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A gentle introduction to logistic regression and lasso regularisation using R

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In this day and age of artificial intelligence and deep learning, it is easy to forget that simple algorithms can work well for a surprisingly large range of practical business problems.  And the simplest place to start is with the granddaddy of data science algorithms: linear regression and its close cousin, logistic regression. Indeed, in his acclaimed MOOC and accompanying textbook, Yaser Abu-Mostafa spends a good portion of his time talking about linear methods, and with good reason too: linear methods are not only a good way to learn the key principles of machine learning, they can also be remarkably helpful in zeroing in on the most important predictors.

My main aim in this post is to provide a beginner level introduction to logistic regression using R and also introduce LASSO (Least Absolute Shrinkage and Selection Operator), a powerful feature selection technique that is very useful for regression problems. Lasso is essentially a regularization method. If you’re unfamiliar with the term, think of it as a way to reduce overfitting using less complicated functions (and if that means nothing to you, check out my prelude to machine learning).  One way to do this is to toss out less important variables, after checking that they aren’t important.  As we’ll discuss later, this can be done manually by examining p-values of coefficients and discarding those variables whose coefficients are not significant. However, this can become tedious for classification problems with many independent variables.  In such situations, lasso offers a neat way to model the dependent variable while automagically selecting significant variables by shrinking the coefficients of unimportant predictors to zero.  All this without having to mess around with p-values or obscure information criteria. How good is that?

Why not linear regression?

In linear regression one attempts to model a dependent variable (i.e. the one being predicted) using the best straight line fit to a set of predictor variables.  The best fit is usually taken to be one that minimises the root mean square error,  which is the sum of square of the differences between the actual and predicted values of the dependent variable. One can think of logistic regression as the equivalent of linear regression for a classification problem.  In what follows we’ll look at binary classification – i.e. a situation where the dependent variable takes on one of two possible values (Yes/No, True/False, 0/1 etc.).

First up, you might be wondering why one can’t use linear regression for such problems. The main reason is that classification problems are about determining class membership rather than predicting variable values, and linear regression is more naturally suited to the latter than the former. One could, in principle, use linear regression for situations where there is a natural ordering of categories like High, Medium and Low for example. However, one then has to map sub-ranges of the predicted values to categories. Moreover, since predicted values are potentially unbounded (in data as yet unseen) there remains a degree of arbitrariness associated with such a mapping.

Logistic regression sidesteps the aforementioned issues by modelling class probabilities instead.  Any input to the model yields a number lying between 0 and 1, representing the probability of class membership. One is still left with the problem of determining the threshold probability, i.e. the probability at which the category flips from one to the other.  By default this is set to p=0.5, but in reality it should be settled based on how the model will be used.  For example, for a marketing model that identifies potentially responsive customers, the threshold for a positive event might be set low (much less than 0.5) because the client does not really care about mailouts going to a non-responsive customer (the negative event). Indeed they may be more than OK with it as there’s always a chance – however small – that a non-responsive customer will actually respond.  As an opposing example, the cost of a false positive would be high in a machine learning application that grants access to sensitive information. In this case, one might want to set the threshold probability to a value closer to 1, say 0.9 or even higher. The point is, the setting an appropriate threshold probability is a business issue, not a technical one.

Logistic regression in brief

So how does logistic regression work?

For the discussion let’s assume that the outcome (predicted variable) and predictors are denoted by Y and X respectively and the two classes of interest are denoted by + and – respectively.  We wish to model the conditional probability that the outcome Y is +, given that the input variables (predictors) are X. The conditional probability is denoted by p(Y=+|X)   which we’ll abbreviate as p(X) since we know we are referring to the positive outcome Y=+.

As mentioned earlier, we are after the probability of class membership so we must ensure that the hypothesis function (a fancy word for the model) always lies between 0 and 1. The function assumed in logistic regression is:

p(X) = \dfrac{\exp^{\beta_0+\beta_1 X}}{1+\exp^{\beta_0 + \beta_1 X}} .....(1)

You can verify that p(X) does indeed lie between 0 and  1 as X varies from -\infty to \infty.  Typically, however, the values of X that make sense are bounded as shown in the example (stolen from Wikipedia) shown in Figure 1. The figure also illustrates the typical S-shaped  curve characteristic of logistic regression.

Figure 1: Logistic function

As an aside, you might be wondering where the name logistic comes from. An equivalent way of expressing the above equation is:

\log(\dfrac{p(X)}{1-p(X)}) = \beta_0+\beta_1 X .....(2)

The quantity on the left is the logarithm of the odds. So, the model is a linear regression of the log-odds, sometimes called logit, and hence the name logistic.

The problem is to find the values of \beta_0  and \beta_1 that results in a p(X) that most accurately classifies all the observed data points – that is, those that belong to the positive class have a probability as close as possible to 1 and those that belong to the negative class have a probability as close as possible to 0. One way to frame this problem is to say that we wish to maximise the product of these probabilities, often referred to as the likelihood:

\displaystyle\log ( {\prod_{i:Y_i=+} p(X_{i}) \prod_{j:Y_j=-}(1-p(X_{j}))})

Where \prod represents the products over i and j, which run over the +ve and –ve classed points respectively. This approach, called maximum likelihood estimation, is quite common in many machine learning settings, especially those involving probabilities.

It should be noted that in practice one works with the log likelihood because it is easier to work with mathematically. Moreover, one minimises the negative  log likelihood which, of course, is the same as maximising the log likelihood.  The quantity one minimises is thus:

L = - \displaystyle\log ( {\prod_{i:Y_i=+} p(X_{i}) \prod_{j:Y_j=-}(1-p(X_{j}))}).....(3)

However, these are technical details that I mention only for completeness. As you will see next, they have little bearing on the practical use of logistic regression.

Logistic regression in R – an example

In this example, we’ll use the logistic regression option implemented within the glm function that comes with the base R installation. This function fits a class of models collectively known as generalized linear models. We’ll apply the function to the Pima Indian Diabetes dataset that comes with the mlbench package. The code is quite straightforward – particularly if you’ve read earlier articles in my “gentle introduction” series – so I’ll just list the code below  noting that the logistic regression option is invoked by setting family=”binomial”  in the glm function call.

Here we go:

#set working directory if needed (modify path as needed)
#setwd(“C:/Users/Kailash/Documents/logistic”)
#load required library
library(mlbench)
#load Pima Indian Diabetes dataset
data(“PimaIndiansDiabetes”)
#set seed to ensure reproducible results
set.seed(42)
#split into training and test sets
PimaIndiansDiabetes[,”train”] <- ifelse(runif(nrow(PimaIndiansDiabetes))<0.8,1,0)
#separate training and test sets
trainset <- PimaIndiansDiabetes[PimaIndiansDiabetes$train==1,]
testset <- PimaIndiansDiabetes[PimaIndiansDiabetes$train==0,]
#get column index of train flag
trainColNum <- grep(“train”,names(trainset))
#remove train flag column from train and test sets
trainset <- trainset[,-trainColNum]
testset <- testset[,-trainColNum]
#get column index of predicted variable in dataset
typeColNum <- grep(“diabetes”,names(PimaIndiansDiabetes))
#build model
glm_model <- glm(diabetes~.,data = trainset, family = binomial)
summary(glm_model)
Call:
glm(formula = diabetes ~ ., family = binomial, data = trainset)
<<output edited>>
Coefficients:
            Estimate  Std. Error z value Pr(>|z|)
(Intercept)-8.1485021 0.7835869 -10.399  < 2e-16 ***
pregnant    0.1200493 0.0355617   3.376  0.000736 ***
glucose     0.0348440 0.0040744   8.552  < 2e-16 ***
pressure   -0.0118977 0.0057685  -2.063  0.039158 *
triceps     0.0053380 0.0076523   0.698  0.485449
insulin    -0.0010892 0.0009789  -1.113  0.265872
mass        0.0775352 0.0161255   4.808  1.52e-06 ***
pedigree    1.2143139 0.3368454   3.605  0.000312 ***
age         0.0117270 0.0103418   1.134  0.256816
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#predict probabilities on testset
#type=”response” gives probabilities, type=”class” gives class
glm_prob <- predict.glm(glm_model,testset[,-typeColNum],type=”response”)
#which classes do these probabilities refer to? What are 1 and 0?
contrasts(PimaIndiansDiabetes$diabetes)
    pos
neg 0
pos 1
#make predictions
##…first create vector to hold predictions (we know 0 refers to neg now)
glm_predict <- rep(“neg”,nrow(testset))
glm_predict[glm_prob>.5] <- “pos”
#confusion matrix
table(pred=glm_predict,true=testset$diabetes)
glm_predict  neg pos
        neg    90 22
        pos     8 33
#accuracy
mean(glm_predict==testset$diabetes)
[1] 0.8039216

 

Although this seems pretty good, we aren’t quite done because there is an issue that is lurking under the hood. To see this, let’s examine the information output from the model summary, in particular the coefficient estimates (i.e. estimates for \beta) and their significance. Here’s a summary of the information contained in the table:

  • Column 2 in the table lists coefficient estimates.
  • Column 3 list s the standard error of the estimates (the larger the standard error, the less confident we are about the estimate)
  • Column 4 the z statistic (which is the coefficient estimate (column 2) divided by the standard error of the estimate (column 3)) and
  • The last column (Pr(>|z|) lists the p-value, which is the probability of getting the listed estimate assuming the predictor has no effect. In essence, the smaller the p-value, the more significant the estimate is likely to be.

From the table we can conclude that only 4 predictors are significant – pregnant, glucose, mass and pedigree (and possibly a fifth – pressure). The other variables have little predictive power and worse, may contribute to overfitting.  They should, therefore, be eliminated and we’ll do that in a minute. However, there’s an important point to note before we do so…

In this case we have only 9 variables, so are able to identify the significant ones by a manual inspection of p-values.  As you can well imagine, such a process will quickly become tedious as the number of predictors increases. Wouldn’t it be be nice if there were an algorithm that could somehow automatically shrink the coefficients of these variables or (better!) set them to zero altogether?  It turns out that this is precisely what  lasso and its close cousin, ridge regression, do.

Ridge and Lasso

Recall that the values of the logistic regression coefficients \beta_0  and \beta_1 are found by minimising the negative log likelihood described in equation (3).  Ridge and lasso regularization work by adding a penalty term to the log likelihood function.  In the case of ridge regression, the penalty term is \beta_1^2 and in the case of lasso, it is |\beta_1| (Remember, \beta_1  is a vector, with as many components as there are predictors).  The quantity to be minimised in the two cases is thus:

L +\lambda \sum \beta_1^2.....(4) – for ridge regression,

and

L +\lambda \sum |\beta_1|.....(5) – for lasso regression.

Where \lambda is a free parameter which is usually selected in such a way that the resulting model minimises the out of sample error. Typically, the optimal value of \lambda is found using grid search with cross-validation, a process akin to the one described in my discussion on cost-complexity parameter  estimation in decision trees. Most canned algorithms provide methods to do this; the one we’ll use in the next section is no exception.

In the case of ridge regression, the effect of the penalty term is to shrink the coefficients that contribute most to the error. Put another way, it reduces the magnitude of the coefficients that contribute to increasing L.  In contrast, in  the case of lasso regression, the effect of the penalty term is to set the these coefficients exactly to zero! This is cool because what it mean that lasso regression works like a feature selector that picks out the most important coefficients, i.e. those that are most predictive (and have the lowest p-values).

Let’s illustrate this through an example. We’ll use the glmnet package which implements a combined version of ridge and lasso (called elastic net). Instead of minimising (4) or (5) above, glmnet minimises:

L +\lambda[ (1-\alpha)\sum [\beta_1^2 + \alpha\sum|\beta_1|]....(6)

where \alpha controls the “mix” of ridge and lasso regularisation, with \alpha=0 being “pure” ridge and  \alpha=1 being “pure” lasso.

Lasso regularisation using glmnet

Let’s reanalyse the Pima Indian Diabetes dataset using glmnet with \alpha=1 (pure lasso). Before diving into code, it is worth noting that glmnet:

  • does not have a formula interface, so one has to input the predictors as a matrix and the class labels as a vector.
  • does not accept categorical predictors, so one has to convert these to numeric values before passing them to glmnet.

The glmnet function model.matrix creates the matrix and also converts categorical predictors to appropriate dummy variables.

Another important point to note is that we’ll use the function cv.glmnet, which automatically performs a grid search to find the optimal value of \lambda.

OK, enough said, here we go:

#load required library
library(glmnet)
#convert training data to matrix format
x <- model.matrix(diabetes~.,trainset)
#convert class to numerical variable
y <- ifelse(trainset$diabetes==”pos”,1,0)
#perform grid search to find optimal value of lambda
#family= binomial => logistic regression, alpha=1 => lasso
# check docs to explore other type.measure options
cv.out <- cv.glmnet(x,y,alpha=1,family=”binomial”,type.measure = “mse” )
#plot result
plot(cv.out)

 

The plot is shown in Figure 2 below:

Figure 2: Error as a function of lambda (select lambda that minimises error)

The plot shows that the log of the optimal value of lambda (i.e. the one that minimises the root mean square error) is approximately -5. The exact value can be viewed by examining the variable lambda_min in the code below. In general though, the objective of regularisation is to balance accuracy and simplicity. In the present context, this means a model with the smallest number of coefficients that also gives a good accuracy.  To this end, the cv.glmnet function  finds the value of lambda that gives the simplest model but also lies within one standard error of the optimal value of lambda. This value of lambda (lambda.1se) is what we’ll use in the rest of the computation. Interested readers should have a look at this article for more on lambda.1se vs lambda.min.

#min value of lambda
lambda_min <- cv.out$lambda.min
#best value of lambda
lambda_1se <- cv.out$lambda.1se
#regression coefficients
coef(cv.out,s=lambda_1se)
10 x 1 sparse Matrix of class “dgCMatrix”
                      1
(Intercept) -4.61706681
(Intercept)  .
pregnant     0.03077434
glucose      0.02314107
pressure     .
triceps      .
insulin      .
mass         0.02779252
pedigree     0.20999511
age          .

 

The output shows that only those variables that we had determined to be significant on the basis of p-values have non-zero coefficients. The coefficients of all other variables have been set to zero by the algorithm! Lasso has reduced the complexity of the fitting function massively…and you are no doubt wondering what effect this  has on accuracy. Let’s see by running the model against our test data:

 

#get test data
x_test <- model.matrix(diabetes~.,testset)
#predict class, type=”class”
lasso_prob <- predict(cv.out,newx = x_test,s=lambda_1se,type=”response”)
#translate probabilities to predictions
lasso_predict <- rep(“neg”,nrow(testset))
lasso_predict[lasso_prob>.5] <- “pos”
#confusion matrix
table(pred=lasso_predict,true=testset$diabetes)
pred  neg pos
   neg 94 28
  pos  4 27
#accuracy
mean(lasso_predict==testset$diabetes)
[1] 0.7908497

 

Which is a bit less than what we got with the more complex model. So, we get  a similar out-of-sample accuracy as we did before, and we do so using a way simpler function (4 non-zero coefficients) than the original one (9  nonzero coefficients). What this means is that the simpler function does at least as good a job fitting the signal in the data as the more complicated one.  The bias-variance tradeoff tells us that the simpler function should be preferred because it is less likely to overfit the training data.

Paraphrasing William of Ockhamall other things being equal, a simple hypothesis should be preferred over a complex one.

Wrapping up

In this post I have tried to provide a detailed introduction to logistic regression, one of the simplest (and oldest) classification techniques in the machine learning practitioners arsenal. Despite it’s simplicity (or I should say, because of it!) logistic regression works well for many business applications which often have a simple decision boundary. Moreover, because of its simplicity it is less prone to overfitting than flexible methods such as decision trees. Further, as we have shown, variables that contribute to overfitting can be eliminated using lasso (or ridge) regularisation, without compromising out-of-sample accuracy. Given these advantages and its inherent simplicity, it isn’t surprising that logistic regression remains a workhorse for data scientists.

Written by K

July 11, 2017 at 10:00 pm

The improbability of success

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Anyone who has tidied up after a toddler intuitively understands that making a mess is far easier than creating order. The fundamental reason for this is that the number of messy states in the universe (or a toddler’s room) far outnumbers the ordered ones.  As this point might not be obvious, I’ll demonstrate it via a simple thought experiment involving marbles:

Throw three marbles onto a flat surface.  When the marbles come to rest, you are most likely to end up with a random configuration  as in Figure 1.

Figure 1: A random configuration of 3 marbles

Indeed, you’d be extremely surprised if the three ended up being collinear as in Figure 2.   Note that Figure 2 is just one example of many collinear possibilities, but the point I’m making is that if the marbles are thrown randomly, they are more likely to end up in a random state than a lined-up one.

Figure 2: an unlikely (ordered) configuration

This raises a couple of questions:

Question: On what basis can one claim that the collinear configuration is tidier or more ordered than the non-collinear one?

Naive answer:  It looks more ordered. Yes, tidiness is in the eye of the beholder so it is necessarily subjective. However, I’ll wager that if one took a poll, an overwhelming number of people would say that the configuration in Figure 2 is more ordered than the one in Figure 1.

More sophisticated answer : The “state” of collinear marbles can be described using 2 parameters, the slope and intercept of the straight line that three marbles lie on (in any coordinate system) whereas the description of the nonlinear state requires 3 parameters. The first state is tidier because it requires fewer parameters.  Another way to think about is that the line can be described by two marbles; the third one is redundant as far as the description of the state is concerned.

Question: Why is a tidier configuration less likely than a messy one?

Answer:  May be you see this intuitively and need no proof, but here’s one just in case. Imagine rolling the three marbles one after the other. The first two, regardless of where they end up, will necessarily lie along a line (two points lie on the straight line joining them). Now, I think it is easy to see that if we throw the third marble randomly, it is highly unlikely end up on that line. Indeed, for the third marble to end up exactly on the same straight line requires a coincidence of near cosmic proportions.

I know, I know, this is not a proof, but I trust it makes the point.

Now, although it is near impossible to get to a collinear end state via random throws, it is possible to approximate it by changing the way we throw the marbles. Here’s how:

  1. Throw the marbles consecutively rather than in one go.
  2. When throwing the third marble, adjust its initial speed and direction in a way that takes into account the positions of the two marbles that are already on the surface. Remember these two already define a straight line.

The third throw is no longer random because it is designed to maximise the chance that the last marble will get as close as possible to the straight line defined by the first two. Done right, you’ll end up with something closer to the configuration in Figure 3 rather than the one in Figure 2.

Figure 3: an “approximately ordered” state

Now you’re probably wondering what this has to do with success. I’ll make the connection via an example that will be familiar to many readers of this blog: an organisation’s strategy. However, as I will reiterate later, the arguments I present are very general and can be applied to just about any initiative or situation.

Typically, a strategy sets out goals for an organisation and a plan to achieve them in a specified timeframe. The goals define a number of desirable outcomes, or states which, by design, are constrained to belong to a (very) small subset of all possible states the organisation can end up in.  In direct analogy with the simple model discussed above it is clear that, left to its own devices, the organisation is more likely to end up in one of the much overwhelmingly larger number of “failed states” than one of the successful ones.  Notwithstanding the popular quote about there being many roads to success, in reality there are a great many more roads to failure.

Of course, that’s precisely why organisations are never “left to their own devices.” Indeed, a strategic plan specifies actions that are intended to make a successful state more likely than an unsuccessful one. However, no plan can guarantee success; it can, at best, make it more likely. As in the marble game, success is ultimately a matter of chance, even when we take actions to make it more likely.

If we accept this, the key question becomes: how can one design a strategy that improves the odds of success?  The marble analogy suggests a way to do this is to:

  1. Define success in terms of an end state that is a natural extension of your current state.
  2. Devise a plan to (approximately) achieve that end state. Such a plan will necessarily build on the current state rather than change it wholesale. Successful change is an evolutionary process rather than a revolutionary one.

My contention is that these points are often ignored by management strategists. More often than not, they will define an end state based on a textbook idealisation, consulting model or (horror!) best practice. The marble analogy shows why copying others is unlikely to succeed.

Figure 4 shows a variant of the marble game in which we have two sets of marbles (or organisations!), one blue, as before, and the other red.


Figure 4: Two distinct configurations of marbles (or organisations)

Now, it is considerably harder to align an additional marble with both sets of marbles than the blue one alone. Here’s why…

To align with both sets, the new marble has to end up close to the point that lies at the intersection of the blue and red lines in Figure 5. In contrast, to align with the blue set alone, all that’s needed is for it to get close to any point on the blue line.

QED!

Figure 5: Why copying others is not a good idea (see text for explanation)

Finally, on a broader note, it should be clear that the arguments made above go beyond organisational strategies. They apply to pretty much any planned action, whether at work or in one’s personal life.

So, to sum up: when developing an organisational (or personal) strategy, the first step is to understand where you are and then identify the minimal actions you need to take in order to get to an “improved” state that is consistent with  your current one. Yes, this is akin to the incremental and evolutionary approach that Agilistas and Leaners have been banging on about for years. However, their prescriptions focus on specific areas: software development and process improvement.  My point is that the basic principles are way broader because they are a direct consequence of a fundamental fact regarding the relative likelihood of order and disorder in a toddler’s room, an organisation, or even the universe at large.

Written by K

April 4, 2017 at 9:16 pm

A gentle introduction to Naïve Bayes classification using R

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Preamble

One of the key problems of predictive analytics is to classify entities or events based on a knowledge of their attributes.  An example: one might want to classify customers into two categories, say, ‘High Value’ or ‘Low Value,’ based on a knowledge of their buying patterns.  Another example: to figure out the party allegiances of  representatives based on their voting records.  And yet another:  to predict the species a particular plant or animal specimen based on a list of its characteristics. Incidentally, if you haven’t been there already, it is worth having a look at Kaggle to get an idea of some of the real world classification problems that people tackle using techniques of predictive analytics.

Given the importance of classification-related problems, it is no surprise that analytics tools offer a range of options. My favourite (free!) tool, R, is no exception: it has a plethora of state of the art packages designed to handle a wide range of problems. One of the problems with this diversity of choice is that it is often confusing for beginners to figure out which one to use in a particular situation. Over the next several months, I intend to write up tutorial articles covering many of the common algorithms, with a particular focus on their strengths and weaknesses; explaining where they work well and where they don’t. I’ll kick-off this undertaking with a simple yet surprisingly effective algorithm – the Naïve Bayes classifier.

Just enough theory

I’m going to assume you have R and RStudio installed on your computer. If you need help with this, please follow the instructions here.

To introduce the Naive Bayes algorithm, I will use the HouseVotes84 dataset, which contains US congressional voting records for 1984. The data set is in the mlbench package which is not part of the base R installation. You will therefore need to install it if you don’t have it already.  Package installation is a breeze in RStudio – just go to Tools > Install Packages and follow the prompts.

The HouseVotes84 dataset describes how 435 representatives voted – yes (y), no (n) or unknown (NA) – on 16 key issues presented to Congress.  The dataset also provides the party affiliation of each representative – democrat or republican.

Let’s begin by exploring the dataset. To do this, we load mlbench, fetch the dataset and get some summary stats on it. (Note: a complete listing of the code in this article can be found here)

#load mlbench library
library(mlbench)
#set working directory if needed (modify path as needed)
setwd(“C:/Users/Kailash/Documents/NaiveBayes”)
#load HouseVotes84 dataset
data(“HouseVotes84”)

It is good to begin by exploring the data visually.  To this end, let’s do some bar plots using the basic graphic capabilities of R:

#barplots for specific issue
plot(as.factor(HouseVotes84[,2]))
title(main=”Votes cast for issue”, xlab=”vote”, ylab=”# reps”)
#by party
plot(as.factor(HouseVotes84[HouseVotes84$Class==’republican’,2]))
title(main=”Republican votes cast for issue 1″, xlab=”vote”, ylab=”# reps”)
plot(as.factor(HouseVotes84[HouseVotes84$Class==’democrat’,2]))
title(main=”Democrat votes cast for issue 1″, xlab=”vote”, ylab=”# reps”)

The plots are shown in Figures 1 through 3.

Fig 1: y and n votes for issue 1

Fig 1: y and n votes for issue 1

Fig 2: Republican votes for issue 1.

Fig 2: Republican votes for issue 1.

Fig 3: Democrat votes for issue 1.

Fig 3: Democrat votes for issue 1.

Among other things, such plots give us a feel for the probabilities associated with how representatives from parties tend to vote on specific issues.

The classification problem at hand is to figure out the party affiliation from a knowledge of voting patterns. For simplicity let us assume that there are only 3 issues voted on instead of the 16 in the actual dataset. In concrete terms we wish to answer the question, “what is the probability that a representative is, say, a democrat (D) given that he or she has voted, say,  (v1 = y, v2=n,v3 = y) on the three issues?” To keep things simple I’m assuming there are no NA values.

In the notation of conditional probability this can be written as,

P(D|v1=y, v2=n,v3=y)

(Note:  If you need a refresher on conditional probability, check out this post for a simple explanation.)

By Bayes theorem, which I’ve explained at length in this post, this can be recast as,

P(D|v1=y, v2=n,v3=y) = \displaystyle \frac{p(D) p(v1=y, v2=n,v3=y|D)}{p(v1=y, v2=n,v3=y)}......(1)

We’re interested only in relative probabilities of the representative being a democrat or republican because the predicted party affiliation depends only on which of the two probabilities is larger (the actual value of the probability is not important). This being the case, we can factor out any terms that are constant.  As it happens, the denominator of the above equation – the probability of a particular voting pattern – is a constant because it depends on the total number of representatives (from both parties)  who voted a particular way.

Now, using the chain rule of conditional probability, we can rewrite the numerator as:

p(D) p(v1=y, v2=n,v3=y|D)

= p(D)p(v1=y|D) p(v2=n,v3=y|D,v1=y)

Basically, the second term on the left hand side, p(v1=y, v2=n,v3=y|D), is the probability of getting a particular voting pattern  (y,n,y) assuming the rep is a Democrat (D). The definition of conditional probability allows us to rewrite this as the probability of getting a n vote for issue v2 and a y vote for issue v3 given that the rep is a Democrat who has voted y on issue v1. Again, this is simply a consequence of the definition of conditional probability.

Another application of the chain rule gives:

p(D) p(v1=y, v2=n,v3=y|D)

= p(D)p(v1=y|d) p(v2=n|D,v1=y) p(v3=y|D,v1=y,v2=n)

Where we have now factored out the n vote on the second issue.

The key assumption of Naïve Bayes is that the conditional probability of each feature given the class is independent of all other features. In mathematical terms this means that,

p(v2=n|D,v1=y) = p(v2=n|D)

and

p(v3=y|D,v1=y,v2=n) = p(v3=y|D)

The quantity of interest, the numerator of equation (1) can then be written as:

p(D) p(v1=y, v2=n,v3=y|D)

= p(D)p(v1=y|D)p(v2=n|D)p(v3=y|D).......(2)

The assumption of independent conditional probabilities is a drastic one.  What it is saying is that the features are completely independent of each other. This is clearly not the case in the situation above: how representatives vote on a particular issue is coloured by their beliefs and values. For example, the conditional probability of voting patterns  on socially progressive issues are definitely not independent of each other. However, as we shall see  in the next section, the Naïve Bayes assumption works well for this problem as it does in many other situations where we know upfront that it is grossly incorrect.

Another good example of the unreasonable efficacy of Naive Bayes is in spam filtering.  In the case of spam, the features are individual words in an email.  It is clear that certain word combinations tend to show up consistently in spam – for example, “online”, “meds”, “Viagra” and “pharmacy.” In other words, we know upfront that their occurrences are definitely not independent of each other. Nevertheless, Naïve Bayes based spam detectors which assume mutual independence of features do remarkably well in distinguishing spam from ham.

Why is this so?

To explain why, I return to a point I mentioned earlier: to figure out  the affiliation associated with a particular voting pattern (say, v1=y, v2=n,v3=y) one only needs to know which of the two probabilities p(R| v1=y, v2=n,v3=y) and p(D| V1=y, V2=n, V3=y) is greater than the other.  That is, the values of these probabilities are not important in determining the party affiliations.

This hints as to why the independence assumption might not be so quite so idiotic. Since the prediction depends only the on the maximum, the algorithm will get it right even if there are dependencies between feature providing the dependencies do not change which class has the maximum probability (once again, note that only the maximal class is important here, not  the value of the maximum).

Yet another reason for the surprising success of Naïve Bayes is that dependencies often cancel out across a large set of features. But, of course, there is no guarantee that this will always happen.

In general, Naïve Bayes algorithms work better for problems in which the dependent (predicted) variable is discrete, even when there are dependencies between features (spam detection is a good example).  They work less well for regression problems – i.e those in  which predicted variables are continuous.

I hope the above has given you an intuitive feel for how Naïve Bayes algorithms work. I don’t know about you, but my head’s definitely spinning after writing out all that mathematical notation.

It’s time to clear our heads by doing some computation.

Naïve Bayes in action

There are a couple of well-known implementations of Naïve Bayes in R. One of them is the naiveBayes method in the e1071 package and the other is NaiveBayes method in  the klaR package.  I’ll use the former for no other reason than it seems to be more popular. That said, I have used the latter too and can confirm that it works just as well.

We’ve already loaded and explored the HouseVotes84 dataset. One of the things you may have noticed when summarising the data is  that there are a fair number of NA values. Naïve Bayes algorithms typically handle NA values either by ignoring records that contain any NA values or by ignoring just the NA values. These choices are indicated by the value of the variable na.action in the naiveBayes algorithm, which is set to na.omit (to ignore the record) or na.pass (to ignore the value).

Just for fun, we’ll take a different approach. We’ll impute NA values for a given issue and party by looking at how other representatives from the same party voted on the issue. This is very much in keeping with the Bayesian spirit: we infer unknowns based on a justifiable belief – that is, belief based on the evidence.

To do this I write two functions: one to  compute the number of NA values for a given issue (vote) and class (party affiliation), and the other to calculate the fraction of yes votes for a given issue (column) and class (party affiliation).

#Functions needed for imputation
#function to return number of NAs by vote and class (democrat or republican)
na_by_col_class <- function (col,cls){return(sum(is.na(HouseVotes84[,col]) & HouseVotes84$Class==cls))}
#function to compute the conditional probability that a member of a party will cast a ‘yes’ vote for
#a particular issue. The probability is based on all members of the party who #actually cast a vote on the issue (ignores NAs).
p_y_col_class <- function(col,cls){
sum_y<-sum(HouseVotes84[,col]==’y’ & HouseVotes84$Class==cls,na.rm = TRUE)
sum_n<-sum(HouseVotes84[,col]==’n’ & HouseVotes84$Class==cls,na.rm = TRUE)
return(sum_y/(sum_y+sum_n))}
#Check that functions work!
> p_y_col_class(2,’democrat’)
[1] 0.6046512
> p_y_col_class(2,’republican’)
[1] 0.1878788
> na_by_col_class(2,’democrat’)
[1] 9
> na_by_col_class(2,’republican’)
> [1] 3

Before proceeding,  you might want to go back to the data and convince yourself that these values are sensible.

We can now impute the NA values based on the above. We do this by randomly assigning values ( y or n) to NAs, based on the proportion of members of a party who have voted y or n. In practice, we do this by invoking the uniform distribution and setting an NA value to y if the random number returned is less than the probability of a yes vote and to n otherwise. This is not as complicated as it sounds; you should be able to figure the logic out from the code below.

#impute missing values.
for (i in 2:ncol(HouseVotes84)) {
if(sum(is.na(HouseVotes84[,i])>0)) {
c1 <- which(is.na(HouseVotes84[,i])& HouseVotes84$Class==’democrat’,arr.ind = TRUE)
c2 <- which(is.na(HouseVotes84[,i])& HouseVotes84$Class==’republican’,arr.ind = TRUE)
HouseVotes84[c1,i] <-
ifelse(runif(na_by_col_class(i,’democrat’))<p_y_col_class(i,’democrat’),’y’,’n’)
HouseVotes84[c2,i] <-
ifelse(runif(na_by_col_class(i,’republican’))<p_y_col_class(i,’republican’),’y’,’n’)}
}

Note that the which function filters  indices by the criteria specified in the arguments and ifelse is a vectorised conditional function which enables us to apply logical criteria to multiple elements of a vector.

At this point it is a good idea to check that the NAs in each column have been set according to the voting patterns of non-NAs for a given party. You can use the p_y_col_class() function to check that the new probabilities are close to the old ones. You might want to do this before you proceed any further.

The next step is to divide the available data into training and test datasets. The former will be used to train the algorithm and produce a predictive model. The effectiveness of the model will then be tested using the test dataset. There is a great deal of science and art behind the creation of training and testing datasets. An important consideration is that both sets must contain records that are representative of the entire dataset. This can be difficult to do, especially when data is scarce and there are predictors that do not vary too much…or vary wildly for that matter. On the other hand, problems can also arise when there are redundant predictors. Indeed, the much of the art of successful prediction lies in figuring out which predictors are likely to lead to better predictions, an area known as feature selection. However, that’s a topic for another time. Our current dataset does not suffer from any of these complications so we’ll simply divide the it in an 80/20 proportion, assigning the larger number of records to the training set.

#divide into test and training sets
#create new col “train” and assign 1 or 0 in 80/20 proportion via random uniform dist
HouseVotes84[,”train”] <- ifelse(runif(nrow(HouseVotes84))<0.80,1,0)
#get col number of train / test indicator column (needed later)
trainColNum <- grep(“train”,names(HouseVotes84))
#separate training and test sets and remove training column before modeling
trainHouseVotes84 <- HouseVotes84[HouseVotes84$train==1,-trainColNum]
testHouseVotes84 <- HouseVotes84[HouseVotes84$train==0,-trainColNum]

Now we’re finally good to build our Naive Bayes model (machine learning folks call this model training rather than model building – and I have to admit, it does sound a lot cooler).

