [4] D. If the classiﬁer is mathematically tractable we can extract the boundaries directly.edu/∼dicook/research/papers/manip. One way to do this is to just show the points where the algorithms diﬀer. 1995. Annals of Eugenics. Cook and A. 7:179–188.pdf. AT&T Labs. and Andreas Weingessel. remove it from the data set and watch as the classiﬁcation boundaries change. e1071: Misc Functions of the Department of Statistics (e1071). 2000. A better algorithm for boundary detection would be very useful. and C. The use of multiple measurements in taxonomic problems. but with the views linked so that you see the same projection of each classiﬁer. QDA. Cabrera. We have a discussed several boundary ﬁnding methods. Buja. 10 . 1997. The grand tour: A tool for viewing multidimensional data. Or imagining dragging a slider that represents a parameter of the algorithm and seeing how the boundaries move. Another way would be to display each classiﬁer in a separate window. [3] D. students could learn how each classiﬁer responds to diﬀerent data sets. [8] J. if the classiﬁer provides posterior probabilities we can use these to ﬁnd uncertain points which lie on boundaries. http://wwwcse. Duda. Hurley. [9] R. Technical report. Hart. We have explored methods of non-random sampling. otherwise we can treat the classiﬁer as a black box and use a k-nearest neighbours technique to remove non-boundary points. [5] Dianne Cook. D. P. 1995. Asimov. and C. Machine Learning. References [1] D. Handbook of Computational Statistics: Data Visualization. and we have demonstrated LDA. www.ucsd. J. Grand tours. David Meyer. Kurt Hornik. Dynamic projections in high-dimensional visualization: Theory and computational methods.edu/users/jdrish/svm. Another extension would be to allow the comparison of two or more classiﬁers. with higher probability of sampling near existing boundary points. 6(1):128–143. 6(4):464–480. Currently.

elsevier.uk¿. and A.com/sd/article/S0167947302002864. 2003. NY. R package version 3. P. Temple Lang. Classiﬁcation and regression by randomforest. rpart: Recursive Partitioning.. Johnson and D. Osuna. D. Applied Multivariate Statistical Analysis (3rd ed). Duncan Temple Lang. S. pages 61–74. [Jan/06] Available publicly from www. 1992. 2(3):18–22.ox. Schuurmans. R port by Brian Ripley ¡ripley@stats. E. and D. and J Platt. Springer-Verlag. Prentice-Hall. Ggobi: Evolving from xgobi into an extensible framework for interactive data visualization. D. The Nature of Statistical Learning Theory (Statistics for Engineering and Information Science). W. Venables and B. [17] Terry M Therneau and Beth Atkinson. Ripley. 2000. 2002. fourth edition. D. R News. Journal of Computational Statistics and Data Analysis. 2005. Advances in Large Margin Classiﬁers. 43:423–444.J. ISBN 0-387-95457-0. 2002.org. N. Swayne. Skolkopf. IEEE Intelligent Systems. Ggobi: software for exploratory graphical analysis of high-dimensional data. A. and Dianne Cook. [18] V. editors. Buja. [12] R.[11] M. 2001-. http://authors. Schoelkopf. [19] W. Springer. In A. Vapnik.ac. [14] John C. [16] Deborah F. Wichern. Platt. Andreas Buja. 1999. Swayne. Support vector machines. Hearst. Modern Applied Statistics with S.A. 1998. [15] Deborah F. NJ. Smola. Englewood Cliﬀs.ggobi. [13] Andy Liaw and Matthew Wiener. Cook. MIT Press. 13(4):18–28. Probabilistic outputs for support vector machines and comparison to regularized likelihood methods. New York. Bartlett. B. B. Dumais. New York. 11 .1-24.

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