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Logistic Regression Analytics Platform


Introduction

The goal in Logistic Regression is to assign probabilities to model scores, creating a reliable ranking system that can be used straightaway to evaluate the risk involved in financial and insurance applications, to rank potential respondents in a marketing campaign, or to evaluate the risk of contracting a disease.

The Logistic Regression Framework of GeneXproTools builds on the models it generates with its evolutionary algorithms, combining the canonical logistic regression technique to estimate probabilities for each model score. And once you know the probability of an event, you can also make categorical predictions about that event (Yes / No or Positive / Negative) and consequently evaluate the confusion matrix both for the Training and Validation/Test data.

Thus, the innovative Logistic Regression Framework of GeneXproTools offers an extremely robust hybrid system in which powerful multivariate nonlinear models, empowered by traditional statistical modeling techniques, are totally created by evolution.


With the Logistic Regression Framework of GeneXproTools you can:


Getting Started

In order to access the Logistic Regression Framework of GeneXproTools you need to:
  1. Create a statistical model that explains a binary dependent variable, using either the Logistic Regression Framework or the Classification Framework of GeneXproTools.
    In the Logistic Regression Framework the default fitness function is the Positive Correl fitness as this kind of function gives the best results with the standard 0/1 class encoding.
    In the Classification Framework you also have access to a wide variety of fitness functions and adaptive rounding thresholds that offer interesting alternatives for exploring the solution space.
  2. In the Logistic Regression Framework, click the Results menu and then choose one of the available analytics tools: Quantile Analysis, ROC Curve, Cutoff Points, Gains Chart, Lift Chart, Log Odds, Logistic Fit, or Confusion Matrix.
    This activates the number-crunching process of the Logistic Regression Analytics Platform that starts with the evaluation of the Quantile Table and finishes with the creation of the Logistic Regression Model and the evaluation of the Confusion Matrix. When all the calculations are done, you just navigate the different options (different Tables and Charts, different Datasets, and different Models) to evaluate the accuracy and generalizability of your logistic regression models.


In the Logistic Regression Analytics Platform of GeneXproTools you can:

  1. Analyze and create Quantile Tables and Charts; perform Quantile Regression; analyze the ROC Curve of your models; visualize the Optimal Cutoff Point for your test scores; study the Gains and Lift Charts of your models; access the Log Odds Chart used to evaluate the slope and intercept of the Logistic Regression Model; visualize how well your logistic regression model fits the data in the Logistic Fit Chart; and compare and analyze Logistic & ROC Confusion Matrices using both 2 x 2 Contingency Tables and innovative quantile-based Distribution Charts.
  2. Copy all the Tables and Charts to the clipboard.
    All the Tables and Charts generated within the Logistic Regression Window can be copied to the clipboard through the context menu. Tables can be copied in their entirety or you can copy just selected rows or individual columns.
  3. Copy the Statistics Report.
    The Stats Report summarizes all the relevant parameters and statistics derived from all the analyses (Quantile Regression, ROC Curve, Cutoff Points, Gains Chart, Lift Chart, Log Odds, Logistic Fit, and Confusion Matrices) performed for the active model and selected dataset. It also contains relevant information about the training and validation/test data, such as class distribution and number of records. And finally, the Stats Report also summarizes some basic information about the model, such as its fitness and accuracy and if any calculation errors occurred during the computation of the model scores. Within the Logistic Regression Window all such calculation errors (which can happen when processing unseen data, which includes not only the validation/test set but also the "training dataset" if it was replaced by a different one or if the model itself was modified by the user in the Change Seed Window) return zero so that the calculations can resume. Note, however, that GeneXproTools flags these errors clearly, highlighting them in light red in all the tables where the model outputs are shown (ROC Table, Cutoff Points Table, Logistic Fit Table, and Confusion Matrix Table).
  4. Choose a different number of bins (quantiles) for your Quantile Table and then see immediately how it affects the Logistic Regression Model through the Logistic Fit Chart.
    The number of bins is an essential parameter for most of the analyses performed in the Logistic Regression Window (Quantile Regression, Gains Chart, Lift Chart, Log Odds and Logistic Regression, Logistic Fit, and Logistic Confusion Matrix) and therefore it is saved for each model. Note, however, that the basic model parameters, namely the slope, intercept, and logistic threshold, of each model are the ones evaluated during training for a specific training data. These parameters can only be changed through the Update Current Threshold or Update All Thresholds in the History Menu. So, for example if you change the number of bins in the Logistic Regression Window, GeneXproTools re-evaluates all the analyses and computations and shows you what-if scenarios if such changes were implemented. However, all the basic model parameters remain fixed unless you make the necessary changes (namely, a different number of bins or a different dataset) and then update the threshold(s). It’s also important to note that in the Logistic Regression Window all the calculations are made for the Training or the Validation datasets as defined in the Data Panel. So, for example if you used a subsample of the training dataset to create your models, you should expect slightly different values for the basic model parameters and on all calculations that depend on them, like for example the Logistic Confusion Matrix.
    By using the ROC-derived accuracy as your golden standard (it is quantile-independent and remains unchanged for a particular model), you can fine-tune the number of bins to get the most of your models. Note, however, that it is not uncommon to get better accuracy on the Logistic Confusion Matrix, which of course is indicative of a very good Logistic Fit.
  5. Access the validation/test dataset so that you can not only test further the predictive accuracy of your model but also build logistic regression models with it.
    The validation/test dataset was never brought into contact with the model during the training process and therefore constitutes an excellent blind test for checking the predictive accuracy of your model on unseen data. You access the validation/test dataset by choosing Validation in the Dataset combobox. GeneXproTools then creates a specific Quantile Table for the validation/test dataset and also performs the complete logistic regression analysis for this dataset. Note, however, that if you want to use this logistic regression model (that is, the slope, intercept and logistic threshold evaluated for the validation/test set) for scoring new cases using the Scoring Engine of GeneXproTools, you’ll have to replace the original training dataset with this one and then recalculate the logistic parameters (the slope and intercept of the Log Odds Chart) with this new operational dataset. As mentioned above, you recalculate the basic model parameters through the Update Current Threshold or Update All Thresholds in the History Menu.
  6. Analyze all the intermediate models created in a run by selecting any model in the Model selector box.
    Each model in the Run History is identified by its ID and respective Training Accuracy for easy access in the Model selector box. Note that when you close the Logistic Regression Window, the last observed model will remain your active model.
    Data modelers are understandably interested in the best-of-run model, but it’s also great fun to get a glimpse of how evolution works by being able to see how intermediate models behave and how their performance becomes better and better with time. But this process is also important to develop a good intuition and learn some tips that might prove useful in making the most of evolution.
  7. Choose to browse all the available Tables and Charts in synchrony or asynchronously by checking the Sync Tables & Charts checkbox.
    By default, the Tables & Charts of the Logistic Regression Framework of GeneXproTools move in synchrony. But you can have them move independently so that you can look at any one table while analyzing a certain chart and vice versa. Another advantage of having Tables & Charts move independently is that it’s much faster to move from chart to chart when using very large datasets.
  8. Access the Logistic Regression Online Help.
    Through the Help button you have access to the Online Knowledge Base of GeneXproTools which includes the Logistic Regression Documentation on all the analyses of the Logistic Regression Analytics Platform.


In order to make predictions or rank new cases within GeneXproTools, you need to:

  1. Go to the Scoring Panel.
    To score a database or Excel file, on the Scoring menu select Databases or go to the Scoring Panel and select the Databases Tab. For scoring data kept in text files, on the Scoring menu select Text Files or go to the Scoring Panel and select the Text Files Tab.
  2. In the Scoring Panel select the model output type in the Model Output combobox and then enter the path for both the source data and output file.
    The Scoring Engine of GeneXproTools uses the JavaScript code of your model to perform the computations as it also includes the code for the Derived Variables (UDFs) and Custom Functions (DDFs).
  3. Then press the Start button to begin the scoring process.
    GeneXproTools saves the scoring results to a file which contains the predictions of your model for all the new cases in the source file. For small datasets (up to 20 variables and 2000 records) GeneXproTools also shows the scoring results in the table of the Scoring Panel; for more than 20 variables GeneXproTools displays only the model output in the Scoring Table.



Quantile Analysis and Regression

Quantile Tables are by themselves powerful analytics tools, but they are also at the heart of the Logistic Regression Model and Logistic Fit. In addition, they are also the basis of powerful analytics tools such as Gains and Lift Charts, which are essential for making good decisions about the quality of a model and to estimate the benefits of using a model.



The number of quantiles or bins is entered in the Quantiles combobox at the top of the Logistic Regression Window. The most commonly used Quantile Tables such as Quartiles, Quintiles, Deciles, Vingtiles, Percentiles, and 1000-tiles are listed by default, but you can type any valid quantile number in the box to build the most appropriate quantile table for your data.

The number of quantiles is an essential parameter for most of the analyses performed in the Logistic Regression Window (obviously Quantile Regression and Analysis, but also Gains Chart, Lift Chart, Log Odds and Logistic Regression, Logistic Fit, and Logistic Confusion Matrix) and therefore it is saved for each model (the number of bins is in fact an essential parameter of all Logistic Regression fitness functions and therefore it can also be changed in the Fitness Functions Tab of the Settings Panel).

On their own, Quantile Tables are widely used in risk assessment applications and in a variety of response models to create rankings or scores. Percentiles, for instance, are very popular and often used for that purpose alone. But in GeneXproTools, Quantile Tables are also used to create a more sophisticated ranking system: the probabilistic ranking system of the Logistic Regression Model. This model estimates unique probabilities for each case, forming a very powerful ranking system, perfectly bounded between 0 and 1.

GeneXproTools shows its Quantile Tables in 100% stacked column charts, where the distribution of both Positive and Negative categories is shown for all the bins. By moving the cursor over each column, GeneXproTools shows both the percentage and absolute values for each class. For more than 20 bins, a scroll bar appears at the bottom of the Quantile Chart and by moving it you can see the distribution over all the range of model outputs.



Besides allowing the visualization of Quantile Tables, GeneXproTools also shows and performs a weighted Quantile Regression. Both the slope and intercept of the regression line, as well as the R-square, are computed and shown in the Quantile Regression Chart.



These parameters form the core of the Quantile Regression Model and can be used both to evaluate rankings and to make discrete classifications in a fashion similar to what is done with the Logistic Regression Model. Within the Logistic Regression Framework of GeneXproTools, however, only the Logistic Regression Model is used to evaluate rankings (probabilities, in this case) and to estimate the most likely class. Furthermore, the Scoring Engine of GeneXproTools also uses the Logistic Regression Model to make predictions, not the Quantile Regression Model.

Note also that in the X-axis of the Quantile Regression Chart, GeneXproTools plots model outputs and therefore you can see clearly how spread out model scores are. Note also that, in the Quantile Regression Chart, upper boundaries are used if the predominant class is “1” and the model is normal, or the predominant class is “0” and the model is inverted; and lower boundaries are used if the predominant class is “1” and the model is inverted, or the predominant class is “0” and the model is normal.

On the companion Statistics Report shown on the right in the Logistic Regression Window (the Quantiles section opens up every time the Quantiles Chart Tab is selected), GeneXproTools also shows the Spread from Top to Bottom, Spread from Top to Middle, and Spread from Middle to Bottom (when the number of bins is even, the middle value is the average of the two middle bins). Note that negative values for the spreads, especially the Spread from Top to Bottom, are usually indicative of an inverted model. In absolute terms, however, the wider the spread the better the model.




ROC Analysis

Receiver Operating Characteristic or ROC Curves are powerful visualization tools that allow a quick assessment of the quality of a model. They are usually plotted in reference to a Baseline or Random Model, with the Area Under the ROC Curve (or AUC for short) as a widely used indicator of the quality of a model.



So, for the Random Model, the area under the ROC curve is equal to 0.5, which means that the further up (or down, for inverted models) a model is from 0.5 the better it is. Indeed, for perfect models on both sides of the random line, what is called ROC heaven takes place when AUC = 1 (for normal models) or AUC = 0 (for inverted models). Below is shown a typical ROC curve obtained for a risk assessment model using a training dataset with 18,253 cases. This model, which has a classification accuracy of 74.15% and an R-square of 0.2445 (R-square values might seem unusually low, but in risk assessment applications R-square values around 0.22 are considered excellent and indicative of a good model), has an AUC of 0.7968. Note that the classification accuracy reported refers to the accuracy of the logistic regression model, not the ROC accuracy evaluated using the ROC Cutoff Point



Below is shown a Gallery of ROC Curves typical of intermediate models generated during a GeneXproTools run. These ROC curves were specifically created for a risk assessment problem with a training dataset with 18,253 cases and using a small population of just 30 programs. The Classification Accuracy, the R-square, and the Area Under the ROC Curve (AUC) of each model, as well as the generation at which they were discovered, are also shown as illustration. From top to bottom, they are as follow (see also the twin Gallery of Logistic Fit Charts in the Logistic Fit section):

  • Generation 0, Accuracy = 65.33%, R-square = 0.0001, AUC = 0.5273
  • Generation 5, Accuracy = 66.03%, R-square = 0.0173, AUC = 0.5834
  • Generation 59, Accuracy = 66.92%, R-square = 0.0421, AUC = 0.6221
  • Generation 75, Accuracy = 68.99%, R-square = 0.1076, AUC = 0.7068
  • Generation 155, Accuracy = 69.93%, R-square = 0.1477, AUC = 0.7597
  • Generation 489, Accuracy = 74.15%, R-square = 0.2445, AUC = 0.7968

Generation 0, Accuracy = 65.33%, R-square = 0.0001, AUC = 0.5273


Generation 5, Accuracy = 66.03%, R-square = 0.0173, AUC = 0.5834


Generation 59, Accuracy = 66.92%, R-square = 0.0421, AUC = 0.6221


Generation 75, Accuracy = 68.99%, R-square = 0.1076, AUC = 0.7068


Generation 155, Accuracy = 69.93%, R-square = 0.1477, AUC = 0.7597


Generation 489, Accuracy = 74.15%, R-square = 0.2445, AUC = 0.7968


ROC Curves and ROC Tables are also useful to evaluate what is called the Optimal Cutoff Point, which is given by the maximum of the Youden index. The Youden index J returns the maximum value of the expression (for inverted models, it returns the minimum):

J = max[SE(t) + SP(t) - 1]


where SE(t) and SP(t) are, respectively, the sensitivity and specificity over all possible threshold values t of the model. Thus, the ROC Cutoff Point corresponds to the model output at the Optimal Cutoff Point.

In the ROC Table, GeneXproTools also shows all “SE + SP -1” values and highlights in light green the row with the Optimal Cutoff Point and corresponding ROC Cutoff Point. These parameters are also shown in the ROC Statistics Report.



The ROC Cutoff Point can be obviously used to evaluate a Confusion Matrix (in the Logistic Regression Window it is called ROC Confusion Matrix in order to distinguish it from the Logistic Confusion Matrix) and, in the Cutoff Points Table, you have access to the Predicted Class, the Match, and Type values used to build the ROC Confusion Matrix (you can see the graphical representation of the ROC Confusion Matrix in the Confusion Matrix section).

The visualization of the ROC Confusion Matrix is a valuable tool and can be used to determine the right number of bins to achieve a good fit with the Logistic Regression Model. But GeneXproTools allows you to do more with the ROC Confusion Matrix and associated ROC Cutoff Point. By allowing the conversion of Logistic Regression runs to the Classification Framework, you can use this model, with its finely adapted ROC Cutoff Point, straightaway to make binary classifications using the Classification Scoring Engine of GeneXproTools. Note, however, that you'll have to change the Rounding Threshold to ROC Threshold in the Settings Panel (when a Logistic Regression run is converted to Classification, the Rounding Threshold is set to Logistic Threshold by default) and then recalculate all model thresholds by selecting Update All Thresholds in the History menu.

The Youden index is also used to evaluate a wide range of useful statistics at the Optimal Cutoff Point (OCP statistics for short). They include:

  • TP (True Positives)
  • TN (True Negatives)
  • FP (False Positives)
  • FN (False Negatives)
  • TPR (True Positives Rate or Sensitivity)
  • TNR (True Negatives Rate or Specificity)
  • FPR (False Positives Rate, also known as 1-Specificity)
  • FNR (False Negatives Rate)
  • PPV (Positive Predictive Value)
  • NPV (Negative Predictive Value)
  • Classification Accuracy (Correct Classifications)
  • Classification Error (Wrong Classifications)

How they are calculated is shown in the table below ("TC" represents the number of Total Cases):

TPR (Sensitivity) TP / (TP + FN)
TNR (Specificity) TN / (TN + FP)
FPR (1-Specificity) FP / (FP + TN)
FNR FN / (FN + TP)
PPV TP / (TP + FP), and TP + FP ≠ 0
NPV TN / (TN + FN), and TN + FN ≠ 0
Classification Accuracy (TP + TN) / TC
Classification Error (FP + FN) / TC

 

It is worth pointing out that OCP statistics are quantile-independent and are therefore a good indicator of what could be achieved with a model in terms of logistic fit and accuracy.  


Cutoff Points

The Cutoff Points Analysis complements the ROC Analysis of the previous section. The Cutoff Points Chart shows clearly the intersection of both the sensitivity (TPR) and specificity (TNR) lines and also the intersection of the FPR line with the FNR line. Seeing how these four lines change with the model output is a great aid to choosing the Ideal Cutoff Point for your test values.

The Ideal Cutoff Point varies from problem to problem, as one might be interested in minimizing or maximizing different things. Sometimes the goal is to minimize the number of false positives; other times the number of false negatives; still other times one might need to maximize the number of true positives or true negatives. With the help of the Cutoff Points Chart of GeneXproTools you can see clearly the best way to move your model threshold to achieve your goals.

Notwithstanding, there is a generic Optimal Cutoff Point. This Optimal Cutoff Point is given by the Youden index and you can see where it exactly lies in the Cutoff Points Chart. When you check the Show ROC CP checkbox, GeneXproTools draws the ROC Cutoff Point in dark brown. GeneXproTools also shows the Logistic Cutoff Point in the Cutoff Points Chart so that you can easily compare both cutoff points. To draw the Logistic Cutoff Point just check the checkbox Show LCP.



The Youden index J returns the maximum value of the expression (for inverted models it returns the minimum):

J = max[SE(t) + SP(t) - 1]


where SE(t) and SP(t) are, respectively, the sensitivity and specificity over all possible threshold values t of the model. Thus, the ROC Cutoff Point corresponds to the model output at the Optimal Cutoff Point.

In the Cutoff Points Table, GeneXproTools also shows all “SE + SP -1” values and highlights in light green the row with the Optimal Cutoff Point and corresponding ROC Cutoff Point. These parameters are also shown in the companion Cutoff Points Statistics Report.



The ROC Cutoff Point can be obviously used to evaluate a Confusion Matrix (in GeneXproTools it is called ROC Confusion Matrix) and, in the Cutoff Points Table, you have access to the Predicted Class, the Match, and Type values used to evaluate the ROC Confusion Matrix (you can see the graphical representation of the ROC Confusion Matrix in the Confusion Matrix section).

The visualization of the ROC Confusion Matrix is a valuable tool and can in fact be used to determine the right number of bins to achieve a good fit with the Logistic Regression Model. But GeneXproTools allows you to do more with the ROC Confusion Matrix and associated ROC Cutoff Point. By allowing the conversion of Logistic Regression runs to the Classification Framework, you can use this model with its ROC Cutoff Point straightaway to make discrete classifications using the Classification Scoring Engine of GeneXproTools. Note, however, that you'll have to change the Rounding Threshold to ROC Threshold in the Settings Panel (when a Logistic Regression run is converted to Classification, the Rounding Threshold is set to Logistic Threshold by default) and then recalculate all model thresholds by selecting Update All Thresholds in the History menu.

The Youden index is also used to evaluate a wide range of useful statistics at the Optimal Cutoff Point (OCP statistics for short). They include:

  • TP (True Positives)
  • TN (True Negatives)
  • FP (False Positives)
  • FN (False Negatives)
  • TPR (True Positives Rate or Sensitivity)
  • TNR (True Negatives Rate or Specificity)
  • FPR (False Positives Rate, also known as 1-Specificity)
  • FNR (False Negatives Rate)
  • PPV (Positive Predictive Value)
  • NPV (Negative Predictive Value)
  • Classification Accuracy (Correct Classifications)
  • Classification Error (Wrong Classifications)

How they are calculated is shown in the table below ("TC" represents the number of Total Cases):

TPR (Sensitivity) TP / (TP + FN)
TNR (Specificity) TN / (TN + FP)
FPR (1-Specificity) FP / (FP + TN)
FNR FN / (FN + TP)
PPV TP / (TP + FP), and TP + FP ≠ 0
NPV TN / (TN + FN), and TN + FN ≠ 0
Classification Accuracy (TP + TN) / TC
Classification Error (FP + FN) / TC

It is worth pointing out that OCP statistics are quantile-independent and are therefore a good indicator of what could be achieved with a model in terms of logistic fit and accuracy.  


Gains Chart

The Gains Chart of GeneXproTools is quantile-based and shows the cumulative gain as more cases are included in a campaign or test. The Lift Curve is compared to both a Random Model and an Ideal Model, showing clearly the advantages of using a model as opposed to not using one.



The Random Line in the Gains Chart represents the average response rate. And the Ideal Line represents a perfect model that is never wrong and therefore could select all the estimated positive responses. So, the further up (or down, for inverted models) the Lift Curve is from the Random Line the better the model.

The Gains Ranking Quality (GRQ) is a good indicator of the quality of a model. It is defined as the relation between the area under the Ideal Model and the area under the Lift Curve. It ranges from -1 to +1, with zero corresponding to the Random Model. The better the model the closer the GRQ gets to either +1 or -1 (for inverted perfect models GRQ = -1, whereas for normal perfect models GRQ = 1). As an additional quality measure, the Area Under the Lift Curve (represented by AUC in the Gains Chart) is also evaluated and shown both in the Gains Chart and in the companion Gains Statistics Report.




Lift Chart

The Lift Chart of GeneXproTools shows both the Lift Curve and Cumulative Lift Curve on the same graph. These curves are also shown in relation to a Random Model and an Ideal Model.



The Random Line in the Lift Chart represents the average response rate. And the Ideal Line represents a perfect model that is never wrong and therefore could select all the estimated positive responses. The point where the Lift Curve crosses the Random Line corresponds approximately to the percentage of the population beyond which the benefits from using the model are lost.

Other useful visual clues from the Lift Chart include the Area Between both Lift Curves (represented by ABC in the Lift Chart). Theoretically, the greater ABC the better the model. The individual areas under each of the Lift Curves are also computed and shown both on the Lift Chart and in the companion Lift Statistics Report.

The Lift Ranking Quality (LRQ) is yet another useful indicator of the accuracy of a model. It corresponds to the ABC area normalized against the area under the Ideal Line. Negative values both for the ABC and LRQ are indicative of an inverted model.




Log Odds and Logistic Regression

The Log Odds Chart is central to the Logistic Regression Model. It’s with its aid that the slope and intercept of the Logistic Regression Model are calculated. And the algorithm is quite simple. As mentioned previously, it’s quantile-based and, in fact, just a few additional calculations are required to evaluate the regression parameters.

So, based on the Quantile Table, one first evaluates the odds ratio for all the bins (you have access to all the values on the Log Odds Table under Odds Ratio). Then the natural logarithm of this ratio (or the Log Odds) is evaluated (the Log Odds values are also shown on the Log Odds Table under Log Odds).



Note, however, that there might be a problem in the evaluation of the log odds if there are bins with zero positive cases. But this problem can be easily fixed with standard techniques. Although rare for large datasets, it can sometimes happen that some of the bins end up with zero positive cases in them. And this obviously results in a calculation error in the evaluation of the natural logarithm of the odds ratio. GeneXproTools handles this with a slight modification to the Laplace estimator to get what is called a complete Bayesian formulation with prior probabilities. In essence, this means that when a particular Quantile Table has bins with only negative cases, then we do the equivalent of priming all the bins with a very small amount of positive cases.

The formula GeneXproTools uses in the evaluation of the Positives Rate values pi for all the quantiles is the following:



where μ is the Laplace estimator that in GeneXproTools has the value of 0.01; Qi and Ti are, respectively, the number of Positive Cases and the number of Total Cases in bin i; and P is the Average Positive Rate of the whole dataset.

So, in the Log Odds Chart, the Log Odds values (adjusted or not with the Laplace strategy) are plotted on the Y-axis against the Model Output in the X-axis. And as for Quantile Regression, here there are also special rules to follow, depending on whether the predominant class is “1” or “0” and whether the model is normal or inverted. To be precise, the Log Odds are plotted against the Model Upper Boundaries if the predominant class is “1” and the model is normal, or the predominant class is “0” and the model is inverted; or against the Lower Boundaries if the predominant class is “1” and the model is inverted, or the predominant class is “0” and the model is normal.

Then a weighted linear regression is performed and the slope and intercept of the regression line are evaluated. And these are the parameters that will be used in the Logistic Regression Equation to evaluate the probabilities.

The regression line can be written as:



where p is the probability of being “1”; x is the Model Output; and a and b are, respectively, the slope and intercept of the regression line. GeneXproTools draws the regression line and shows both the equation and the R-square in the Log Odds Chart.



And now solving the logistic equation above for p, gives:



which is the formula for evaluating the probabilities with the Logistic Regression Model. The probabilities estimated for each case are shown in the Logistic Fit Table.

Besides the slope and intercept of the Logistic Regression Model, another useful and widely used parameter is the exponent of the slope, usually represented by Exp(slope). It describes the proportionate rate at which the predicted odds ratio changes with each successive unit of x. GeneXproTools also shows this parameter both in the Log Odds Chart and in the companion Log Odds Stats Report.  


Logistic Fit Chart

The Logistic Fit Chart is a very useful graph that allows not only a quick visualization of how good the Logistic Fit is (the shape and steepness of the sigmoid curve are excellent indicators of the robustness and accuracy of the model), but also how the model outputs are distributed all over the model range.



The blue line (the sigmoid curve) on the graph is the logistic transformation of the model output x, using the slope a and intercept b calculated in the Log Odds Chart and is evaluated by the already familiar formula for the probability p:



Since the proportion of Positive responses (1’s) and Negative responses (0’s) must add up to 1, both probabilities can be read on the vertical axis on the left. Thus, the probability of “1” is read directly on the vertical axis; and the probability of “0” is the distance from the line to the top of the graph, which is 1 minus the axis reading.

But there’s still more information on the Logistic Fit Chart. By plotting the dummy data points, which consist of up to 1000 randomly selected model scores paired with dummy random ordinates, one can clearly visualize how model scores are distributed. Are they all clumped together or are they finely distributed, which is the telltale sign of a good model? This is valuable information not only to guide the modeling process (not only in choosing model architecture and composition but also in the exploration of different fitness functions and class encodings that you can use to model your data), but also to sharpen one’s intuition and knowledge about the workings of learning evolutionary systems.

Indeed, browsing through the different models created in a run might prove both insightful and great fun. And you can do that easily as all the models in the Run History are accessible through the Model selector box in the Logistic Regression Window. Good models will generally allow for a good distribution of model outputs, resulting in a unique score for each different case. Bad models, though, will usually concentrate most of their responses around certain values and consequently are unable to distinguish between most cases. These are of course rough guidelines as the distribution of model outputs depends on multiple factors, including the type and spread of input variables and the complexity of the problem. For example, a simple problem may be exactly solved by a simple step function.

Below is shown a Gallery of Logistic Fit Charts typical of intermediate models generated during a GeneXproTools run. It was generated using the same models used to create the twin ROC Curve Gallery presented in the ROC Analysis section. The models were created for a risk assessment problem with a training dataset with 18,253 cases and using a small population of just 30 programs. The Classification Accuracy, the R-square, and the Area Under the ROC Curve (AUC) of each model, as well as the generation at which they were discovered, are also shown as illustration. From top to bottom, they are as follow:

  • Generation 0, Accuracy = 65.33%, R-square = 0.0001, AUC = 0.5273
  • Generation 5, Accuracy = 66.03%, R-square = 0.0173, AUC = 0.5834
  • Generation 59, Accuracy = 66.92%, R-square = 0.0421, AUC = 0.6221
  • Generation 75, Accuracy = 68.99%, R-square = 0.1076, AUC = 0.7068
  • Generation 155, Accuracy = 69.93%, R-square = 0.1477, AUC = 0.7597
  • Generation 489, Accuracy = 74.15%, R-square = 0.2445, AUC = 0.7968

Generation 0, Accuracy = 65.33%, R-square = 0.0001, AUC = 0.5273


Generation 5, Accuracy = 66.03%, R-square = 0.0173, AUC = 0.5834


Generation 59, Accuracy = 66.92%, R-square = 0.0421, AUC = 0.6221


Generation 75, Accuracy = 68.99%, R-square = 0.1076, AUC = 0.7068


Generation 155, Accuracy = 69.93%, R-square = 0.1477, AUC = 0.7597


Generation 489, Accuracy = 74.15%, R-square = 0.2445, AUC = 0.7968


Besides its main goal, which is to estimate the probability of a response, the Logistic Regression Model can also be used to make categorical or binary predictions. From the logistic regression equation introduced in the previous section, we know that when a Positive event has the same probability of happening as a Negative one, the log odds term in the logistic regression equation becomes zero, giving:



where x is the model output at the Logistic Cutoff Point; and a and b are, respectively, the slope and the intercept of the regression line.

The Logistic Cutoff Point can be obviously used to evaluate a Confusion Matrix (in the Logistic Regression Window it is called Logistic Confusion Matrix to distinguish it from the ROC Confusion Matrix), in which model scores with Prob[1] higher than or equal to 0.5 correspond to a Positive case and a Negative otherwise.

In the Logistic Fit Table, GeneXproTools shows the Most Likely Class, the Match, and Type values of the Logistic Confusion Matrix (you can see the graphical representation of the Logistic Confusion Matrix in the Confusion Matrix Tab). For easy visualization, the model output closest to the Logistic Cutoff Point is highlighted in light green in the Logistic Fit Table. Note that the exact value of the Logistic Cutoff Point is shown in the companion Logistic Fit Stats Report.




Confusion Matrix

In the Logistic Regression Window, GeneXproTools evaluates and shows two different Confusion Matrices: the Logistic Confusion Matrix and the ROC Confusion Matrix.



The Logistic Confusion Matrix is derived from the logistic regression model and evaluates the Most Likely Class using the predicted probabilities evaluated for each record. Thus, probabilities higher than or equal to 0.5 (the Logistic Cutoff Point) indicate a Positive response or a Negative response otherwise. The model output closest to the Logistic Cutoff Point is highlighted in light green in the Confusion Matrix Table. Note that the exact value of the Logistic Cutoff Point is shown in the companion Logistic Confusion Matrix Stats Report.

In the Confusion Matrix Table you have access not only to the predicted probabilities for each case but also to the Most Likely Class plus how these predictions compare to actual target values. In the Confusion Matrix Table, GeneXproTools also shows the Type of each classification (true positive, true negative, false positive, or false negative) for all sample cases. These results are then displayed graphically, both in a 2-way table (the Confusion Matrix) and in a quantile-based distribution chart (the Confusion Matrix Distribution Chart).

The ROC Confusion Matrix, on the other hand, is evaluated using the Optimal Cutoff Point (or ROC Cutoff Point), a parameter derived from the ROC Curve. This means that for model scores higher than or equal to the ROC Cutoff Point, a Positive response is predicted and a Negative response otherwise. Note that, despite displaying in the Confusion Matrix Tab the diagram representation of the ROC Confusion Matrix, the confusion matrix data (Predicted Class, Match, and Type) are shown in the Cutoff Points Table.

Note, however, that the statistics evaluated at the Optimal Cutoff Point (or OCP statistics, for short) might result in slightly different values than the ones derived from the ROC Confusion Matrix. Remember that OCP statistics are evaluated using the direct readings of all the parameters at the Optimal Cutoff Point (this point, which is highlighted in green both in the ROC Curve Table and Cutoff Points Table, is also highlighted in the Confusion Matrix Table in green for a comparison with the Logistic Cutoff Point). For inverted models, for instance, the ROC Confusion Matrix was adjusted to match the default predictions of binomial logistic regression, which always predicts the “1” or positive class. The OCP statistics, however, are not adjusted for inversion and correspond to the actual values for the model. Also note that if you decide to export an inverted model to the Classification Framework, the confusion matrix you’ll get there using the ROC Cutoff Point will match the OCP statistics rather than the ROC Confusion Matrix.

Besides the canonical confusion matrix, GeneXproTools also shows a new kind of confusion matrix. This new confusion matrix plots the distribution of all the classification outcomes (TP, TN, FP, FN) along the different quantiles or bins. This shows clearly what each model is doing, and where their strengths and weaknesses lie. And by comparing both Confusion Matrix Distribution Charts (logistic and ROC), you can also see how both systems are operating. This is valuable information that you can use in different ways, but most importantly you can use it to fine-tune the number of quantiles in your system so that you can get the most of the logistic fit (as a reminder, the ROC Confusion Matrix is quantile-independent and can be used as reference for fine-tuning the logistic regression model that is quantile dependent).




Modeling Strategies

The addition of the Logistic Regression Analytics Platform to GeneXproTools started in response to specific user requests and the analysis of how GeneXproTools is being used in the wild.

The implementation of the Logistic Regression Analytics Platform uses the Logistic Regression Framework in the model creation phase, with a total of 59 built-in Fitness Functions. The default fitness function for Logistic Regression is the Positive Correl fitness function, as correlation-based fitness functions are extremely efficient at finding very good logistic regression models. In GeneXproTools several correlation-based fitness functions are implemented, with the Enhanced Series combining bounded positive correlations with different error measures:



The innovative Classification Scatter Plot and Binomial Fit Charts of the Run Panel (Binomial Fit by Target, Binomial Fit by Model, and Binomial Fit by Target & Model) are very useful to get an idea of the kind of range the evolving models are exploring. Indeed, different fitness functions work on different ranges and therefore explore the solution space differently. Indeed, the reason why both correlation-based fitness functions work so well with the standard 0/1 class encoding is that they can get free of the restricting 0/1 target range of the standard class encoding. For instance, a fitness function such as the one based exclusively on the Mean Squared Error (MSE) will only be able to drive evolution towards optimal solutions around the boundaries of the standard 0/1 class encoding. Note, however, that the MSE fitness function of GeneXproTools for Logistic Regression is richer than a simplistic fitness function based on the MSE alone, as it combines the MSE with the Cost/Gain Matrix and implements a control for favoring solutions with continuous model outputs.



Notwithstanding, if you use a different Class Encoding, say [-1000, 1000], you'll be able to explore different solution spaces with most fitness functions. For example, a fitness function based on the MSE alone, although still confined to the target range, would have much more room to explore and come up with good ranges for the model scores. This is of course the most important prerequisite for designing a good model. And you can observe this change in behavior straightaway with the help of the Classification Scatter Plot and different Binomial Fit Charts (sorted either by target or model or by target & model), available both in the Run Panel and Results Panel.



GeneXproTools allows you to Change the Class Representation easily and therefore you can experiment with different class encodings without much trouble (and you can just as easily revert to the standard 0/1 encoding if you feel more comfortable with it, although it has no bearing on the real meaning of the binary representation and how everything is processed and shown in the Logistic Regression Window, with the minimum value always representing the standard "0" or Negative cases, and the maximum value representing the standard "1" or Positive cases).

To change the Class Encoding within GeneXproTools, choose Class Encoding in the Data menu. This opens the Class Encoding Window of GeneXproTools. In the Class Encoding Window, you can choose your encoding from several default values, but you can also experiment with all kinds of binary encodings, including systems with floating-point values, by entering any pair of two different numbers in the Change To box in the Other Encodings option.



Also notice that you can invert your class representation by checking the Invert Class Representation checkbox. This means that what you had originally represented as “0” will become “1” and vice versa. This might prove useful in certain modeling situations, but please keep in mind that GeneXproTools will be handling what you originally had as negative cases as 1’s. And this means that within the Logistic Regression Framework all the predictions and analyses will be made for these new 1’s because the Logistic Regression Technique is by default designed to always predict the 1’s. Remember, however, that you can always revert to the original encoding by inverting the representation once more.

Also worth mentioning in this section about modeling strategies is the fact that GeneXproTools allows the conversion of Classification runs to Logistic Regression and vice versa. This obviously means that you can explore all the fitness functions available for Classification (there are a total of 52 built-in fitness functions for Classification) to evolve your models. Then, in the Logistic Regression Framework you have access to all the analyses of the Logistic Regression Analytics Platform, including the evaluation of Quantile Tables, analysis of Gains and Lift Charts, the complete ROC Analysis with the Cutoff Points Charts, and of course the evaluation of the probabilities with the Logistic Regression Algorithm and also the comparison of the Logistic and ROC Confusion Matrices.

When a Logistic Regression run is converted to Classification, the Logistic Cutoff Point is automatically set up as default in the Fitness Function Tab. This ensures that the Logistic Cutoff Point evaluated for each model in the Logistic Regression Framework remains unchanged in the new Classification run.

It is also worth pointing out that, when you convert a Logistic Regression run to Classification, you can also use the ROC Cutoff Point as your Rounding Threshold. Note, however, that in this case you'll have to change the Rounding Threshold to ROC Threshold in the Fitness Function Tab. The confusion matrix you'll get in this case on the Classification Framework will match obviously the ROC Confusion Matrix.  


Testing a Model

The predictive accuracy of logistic regression models can be evaluated like all the models are evaluated in GeneXproTools. That is, as soon as evolution stops, and if a validation/test set is available, both the fitness and classification accuracy are immediately evaluated for the validation dataset and the results are shown straightaway on the Run Panel. Furthermore, an additional set of statistics, including the Correlation Coefficient, the R-square, the Recall, the Precision and the Area Under the ROC Curve, are evaluated and shown in the Results Panel for both the training and validation datasets.



When both the Fitness and Classification Accuracy obtained for the validation set are about the same as the values obtained for the training set, this is a good indicator that your model is a good one and therefore can be used to make accurate predictions.

Additionally, within the Logistic Regression Window, GeneXproTools allows you to run the whole set of analytics tools on the validation dataset, namely the evaluation and analysis of Quantile Tables, ROC Curves & Tables, Cutoff Points, Gains and Lift Charts, Log Odds Analysis & Logistic Regression and Logistic Fit, and ROC & Logistic Confusion Matrices. For that you just have to select Validation in the Dataset combobox in the Logistic Regression Window.



Note, however, that this additional testing procedure builds its own Quantile Table and also evaluates and uses its own slope and intercept for the Logistic Regression Model. This means that the logistic regression parameters evaluated for the training dataset are not operational during this testing and new ones are being evaluated for the validation dataset, which might prove useful as a form of further testing the model.

It’s worth emphasizing that the logistic regression model that GeneXproTools deploys during scoring, either internally or using the generated code for deployment to Excel or elsewhere, uses the slope and intercept evaluated for the training dataset that was used during the learning process, unless an update of the threshold was carried out using the Update Current Threshold or Update All Thresholds functionality accessible though the History menu.


Making Categorical and Probabilistic Predictions

The goal in Logistic Regression is to assign probabilities to model scores, creating a reliable ranking system that can be used straightaway to evaluate the risk involved in financial and insurance applications, to rank potential respondents in a marketing campaign, or to evaluate the risk of contracting a disease.

The Logistic Regression Framework of GeneXproTools builds on the model scores it generates with its innovative hybrid system where Evolutionary Algorithms are combined with the canonical Logistic Regression Technique. This powerful logistic regression model is then used to estimate probabilities for each model score, which in turn can be used to make categorical predictions for each outcome. These categorical or binary predictions are summarized in the Logistic Confusion Matrix of the Logistic Regression Window and also in the Confusion Matrix of the Run Panel and the Results Panel.



GeneXproTools scores new cases using the JavaScript code it generates for your logistic regression model, allowing you to choose the kind of model output through the Model Output combobox. By choosing either Probability[1] or Most Likely Class in the Model Output combobox, you have access to the complete code of your logistic regression models.



Moreover, in the Model Panel, you can also access all the generated code in all the programming languages available in GeneXproTools (19 built-in programming languages plus all programming languages you add through the Custom Grammars of GeneXproTools).



Additionally, by deploying your models and ensembles to Excel, you have very conveniently within Excel the complete code of your logistic regression models in Excel VBA. This way you can make predictions straightaway with your logistic regression models in Excel.



In order to score new cases with the Scoring Engine of GeneXproTools you need to:

  1. Go to the Scoring Panel and select the type of model output in the Model Output combobox.
    You can choose either Probability[1], Most Likely Class, or Raw Model Output.
  2. Enter the path for the scoring data or connect to the Excel file or database where your new cases are kept.
  3. Enter the path for the file in which the scoring results will be saved.
    If you also want to include the input values in the output file, you have to choose Predictor Variables Plus Output in the Content combobox.
  4. Press the Start button to score your new cases.
    GeneXproTools shows the scoring results for the first 2000 cases in the Scoring Table of the Scoring Panel for a quick preview. All the scoring results, however, are saved to file.


The Scoring Engine of GeneXproTools allows you to score as many new cases as you wish without exiting the GeneXproTools environment. But you can also score your new cases outside GeneXproTools using the code it automatically generates for your models in any of the 19 programming languages it supports for Logistic Regression.



And as mentioned above, through the innovative functionality of Excel Deployment of Models & Ensembles, the generated Excel VBA code of your models can be immediately used to automatically deploy the code of all your logistic regression models to Excel where you then can conveniently carry out the scoring of your models and your model ensembles.




Evaluating the Variable Importance of Model Variables

GeneXproTools uses a sophisticated stochastic method to compute the variable importance of all the variables in a model. For all logistic regression models the importance of each model variable is computed by randomizing its input values and then computing the decrease in the R-square between the model output and the target. The results for all variables are then normalized so that they add up to 1.

GeneXproTools evaluates the variable importance of all the variables (original and derived) in a model and shows the results in the Statistics Report in the Data Panel. The variable importance is also shown graphically in the Variable Importance Chart. The Variable Importance Chart is available through the Statistics Charts in the Data Panel when Model Variables is selected in the Variables combobox.




Converting Classification Runs to Logistic Regression

GeneXproTools allows you to convert runs created within the Classification Framework to Logistic Regression. This means that you’ll be able to generate probabilities with these models using the Logistic Regression Algorithm implemented in the Logistic Regression Framework. Note, however, that you'll only be able to reap all the benefits of the Logistic Regression Algorithm if your classification models were created with the Logistic Threshold; for other threshold types you'll likely see a slight decrease in accuracy when you convert your Classification runs to Logistic Regression. Notwithstanding, converting your Classification runs to Logistic Regression might prove useful even in those cases, as the algorithm that generates the probabilities in the Classification Framework is less robust than the powerful and innovative Logistic Regression Algorithm implemented in the Logistic Regression Framework.

You can convert any Classification run to the Logistic Regression Framework. But you may also consider creating new ones with the sole purpose of exploring all the Classification fitness functions (there are a total of 52 built-in fitness functions in the Classification Framework, which are a nice addition to the 59 built-in fitness functions of Logistic Regression). Then, in the Logistic Regression Framework you have access to all the analyses of the Logistic Regression Analytics Platform, including the evaluation of Quantile Tables, analysis of Gains and Lift Charts, the complete ROC Analysis with the Cutoff Points Charts, and of course the evaluation of the probabilities with the Logistic Regression Algorithm and also the comparison of the Logistic and ROC Confusion Matrices. In addition, you can use these models as seed (either in the Logistic Regression Framework or back in the Classification Framework) to create better models from them. You can obviously repeat this process for as long as you wish, until you obtain the right model for your data.

To convert a Classification run to Logistic Regression you need to:

  1. Within the Classification Framework, choose Convert To Logistic Regression in the File menu.
    This opens the Save As dialog box and also asks if you want to save the current run before converting it to Logistic Regression. This way you will be able to come back to it if you need to.
  2. Type the run name for the new Logistic Regression run and then click Save.
    When you click Save, GeneXproTools takes you immediately to the Logistic Regression Framework. Note that the model statistics of the converted models in the run History will only match the ones evaluated in the Classification Framework if the classification models were created with the Logistic Threshold; if a different threshold was used you’ll get slightly different values when you do Refresh All to update all calculations in the History Panel or when you analyze your models in the Results Panel. Model statistics are also updated when you go to the Data Panel.

Converting Logistic Regression Runs to Classification

GeneXproTools also allows you to convert Logistic Regression runs to Classification. This means that, among other things, you can easily access all the Classification fitness functions to drive model evolution (there are a total of 52 built-in fitness functions in the Classification Framework, which are a nice addition to the 59 built-in fitness functions of Logistic Regression). By going back and forth between both platforms, you can explore different modeling tools to fine-tune your models.

When a Logistic Regression run is converted to Classification, the Logistic Cutoff Point is automatically set up as default in the Fitness Function Tab. This ensures that the Logistic Cutoff Point evaluated for each model in the Logistic Regression Framework remains unchanged in the new Classification run.

It is also worth pointing out that when you convert a Logistic Regression run to Classification you can also use the ROC Cutoff Point as your Rounding Threshold. Note, however, that in this case you'll have to change the Rounding Threshold to ROC Threshold in the Fitness Function Tab. The confusion matrix you'll get in this case on the Classification Framework will match obviously the ROC Confusion Matrix.  

To convert a Logistic Regression run to Classification you need to:

  1. Within the Logistic Regression Framework, choose Convert To Classification in the File menu.
    This opens the Save As dialog box and also asks if you want to save the current run before converting it to Classification. This way you will be able to come back to it if you need to.
  2. Type the run name for the new Classification run and then click Save.
    When you click Save, GeneXproTools takes you immediately to the Classification Framework. When converting a Logistic Regression run to Classification, GeneXproTools will try to match the fitness function whenever possible (for example, the ROC Measure fitness function or the Positive Correl fitness function exist in both frameworks, but the R-square fitness function or the Symmetric ROC fitness function exist only in the Logistic Regression Framework); when a match is not possible, the Positive Correl fitness function is set by default. Thus, in the History Panel the fitness values that are shown there upon conversion correspond to the ones evaluated in the Logistic Regression Framework. By choosing Refresh All you can rapidly update these values to their true values in this new context.

Importing Regression Models to Logistic Regression

GeneXproTools allows you to import models created within the Regression Framework to Logistic Regression, as long as their structure and composition are compatible.



When Regression models are imported into a Logistic Regression run, GeneXproTools evaluates automatically all the logistic regression parameters for all the models, namely the Slope, Intercept and Logistic Cutoff Point. This allows you to generate probabilities with these models straightaway using the Logistic Regression Algorithm implemented in the Logistic Regression Framework.



Then, in the Logistic Regression Framework you have access to all the analyses of the Logistic Regression Analytics Platform, including the evaluation of Quantile Tables, analysis of Gains and Lift Charts, the complete ROC Analysis with the Cutoff Points Charts, and of course the evaluation of the probabilities with the Logistic Regression Algorithm and also the comparison of the Logistic and ROC Confusion Matrices. In addition, you can use these models as seed to create better models from them.



The main advantage of importing models created in the Regression Framework to Logistic Regression is that you can use all the Regression fitness functions to drive model evolution (there are a total of 49 built-in fitness functions in the Regression Framework, which are a nice addition to the 59 built-in fitness functions of Logistic Regression). By going back and forth between both platforms, you can explore different modeling tools to fine-tune your models. Below is shown a model created in the Regression Framework using the RMSE fitness function.



And now the same model imported to the Logistic Regression Framework, where it can be either used as seed to create a better model or deployed straightaway and evaluated.





Last modified: October 24, 2013


Cite this as:

Ferreira, C. "Logistic Regression Analytics Platform." From GeneXproTools Tutorials – A Gepsoft Web Resource.
https://www.gepsoft.com/tutorials/LogisticRegressionAnalyticsPlatform.htm

 

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