The code to train the model is anticlimactically simple:

#load e1071 library and invoke naiveBayes method
library(e1071)
nb_model <- naiveBayes(Class~.,data = trainHouseVotes84)

Here we’ve invokedthe naiveBayes method from the e1071 package. The first argument uses R’s formula notation.In this notation, the dependent variable (to be predicted) appears on the left hand side of the ~ and the independent variables (predictors or features) are on the right hand side. The dot (.) is simply shorthand for “all variable other than the dependent one.” The second argument is the dataframe that contains the training data. Check out the documentation for the other arguments of naiveBayes; it will take me too far afield to cover them here. Incidentally, you can take a look at the model using the summary() or str() functions, or even just entering the model name in the R console:

nb_model
summary(nb_model)
str(nb_model)

Note that I’ve suppressed the output above.

Now that we have a model, we can do some predicting. We do this by feeding our test data into our model and comparing the predicted party affiliations with the known ones. The latter is done via the wonderfully named confusion matrix – a table in which true and predicted values for each of the predicted classes are displayed in a matrix format. This again is just a couple of lines of code:

#…and the moment of reckoning
nb_test_predict <- predict(nb_model,testHouseVotes84[,-1])
#confusion matrix
table(pred=nb_test_predict,true=testHouseVotes84$Class)
pred true democrat republican
democrat 38 3
republican 5 22

The numbers you get will be different because your training/test sets are almost certainly different from mine.

In the confusion matrix (as defined above), the true values are in columns and the predicted values in rows. So, the algorithm has correctly classified 38 out of 43 (i.e. 38+5) Democrats and 22 out of 25 Republicans (i.e. 22+3). That’s pretty decent. However, we need to keep in mind that this could well be quirk of the choice of dataset. To address this, we should get a numerical measure of the efficacy of the algorithm and for different training and testing datasets. A simple measure of efficacy would be the fraction of predictions that the algorithm gets right. For the training/testing set above, this is simply 60/68 (see the confusion matrix above). The simplest way to calculate this in R is:

#fraction of correct predictions
mean(nb_test_predict==testHouseVotes84$Class)
[1] 0.8823529

A natural question to ask at this point is: how good is this prediction. This question cannot be answered with only a single run of the model; we need to do many runs and look at the spread of the results. To do this, we’ll create a function which takes the number of times the model should be run and the training fraction as inputs and spits out a vector containing the proportion of correct predictions for each run. Here’s the function

#function to create, run and record model results
nb_multiple_runs <- function(train_fraction,n){
fraction_correct <- rep(NA,n)
for (i in 1:n){
HouseVotes84[,”train”] <- ifelse(runif(nrow(HouseVotes84))<train_fraction,1,0)
trainColNum <- grep(“train”,names(HouseVotes84))
trainHouseVotes84 <- HouseVotes84[HouseVotes84$train==1,-trainColNum]
testHouseVotes84 <- HouseVotes84[HouseVotes84$train==0,-trainColNum]
nb_model <- naiveBayes(Class~.,data = trainHouseVotes84)
nb_test_predict <- predict(nb_model,testHouseVotes84[,-1])
fraction_correct[i] <- mean(nb_test_predict==testHouseVotes84$Class)
}
return(fraction_correct)
}

I’ve not commented the above code as it is essentially a repeat of the steps described earlier. Also, note that I have not made any effort to make the code generic or efficient.

Let’s do 20 runs with the same training fraction (0.8) as before:

#20 runs, 80% of data randomly selected for training set in each run
fraction_correct_predictions <- nb_multiple_runs(0.8,20)
fraction_correct_predictions
[1] 0.9417476 0.9036145 0.9294118 0.9302326 0.9213483 0.9404762 0.8777778 0.9102564
[9] 0.9102564 0.9080460 0.9139785 0.9200000 0.9090909 0.9239130 0.9605263 0.9333333
[17] 0.9052632 0.8977273 0.9642857 0.8518519
#summary of results
summary(fraction_correct_predictions)
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.8519 0.9074 0.9170 0.9177 0.9310 0.9643
#standard deviation
sd(fraction_correct_predictions)
[1] 0.02582419

We see that the outcome of the runs are quite close together, in the 0.85 to 0.95 range with a standard deviation of 0.025. This tells us that Naive Bayes does a pretty decent job with this data.

Wrapping up

I originally intended to cover a few more case studies in this post, a couple of which highlight the shortcomings of the Naive Bayes algorithm. However, I realize that doing so would make this post unreasonably long, so I’ll stop here with a few closing remarks, and a promise to write up the rest of the story in a subsequent post.

To sum up: I have illustrated the use of a popular Naive Bayes implementation in R and attempted to convey an intuition for how the algorithm works.  As we have seen, the algorithm works quite well in the example case, despite the violation of the assumption of independent conditional probabilities.

The reason for the unreasonable effectiveness of the algorithm is two-fold. Firstly, the algorithm picks the predicted class based on the largest predicted probability, so ordering is more important than the actual value of the probability. Secondly, in many cases, a bias one way for a particular vote may well be counteracted by a bias the other way for another vote. That is, biases tend to cancel out, particularly if there are a large number of features.

That said, there are many cases in which the algorithm fails miserably – and we’ll look at some of these in a future post.  However, despite its well known shortcomings, Naive Bayes is often the first port of call in prediction problems simply because it is easy to set up and is fast compared to many of the iterative algorithms we will explore later in this series of articles.

Endnote

Thanks for reading! If you liked this piece, you might enjoy the other articles in my “Gentle introduction to analytics using R” series. Here are the links:

A gentle introduction to text mining using R

A gentle introduction to cluster analysis using R

A gentle introduction to topic modeling using R

Written by K

November 6, 2015 at 7:33 am

Three types of uncertainty you (probably) overlook

with 5 comments

Introduction – uncertainty and decision-making

Managing uncertainty deciding what to do in the absence of reliable information – is a significant part of project management and many other managerial roles. When put this way, it is clear that managing uncertainty is primarily a decision-making problem. Indeed, as I will discuss shortly, the main difficulties associated with decision-making are related to specific types of uncertainties that we tend to overlook.

Let’s begin by looking at the standard approach to decision-making, which goes as follows:

  1. Define the decision problem.
  2. Identify options.
  3. Develop criteria for rating options.
  4. Evaluate options against criteria.
  5. Select the top rated option.

As I have pointed out in this post, the above process is too simplistic for some of the complex, multifaceted decisions that we face in life and at work (switching jobs, buying a house or starting a business venture, for example). In such cases:

  1. It may be difficult to identify all options.
  2. It is often impossible to rate options meaningfully because of information asymmetry – we know more about some options than others. For example, when choosing whether or not to switch jobs, we know more about our current situation than the new one.
  3. Even when ratings are possible, different people will rate options differently – i.e. different people invariably have different preferences for a given outcome. This makes it difficult to reach a consensus.

Regular readers of this blog will know that the points listed above are characteristics of wicked problems.  It is fair to say that in recent years, a general awareness of the ubiquity of wicked problems has led to an appreciation of the limits of classical decision theory. (That said,  it should be noted that academics have been aware of this for a long time: Horst Rittel’s classic paper on the dilemmas of planning, written in 1973, is a good example. And there are many others that predate it.)

In this post  I look into some hard-to-tackle aspects of uncertainty by focusing on the aforementioned shortcomings of classical decision theory. My discussion draws on a paper by Richard Bradley and Mareile Drechsler.

This article is organised as follows: I first present an overview of the standard approach to dealing with uncertainty and discuss its limitations. Following this, I elaborate on three types of uncertainty that are discussed in the paper.

Background – the standard view of uncertainty

The standard approach to tackling uncertainty was  articulated by Leonard Savage in his classic text, Foundations of Statistics. Savage’s approach can be summarized as follows:

  1. Figure out all possible states (outcomes)
  2. Enumerate actions that are possible
  3. Figure out the consequences of actions for all possible states.
  4. Attach a value (aka preference) to each consequence
  5. Select the course of action that maximizes value (based on an appropriately defined measure, making sure to factor in the likelihood of achieving the desired consequence)

(Note the close parallels between this process and the standard approach to decision-making outlined earlier.)

