The Naive Bayes classifier is one of the most versatile machine learning algorithms that I have seen around during my meager experience as a graduate student, and I wanted to do a toy implementation for fun. At its core, the implementation is reduced to a form of counting, and the entire Python module, including a test harness took only 50 lines of code. I haven’t really evaluated the performance, so I welcome any comments. I am a Python amateur, and am sure that experienced Python hackers can trim a few rough edges off this code.

Intuition and Design

Here is definition a of the classifier functionality (from wikipedia):

Now this means, that for each possible class label, multiply together the conditional probability of each feature, given the class label. This means, for us to implement the classifier, all we need to do, is compute these individual conditional probabilities for each label, for each feature, p(Fi | Cj), and multiply them together with the prior probability for that label p(Cj). The label for which we get the largest product, is the label returned by the classifier.

In order to compute these individual conditional probabilities, we use the Maximum Likelihood Estimation method. In a very short sentence, we approximate these probabilities using the counts from the input/training vectors.

Hence we have: p(Fi | Cj) = count( Fi ^ Cj) / count(Cj)

That is, we count from the training corpus, the ratio of the number of occurrences of the feature Fi and the label Cj together to the total number of occurrences of the label Cj.

Zero Probability Problem

What if we have never seen a particular feature Fa and a particular label Cb together in the training dataset? Whenever they occur in the test data, p(Fa | Cb) will be zero. Hence the overall product will also be zero. This is a problem with maximum likelihood estimates. Just because a particular observation was not made during training does not mean that it will never occur in the test data. In order to remedy this issue, we use what is known as smoothing. The simplest kind of smoothing that we use in this code, is called “add one smoothing”. Essentially, the probability for an unseen event should be greater than one. We achieve this by adding one to each zero count. The net effect should be that we redistribute some of the probability mass from the non-zero count observations to the zero-count observations. Hence, we also need to increase the total count for each label by the number of possible observations, in order to maintain the total probability mass at 1.

For example, if we have two classes C = 0 and C = 1, then after smoothing, the smoothed MLE probabilities can be written as:

p-smoothed(Fi | Cj) = [count(Fi ^ Cj) + 1]/[count(Cj) + N] where N is the total number of observations across all features in the training corpus.

Code

For simplicity, we will use Weka’s ARFF file format as input. We have a single class called Model which has a few dictionaries and lists to store the counts and feature vector details. In this implementation, we only deal with discrete valued features.

The dictionary ‘features’ saves all possible values for a feature. ‘featureNameList‘ is simply a list that contains the names of the features in the same order that it appears in the ARFF file. This is because our features dictionary does not have any intrinsic order, and we need to maintain feature order explicitly. ‘featureCounts‘ contains the actual counts for co-occurrence of each feature value with each label value. The keys for this dictionary are tuples of the form (class_label, feature_name, feature_value). Hence, if we have observed the feature F1 with the value ‘x’ for the label ‘yes’, fifteen times, then we will have the entry {(‘yes’, ‘F1’, 15)} in the dictionary. Note how the default values for counts in this dictionary is ‘1’ instead of ‘0’. This is because we are smoothing the counts. The ‘featureVectors‘ list actually contains all the input feature vectors from the ARFF file. The last feature in this vector is the class label itself, as is the convention with weka ARFF files. Finally, ‘labelCounts‘ stores the counts of the class labels themselves, i.e. now many times did we see the label Ci during training.

We also have the following member functions in the Model class:



The above method simply reads the feature names (including class labels), their possible values, and the feature vectors themselves; and populate the appropriate data structures defined above.



The TrainClassifier method simply counts the number of co-occurrences of each feature value with each class label, and stores them in the form of 3-tuples. These counts are automatically smoothed by using add-one smoothing as the default value of count for this dictionary is ‘1’. The counts of the labels is also adjusted by incrementing these counts by the total number of observations.

Finally, we have the Classify method, that accepts as argument, a single feature vector (as a list), and computes the product of individual conditional probabilities (smoothed MLE) for each label. The final computed probabilities for each label are stored in the ‘probabilityPerLabel‘ dictionary. In the last line, we return the entry from probabilityPerLabel which has the highest probability. Note that the multiplication is actually done as addition in the log domain as the numbers involved are extremely small. Also, one of the factors used in this multiplication, is the prior probability of having this class label.

Here is the complete code, including a test method:

Download the sample ARFF file to try it out.

Update: I found a bug in the last but one(th) line of the GetValues() function. This line gets the possible attribute values from the arff file and stores them in self.featureNameList. This method did not deal with whitespaces correctly. Update this line to: