The Importance of Scoring Data

The intuition behind

Events can occur, or not... although we don't have tomorrow's newspaper :newspaper:, we can make a good guess about how is it going to be.

The future is undoubtedly attached to uncertainty, and this uncertainty can be estimated.

And there are differents targets...

For now, this book will cover the classical: Yes/No target -also known as binary or multiclass prediction.

So, this estimation is the value of truth of an event to happen, therefore a probabilistic value between 0 and 1.

two-label vs. multi-label outcome :

Please note this chapter is written for a binary outcome (two-label outcome), but multi-label target can be seen as a general approach of a binary class.

For example, having a target with 4 different values, there can be 4 models that predict the likelihood of belonging to particular class, or not. And then a higher model which takes the results of those 4 models and predict the final class.

Say what? :hushed:

Some examples:

  • Is this client going to buy this product?
  • Is this patient going to get better?
  • Is certain event going to happen in the next few weeks?

The answers to these last questions are True or False, but the essence is to have a score, or a number indicating the likelihood of a certain event to happen.

But we need more control...

Many machine learning resources show the simplified version -which is good to start- getting the final class as an output. Let's say:

Simplified approach:

  • Question: Is this person going to have a heart disease?
  • Answer: "No"

But there is something else before the "Yes/No" answer, and this is the score:

  • Question: What is the likelihood for this person of having heart disease?
  • Answer: "25%"

So first you get the score, and then according to your needs you set the cut point. And this is really important.

Let see an example

Example table showing the following

  • id=identity
  • x1,x2 and x3 input variables
  • target=variable to predict

Forgetting about input variables... After the creation of the predictive model, like a random forest, we are interested in the scores. Even though our final goal is to deliver a yes/no predicted variable.

For example, the following 2 sentences express the same: The likelihood of being yes is 0.8 <=> The probability of being no is 0.2

Maybe it is understood, but the score usually refers to the less representative class: yes.

:raised_hand: R Syntax -skip it if you don't want to see code-

Following sentence will return the score:

score = predict(randomForestModel, data, type = "prob")[, 2]

Please note for other models this syntax may vary a little, but the concept will remain the same. Even for other languages.

Where prob indicates we want the probabilities (or scores).

The predict function + type="prob" parameter returns a matrix of 15 rows and 2 columns: the 1st indicates the likelihood of being no while the 2nd one shows the same for class yes.

Since target variable can be no or yes, the [, 2] return the likelihood of being -in this case- yes (which is the complement of the no likelihood).

It's all about the cut point :straight_ruler:

Now the table is ordered by descending score.

This is meant to see how to extract the final class having by default the cut point in 0.5. Tweaking the cut point will lead to a better classification.

Accuracy metrics or the confusion matrix are always attached to a certain cut point value.

After assigning the cut point, we can see the classification results getting the famous:

  • :white_check_mark:True Positive (TP): It's true, that the classification is positive, or, "the model hit correctly the positive (yes) class".
  • :white_check_mark:True Negative (TN): Same as before, but with negative class (no).
  • :x:False Positive (FP): It's false, that the classification is positive, or, "the model missed, it predicted yes but the result was no
  • :x:False Negative (FN): Same as before, but with negative class, "the model predicted negative, but it was positive", or, "the model predicted no, but the class was yes"

The best and the worst scenario

The analysis of the extremes will help to find the middle point.

:thumbsup: The best scenario is when TP and TN rates are 100%. That means the model correctly predicts all the yes and all the no; (as a result, FP and FN rates are 0%).

But wait :raised_hand:! If you find a perfect classification, probably it's because of overfitting!

:thumbsdown: The worst scenario -the opposite to last example- is when FP and FN rates are 100%. Not even randomness can achieve such an awful scenario.

Why? If the classes are balanced, 50/50, flipping a coin will assert around half of the results. This is the common baseline to test if the model is better than randomness.

In the example provided, class distribution is 5 for yes, and 10 for no; so: 33,3% (5/15) is yes.

Comparing classifiers

Comparing classification results

:question: Trivia: Is a model which correcltly predict this 33.3% (TP rate=100%) a good one?

Answer: It depends on how many 'yes', the model predicted.

A classifier that always predicts yes, will have a TP of 100%, but is absolutely useless since lots of yes will be actually no. As a matter of fact, FP rate will be high.

Comparing ordering label based on score

A classifier must be trustful, and this is what ROC curves measures when plotting the TP vs FP rates. The higher the proportion of TP over FP, the higher the Area Under Roc Curve (AUC) is.

The intuition behind ROC curve is to get an sanity measure regarding the score: how well it orders the label. Ideally, all the positive labels must be at the top, and the negative ones at the bottom.

model 1 will have a higher AUC than model 2.

Wikipedia has an extensive and good article on this:

There is the comparission of 4 models, given a cutpoint of 0.5:

Hands on R!

We'll be analyzing 3 scenarios based on 3 cut-points.

# install.packages("rpivotTable") 
# rpivotTable: it creates a pivot table dinamically, it also supports plots, more info at:


## reading the data
data=read.delim(file="", sep="\t", header = T, stringsAsFactors=F)

Scenario 1 Cut point @ 0.5

Classical confusion matrix, indicating how many cases fall in the intersection of real vs predicted value:

data$predicted_target=ifelse(data$score>=0.5, "yes", "no")

rpivotTable(data = data, rows = "predicted_target", cols="target", aggregatorName = "Count", rendererName = "Table", width="100%", height="400px")

Another view, now each column sums 100%. Good to answer the following questions:

rpivotTable(data = data, rows = "predicted_target", cols="target", aggregatorName = "Count as Fraction of Columns", rendererName = "Table", width="100%", height="400px")

  • What is the percentage of real yes values captured by the model? Answer: 80% Also known as Precision (PPV)
  • What is the percentage of yes thrown by the model? 40%.

So, from the last two sentences:

The model throws 4 out of 10 predictions as yes, and from this segment -the yes- it hits 80%.

Another view: The model correctly hits 3 cases for each 10 yes predictions (0.4/0.8=3.2, or 3, rounding down).

Note: The last way of analysis can be found when building an association rules (market basket analysis), and a decision tree model.

Scenario 2 Cut point @ 0.4

Time to change the cut point to 0.4, so the amount of yes will be higher:

data$predicted_target=ifelse(data$score>=0.4, "yes", "no")

rpivotTable(data = data, rows = "predicted_target", cols="target", aggregatorName = "Count as Fraction of Columns", rendererName = "Table", width="100%", height="400px")

Now the model captures 100% of yes (TP), so the total amount of yes produced by the model increased to 46.7%, but at no cost since the TN and FP remained the same :thumbsup:.

Scenario 3 Cut point @ 0.8

Want to decrease the FP rate? Set the cut point to a higher value, for example: 0.8, which will cause the yes produced by the model decreases:

data$predicted_target=ifelse(data$score>=0.8, "yes", "no")

rpivotTable(data = data, rows = "predicted_target", cols="target", aggregatorName = "Count as Fraction of Columns", rendererName = "Table", width="100%", height="400px")

Now the FP rate decreased to 10% (from 20%), and the model still captures the 80% of TP which is the same rate as the one obtained with a cut point of 0.5 :thumbsup:.

Decreasing the cut point to 0.8 improved the model at no cost.


  • This chapter has focused on the essence of predicting a binary variable: To produce a score or likelihood number which orders the target variable.

  • A predictive model maps the input with the output.

  • There is not a unique and best cut point value, it relies on the project needs, and is constrained by the rate of False Positive and False Negative we can accept.

This book addresses general aspects on model performance in Knowing the error.

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