To keep things concrete it is useful to see how this process would work in a simple real-life example. Bradley and Drechsler quote the following example from Savage’s book that does just that:

…[consider] someone who is cooking an omelet and has already broken five good eggs into a bowl, but is uncertain whether the sixth egg is good or rotten. In deciding whether to break the sixth egg into the bowl containing the first five eggs, to break it into a separate saucer, or to throw it away, the only question this agent has to grapple with is whether the last egg is good or rotten, for she knows both what the consequence of breaking the egg is in each eventuality and how desirable each consequence is. And in general it would seem that for Savage once the agent has settled the question of how probable each state of the world is, she can determine what to do simply by averaging the utilities (Note: utility is basically a mathematical expression of preference or value) of each action’s consequences by the probabilities of the states of the world in which they are realised…

In this example there are two states (egg is good, egg is rotten), three actions (break egg into bowl, break egg into separate saucer to check if it rotten, throw egg away without checking) and three consequences (spoil all eggs, save eggs in bowl and save all eggs if last egg is not rotten, save eggs in bowl and potentially waste last egg). The problem then boils down to figuring out our preferences for the options (in some quantitative way) and the probability of the two states.  At first sight, Savage’s approach seems like a reasonable way to deal with uncertainty.  However, a closer look reveals major problems.

Problems with the standard approach

Unlike the omelet example, in real life situations it is often difficult to enumerate all possible states or foresee all consequences of an action. Further, even if states and consequences are known, we may not what value to attach to them – that is, we may not be able to determine our preferences for those consequences unambiguously. Even in those situations  where we can,  our preferences for may be subject to change  – witness the not uncommon situation where lottery winners end up wishing they’d never wonThe standard prescription works therefore works only in situations where all states, actions and consequences are known – i.e. tame situations, as opposed to wicked ones.

Before going any further, I should mention that Savage was cognisant of the limitations of his approach. He pointed out that it works only in what he called small world situations–  i.e. situations in which it is possible to enumerate and evaluate all options.  As Bradley and Drechsler put it,

Savage was well aware that not all decision problems could be represented in a small world decision matrix. In Savage’s words, you are in a small world if you can “look before you leap”; that is, it is feasible to enumerate all contingencies and you know what the consequences of actions are. You are in a grand world when you must “cross the bridge when you come to it”, either because you are not sure what the possible states of the world, actions and/or consequences are…

In the following three sections  I elaborate on the complications mentioned above emphasizing, once again, that many real life situations are prone to such complications.

State space uncertainty

The standard view of uncertainty assumes that all possible states are given as a part of the problem definition – as in the omelet example discussed earlier.  In real life, however, this is often not the case.

Bradley and Drechsler identify two distinct cases of state space uncertainty. The first one is when we are unaware that we’re missing states and/or consequences. For example, organisations that embark on a restructuring program are so focused on the cost-related consequences that they may overlook factors such as loss of morale and/or loss of talent (and the consequent loss of productivity). The second, somewhat rarer, case is when we are aware that we might be missing something but we don’t quite know what it is. All one can do here, is make appropriate contingency plans based on  guesses regarding possible consequences.

Figuring out possible states and consequences is largely a matter of scenario envisioning based on knowledge and practical experience. It stands to reason that this is best done by leveraging the collective experience and wisdom of people from diverse backgrounds. This is pretty much the rationale behind collective decision-making techniques such as Dialogue Mapping.

Option uncertainty

The standard approach to tackling uncertainty assumes that the connection between actions and consequences is well defined. This is often not the case, particularly for wicked problems.  For example, as I have discussed in this post, enterprise transformation programs with well-defined and articulated objectives often end up having a host of unintended consequences. At an even more basic level, in some situations it can be difficult to identify sensible options.

Option uncertainty is a fairly common feature in real-life decisions. As Bradley and Drechsler put it:

Option uncertainty is an endemic feature of decision making, for it is rarely the case that we can predict consequences of our actions in every detail (alternatively, be sure what our options are). And although in many decision situations, it won’t matter too much what the precise consequence of each action is, in some the details will matter very much.

…and unfortunately, the cases in which the details matter are precisely those problems in which they are the hardest to figure out – i.e. in wicked problems.

Preference uncertainty

An implicit assumption in the standard approach is that once states and consequences are known, people will be able to figure out their relative preferences for these unambiguously. This assumption is incorrect, as there are at least two situations in which people will not be able to determine their preferences. Firstly, there may be  a lack of factual information about one or more of the states. Secondly, even when one is able to get the required facts, it is hard to figure out how we would value the consequences.

A common example of the aforementioned situation is the job switch dilemma. In many (most?) cases in which one is debating whether or not to switch jobs, one lacks enough factual information about the new job – for example, the new boss’ temperament, the work environment etc. Further, even if one is able to get the required information, it is impossible to know how it would be to actually work there.  Most people would have struggled with this kind of uncertainty at some point in their lives. Bradley and Drechsler term this ethical uncertainty. I prefer the term preference uncertainty, as it has more to do with preferences than ethics.

Some general remarks

The first point to note is that the three types of uncertainty noted above map exactly on to the three shortcomings of classical decision theory discussed in the introduction.  This suggests a connection between the types of uncertainty and wicked problems. Indeed, most wicked problems are exemplars of one or more of the above uncertainty types.  For example, the paradigm-defining super-wicked problem of climate change displays all three types of uncertainty.

The three types of uncertainty discussed above are overlooked by the standard approach to managing uncertainty.  This happens in a number of ways. Here are two common ones:

  1. The standard approach assumes that all uncertainties can somehow be incorporated into a single probability function describing all possible states and/or consequences. This is clearly false for state space and option uncertainty: it is impossible to define a sensible probability function when one is uncertain about the possible states and/or outcomes.
  2. The standard approach assumes that preferences for different consequences are known. This is clearly not true in the case of preference uncertainty…and even for state space and option uncertainty for that matter.

In their paper, Bradley and Dreschsler arrive at these three types of uncertainty from considerations different from the ones I have used above. Their approach, while more general, is considerably more involved. Nevertheless, I would recommend that readers who are interested should take a look at it because they cover a lot of things that I have glossed over or ignored altogether.

Just as an example, they show how the aforementioned uncertainties can be reduced. There is a price to be paid, however: any reduction in uncertainty results in an increase in its severity. An example might help illustrate how this comes about. Consider a situation of state space uncertainty. One can reduce- or even, remove – this by defining a catch-all state (labelled, say, “all other outcomes”). It is easy to see that although one has formally reduced state space uncertainty to zero, one has increased the severity of the uncertainty because the catch-all state is but a reflection of our ignorance and our refusal to do anything about it!

There are many more implications of the above. However, I’ll point out just one more that serves to illustrate the very practical implications of these uncertainties. In a post on the shortcomings of enterprise risk management, I pointed out that the notion of an organisation-wide risk appetite is problematic because it is impossible to capture the diversity of viewpoints through such a construct. Moreover,  rule or process based approaches to risk management tend to focus only on those uncertainties that can be quantified, or conversely they assume that all uncertainties can somehow be clumped into a single probability distribution as prescribed by the standard approach to managing uncertainty. The three types of uncertainty discussed above highlight the limitations of such an approach to enterprise risk.

Conclusion

The standard approach to managing uncertainty assumes that all possible states, actions and consequences are known or can be determined. In this post I have discussed why this is not always so.  In particular, it often happens that we do not know all possible outcomes (state space uncertainty), consequences (option uncertainty) and/or our preferences for consequences (preference or ethical uncertainty).

As I was reading the paper, I felt the authors were articulating issues that I had often felt uneasy about but chose to overlook (suppress?).  Generalising from one’s own experience is always a fraught affair, but  I reckon we tend to deny these uncertainties because they are inconvenient – that is, they are difficult if not impossible to deal with within the procrustean framework of the standard approach.  What is needed as a corrective is a recognition that the pseudo-quantitative approach that is commonly used to manage uncertainty may not the panacea it is claimed to be. The first step towards doing this is to acknowledge the existence of the uncertainties that we (probably) overlook.

Written by K

February 25, 2015 at 9:08 pm

On the statistical downsides of blogging

with 22 comments

Introduction

The stats on the 200+ posts I’ve written since I started blogging make it pretty clear that:

  1. Much of what I write does not get much attention – i.e. it is not of interest to most readers.
  2. An interesting post – a rare occurrence in itself  – is invariably followed by a series of uninteresting ones.

In this post, I ignore the very real possibility that my work is inherently uninteresting and discuss how the above observations can be explained via concepts of probability.

Base rate of uninteresting ideas

A couple of years ago I wrote a piece entitled, Trumped by Conditionality, in which I used conditional probability to show that majority of the posts on this blog will be uninteresting despite my best efforts.  My argument was based on the following observations:

  1. There are many more uninteresting ideas than interesting ones.  In statistical terminology one would say that the base rate of uninteresting ideas is high.   This implies that if I write posts without filtering out bad ideas, I will write uninteresting posts far more frequently than interesting ones.
  2. The base rate as described above is inapplicable in real life because I do attempt to filter out the bad ideas. However, and this is the key:  my ability to distinguish between interesting and uninteresting topics is imperfect. In other words, although I can generally identify an interesting idea correctly , there is a small (but significant) chance that I will incorrectly identify an uninteresting topic as being interesting.

Now,  since uninteresting ideas vastly outnumber interesting ones and my ability to filter out uninteresting ideas is imperfect, it follows that  the majority of the topics I choose to write about will be uninteresting.   This is essentially the first point I made in the introduction.

Regression to the mean

The observation that good (i.e. interesting) posts are generally followed by a series of not so good ones is a consequence of a statistical phenomenon known as regression to the mean.  In everyday language this refers to the common observation that an extreme event is generally followed by a less extreme one.   This is simply a consequence of the fact that for many commonly encountered phenomena extreme events are much less likely to occur than events that are close to the average.

In the case at hand we are concerned with the quality of writing. Although writers might improve through practice, it is pretty clear that they cannot write brilliant posts every time they put fingers to keyboard. This is particularly true of bloggers and syndicated columnists who have to produce pieces according to a timetable – regardless of practice or talent, it is impossible to produce high quality pieces on a regular basis.

It is worth noting that people often incorrectly ascribe causal explanations to phenomena that can be explained by regression to the mean.  Daniel Kahneman and Amos Tversky describe the following example in their classic paper on decision-related cognitive biases:

…In a discussion of flight training, experienced instructors noted that praise for an exceptionally smooth landing is typically followed by a poorer landing on the next try, while harsh criticism after a rough landing is usually followed by an improvement on the next try. The instructors concluded that verbal rewards are detrimental to learning, while verbal punishments are beneficial, contrary to accepted psychological doctrine. This conclusion is unwarranted because of the presence of regression toward the mean. As in other cases of repeated examination, an improvement will usually follow a poor performance and a deterioration will usually follow an outstanding performance, even if the instructor does not respond to the trainee’s achievement on the first attempt

So, although I cannot avoid the disappointment that follows the high of writing a well-received post, I can take (perhaps, false) comfort in the possibility that I’m a victim of statistics.

In closing

Finally, l would be remiss if I did not consider an explanation which, though unpleasant, may well be true: there is the distinct possibility that everything I write about is uninteresting. Needless to say, I reckon the explanations (rationalisations?) offered above are far more likely to be correct 🙂

Written by K

June 1, 2012 at 6:12 am

Posted in Probability, Statistics, Writing

Tagged with

The shape of things to come: an essay on probability in project estimation

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Introduction

Project estimates are generally based on assumptions about future events and their outcomes.   As the future is uncertain, the concept of  probability  is  sometimes  invoked in the estimation process.   There’s enough been written about how probabilities can be used in developing estimates; indeed there are a good number of articles on this blog – see this post or this one, for example.  However, most of these writings focus on the practical applications of probability rather than on the concept itself – what it means and how it should be interpreted.  In this article I address the latter point in a way that will (hopefully!) be of interest to those working in project management and related areas.

Uncertainty is a shape, not a number

Since the future can unfold in a number of different ways one can describe it only in terms of a range of possible outcomes.   A good way to explore the implications of this statement is through a simple estimation-related example:

Assume you’ve been asked to do a particular task relating to your area of expertise.  From experience you know that this task usually takes 4 days to complete. If things go right, however,  it could take as little as 2 days. On the other hand, if things go wrong it could take as long as 8 days.  Therefore, your range of possible finish times (outcomes) is anywhere between 2 to 8 days.

Clearly, each of these outcomes is not equally likely.  The most likely outcome is that you will finish the task in 4 days. Moreover, the likelihood of finishing in less than  2 days or more than 8 days is zero. If we plot the likelihood of completion against completion time, it would look something like Figure 1.

Figure 1: Likelihood of finishing on day 2, day 4 and day 8.

Figure 1 begs a couple of questions:

  1. What are the relative likelihoods of completion for all intermediate times – i.e. those between 2  to 4 days and 4 to 8 days?
  2. How can one quantify the likelihood of intermediate times? In other words, how can one get a numerical value of the likelihood for all times between 2 to 8 days?  Note that we know from the earlier discussion that this must be zero for any time less than 2 or greater than 8 days.

The two questions are actually related:  as we shall soon see, once we know the relative likelihood of completion at all times (compared to the maximum), we can work out its numerical value.

Since we don’t know anything about intermediate times (I’m assuming there is no historical data available, and I’ll have more to say about this later…), the simplest thing to do is to assume that the likelihood increases linearly (as a straight line) from 2 to 4 days and decreases in the same way from 4 to 8 days as shown in Figure 2. This gives us the well-known triangular distribution.

Note: The term distribution is simply a fancy word for a plot of  likelihood vs. time.

Figure 2: Triangular distribution fitted to points in Figure 1

Of course, this isn’t the only possibility; there are an infinite number of others. Figure 3 is another (admittedly weird) example.

FIgure 3: Another distribution that fits the points in Figure 1

Further, it is quite possible that the upper limit (8 days) is not a hard one. It may be that in exceptional cases the task could take much longer (say, if you call in sick for two weeks) or even not be completed at all (say, if you leave for that mythical greener pasture).  Catering for the latter possibility, the shape of the likelihood might resemble Figure 4.

Figure 4: A distribution that allows for a very long (potentially) infinite completion time

From the figures above, we see that uncertainties are shapes rather than single numbers, a notion popularised by Sam Savage in his book, The Flaw of Averages. Moreover, the “shape of things to come” depends on a host of factors, some of which may not even be on the radar when a future event is being estimated.

Making likelihood precise

Thus far, I have used the word “likelihood” without bothering to define it.  It’s time to make the notion more precise.  I’ll begin by asking the question: what common sense properties do we expect a quantitative measure of likelihood to have?

Consider the following:

  1. If an event is impossible, its likelihood should be zero.
  2. The sum of likelihoods of all possible events should equal complete certainty. That is, it should be a constant. As this constant can be anything, let us define it to be 1.

In terms of the example above, if we denote time by t and the likelihood by P(t)  then:

P(t) = 0 for t< 2 and  t> 8

And

\sum_{t}P(t) = 1 where 2\leq t< 8

Where \sum_{t} denotes the sum of all non-zero likelihoods – i.e. those that lie between 2 and 8 days. In simple terms this is the area enclosed by the likelihood curves and the x axis in figures 2 to 4.  (Technical Note:  Since t is a continuous variable, this should be denoted by an integral rather than a simple sum, but this is a technicality that need not concern us here)

P(t) is , in fact, what mathematicians call probability– which explains why I have used the symbol P rather than L. Now that I’ve explained what it  is, I’ll use the word “probability” instead of ” likelihood” in the remainder of this article.

With these assumptions in hand, we can now obtain numerical values for the probability of completion for all times between 2 and 8 days. This can be figured out by noting that the area under the probability curve (the triangle in figure 2 and the weird shape in figure 3) must equal 1.  I won’t go into any further details here, but those interested in the maths for the triangular case may want to take a look at this post  where the details have been worked out.

The meaning of it all

(Note:  parts of this section borrow from my post on the interpretation of probability in project management)

So now we understand how uncertainty is actually a shape corresponding to a range of possible outcomes, each with their own probability of occurrence.  Moreover, we also know, in principle, how the probability can be calculated for any valid value of time (between 2 and 8 days). Nevertheless, we are still left with the question as to what a numerical probability really means.

As a concrete case from the example above, what do we mean when we say that there is 100% chance (probability=1) of finishing within 8 days?   Some possible interpretations of such a statement include:

  1.  If the task is done many times over, it will always finish within 8 days. This is called the frequency interpretation of probability, and is the one most commonly described in maths and physics textbooks.
  2. It is believed that the task will definitely finish within 8 days. This is called the belief interpretation.  Note that this interpretation hinges on subjective personal beliefs.
  3. Based on a comparison to similar tasks, the  task will finish within 8 days. This is called the support interpretation.

Note that these interpretations are based on a paper by Glen Shafer. Other papers and textbooks frame these differently.

The first thing to note is how different these interpretations are from each other.  For example, the first one offers a seemingly objective interpretation whereas the second one is unabashedly subjective.

So, which is the best – or most correct – one?

A person trained in science or mathematics might  claim that the frequency interpretation wins hands down because it lays out an objective, well -defined procedure for calculating probability: simply perform the same task many times and note the completion times.

Problem is, in real life situations it is impossible to carry out exactly the same task over and over again. Sure, it may be possible to almost the same  task, but even straightforward tasks  such as vacuuming a room or baking a cake can hold hidden surprise (vacuum cleaners do malfunction and a friend may call when one is mixing the batter for a cake). Moreover, tasks that are complex (as is often the case in the project work) tend to be unique and can never be performed in exactly the same way twice.  Consequently, the frequency interpretation is great in theory but not much use in practice.

“That’s OK,”  another estimator might say,” when drawing up an estimate, I compared it to other similar tasks that I have done before.”

This is essentially the support interpretation (interpretation 3 above).  However, although this seems reasonable, there is a problem: tasks that are superficially similar will differ in the details, and these small differences may turn out to be significant when one is actually carrying out the task.  One never knows beforehand which variables are important. For example, my ability to finish a particular task within a stated time depends not only on my skill but also on things such as my workload, stress levels and even my state of mind. There are many external factors that one might not even recognize as being significant. This is a manifestation of the reference class problem.

So where does that leave us? Is probability just a matter of subjective belief?

No, not quite:  in reality, estimators will use some or all of three interpretations to arrive at “best guess” probabilities.  For example, when estimating a project task, a person will likely use one or more of the following pieces of information:

  1. Experience with similar tasks.
  2. Subjective belief regarding task complexity and potential problems. Also, their “gut feeling” of how long they think it ought to take. These factors often drive excess time or padding that people work into their estimates.
  3. Any relevant historical data (if available)

Clearly, depending on the situation at hand, estimators may be forced to rely on one piece of information more than others. However, when called upon to defend their estimates, estimators may use other arguments to justify their conclusions depending on who they are talking to. For example,  in discussions involving managers, they may use hard data presented in a way that supports their estimates, whereas when talking to their peers they may emphasise their gut feeling based on differences between the task at hand and similar ones they have done in the past.  Such contradictory representations tend to obscure the means by which the estimates were actually made.

Summing up

Estimates are invariably made in the face of uncertainty. One way to get a handle on this is by estimating the probabilities associated with possible outcomes.  Probabilities can be reckoned in a number of different ways. Clearly, when using them in estimation, it is crucial to understand how probabilities have been derived and the assumptions underlying these. We have seen three ways in which probabilities are interpreted corresponding to three different ways in which they are arrived at.  In reality, estimators may use a mix of the three approaches so it isn’t always clear how the numerical value should be interpreted. Nevertheless, an awareness of what probability is and its different interpretations may help managers ask the right questions to better understand the estimates made by their teams.

Written by K

April 3, 2012 at 11:40 pm

On the accuracy of group estimates

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Introduction

The essential idea behind group estimation is that an estimate made by a group is likely to be more accurate than one made by an individual in the group. This notion is the basis for the Delphi method and its variants. In this post, I use arguments involving probabilities to gain some insight into the conditions under which group estimates are more accurate than individual ones.

An insight from conditional probability

Let’s begin with a simple group estimation scenario.

Assume we have two individuals of similar skill who have been asked to provide independent estimates of some quantity, say  a project task duration. Further, let us assume that each individual has a probability p of making a correct estimate.

Based on the above, the probability that they both make a correct estimate, P(\textnormal{both correct}),  is:

P(\textnormal{both correct}) = p*p = p^2,

This is a consequence of our assumption that the individual estimates are independent of each other.

Similarly,  the probability that they both get it wrong, P(\textnormal{both wrong}), is:

P(\textnormal{both wrong}) = (1-p)*(1-p) = (1-p)^2,

Now we can ask the following question:

What is the probability that both individuals make the correct estimate if we know that they have both made the same estimate?

This can be figured out using Bayes’ Theorem, which in the context of the question can be stated as follows:

P(\textnormal{both correct\textbar same estimate})= \displaystyle{\frac{ P(\textnormal{same estimate\textbar both correct})*P(\textnormal{both correct})}{ P(\textnormal{same estimate})}}

In the above equation, P(\textnormal{both correct\textbar same estimate}) is the probability that both individuals get it right given that they have made the same estimate (which is  what we want to figure out). This is an example of a conditional probability – i.e.  the probability that an event occurs given that another, possibly related event has already occurred.  See this post for a detailed discussion of conditional probabilities.

Similarly, P(\textnormal{same estimate\textbar both correct}) is the conditional probability that both estimators make the same estimate given that they are both correct. This probability is 1.

Question: Why? 

Answer: If both estimators are correct then they must have made the same estimate (i.e. they must both within be an acceptable range of the right answer).

Finally, P(\textnormal{same estimate}) is the probability that both make the same estimate. This is simply the sum of the probabilities that both get it right and both get it wrong. Expressed in terms of p this is, p^2+(1-p)^2.

Now lets apply Bayes’ theorem to the following two cases:

  1. Both individuals are good estimators – i.e. they have a high probability of making a correct estimate. We’ll assume they both have a 90% chance of getting it right (p=0.9).
  2. Both individuals are poor estimators – i.e. they have a low probability of making a correct estimate. We’ll assume they both have a 30% chance of getting it right (p=0.3)

Consider the first case. The probability that both estimators get it right given that they make the same estimate is:

P(\textnormal{both correct\textbar same estimate})= \displaystyle\frac{1*0.9*0.9}{0.9*0.9+0.1*0.1}= \displaystyle \frac{0.81}{0.82}= 0.9878

Thus we see that the group estimate has a significantly better chance of being right than the individual ones:  a probability of 0.9878 as opposed to 0.9.

In the second case, the probability that both get it right is:

P(\textnormal{both correct\textbar same estimate})= \displaystyle \frac{1*0.3*0.3}{0.3*0.3+0.7*0.7}= \displaystyle \frac{0.09}{0.58}= 0.155

The situation is completely reversed: the group estimate has a much smaller chance of being right than an  individual estimate!

In summary:  estimates provided by a group consisting of individuals of similar ability working independently are more likely to be right (compared to individual estimates) if the group consists of  competent estimators and more likely to be wrong (compared to individual estimates) if the group consists of  poor estimators.

Assumptions and complications

I have made a number of simplifying assumptions in the above argument. I discuss these below with some commentary.

  1. The main assumption is that individuals work independently. This assumption is not valid for many situations. For example, project estimates are often made  by a group of people working together.  Although one can’t work out what will happen in such situations using the arguments of the previous section, it is reasonable to assume that given the right conditions, estimators will use their collective knowledge to work collaboratively.   Other things being equal,  such collaboration would lead a group of skilled estimators to reinforce each others’ estimates (which are likely to be quite similar) whereas less skilled ones may spend time arguing over their (possibly different and incorrect) guesses.  Based on this, it seems reasonable to conjecture that groups consisting of good estimators will tend to make even better estimates than they would individually whereas those consisting of poor estimators have a significant chance of making worse ones.
  2. Another assumption is that an estimate is either good or bad. In reality there is a range that is neither good nor bad, but may be acceptable.
  3. Yet another assumption is that an estimator’s ability can be accurately quantified using a single numerical probability.  This is fine providing the number actually represents the person’s estimation ability for the situation at hand. However, typically such probabilities are evaluated on the basis of  past estimates. The problem is, every situation is unique and history may not be a good guide to the situation at hand. The best way to address this is to involve people with diverse experience in the estimation exercise.  This will almost often lead to  a significant spread of estimates which may then have to be refined by debate and negotiation.

Real-life estimation situations have a number of other complications.  To begin with, the influence that specific individuals have on the estimation process may vary – a manager who is  a poor estimator may, by virtue of his position, have a greater influence than others in a group. This will skew the group estimate by a factor that cannot be estimated.  Moreover, strategic behaviour may influence estimates in a myriad other ways. Then there is the groupthink factor  as well.

…and I’m sure there are many others.

Finally I should mention that group estimates can depend on the details of the estimation process. For example, research suggests that under certain conditions competition can lead to better estimates than cooperation.

Conclusion

In this post I have attempted to make some general inferences regarding the validity of group estimates based on arguments involving conditional probabilities. The arguments suggest that, all other things being equal, a collective estimate from a bunch of skilled estimators will generally be better than their individual estimates whereas an estimate from a group of less skilled estimators will tend to be worse than their individual estimates. Of course, in real life, there are a host of other factors  that can come into play:  power, politics and biases being just a few. Though these are often hidden, they can  influence group estimates in inestimable ways.

Acknowledgement

Thanks go out to George Gkotsis and Craig Brown for their comments which inspired this post.

Written by K

December 1, 2011 at 5:16 am

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