Encoding in Python 2.x

One of the annoying things where I always forget the specifics. So here it is…

Reading a file line-by-line in python and writing it to another file is easy:

input_file = open("input.txt")
outputFile = open("output.txt", "w")
for line in input_file:
   outputFile.write(line + "\n")

But whenever encodings are involved, everything gets complicated. What is the encoding of line? Actually, not really anything, without specification, line is just a Byte-String (type 'str') with no encoding.

Because this is usually not what we want, the first step is to convert the read line to Unicode. This is done with the method decode. The method has two parameters. The fist is the encoding that should be used. This is a predefined String value which you can guess it for the more common encodings (or look it up in the documentation). If left out, ASCII is assumed. The second parameter defines how to handle unknown byte patterns. The value 'strict' will abort with UnicodeDecodeError, 'ignore' will leave the character out of the Unicode result, and 'replace' will replace every unknown pattern with U+FFFD. Let’s assume our input file and therefor the line we read from there is in Latin-1. We convert this to Unicode with:

lineUnicode = line.decode('latin-1','strict')

or equivalently

lineUnicode = unicode(line, encoding='latin-1', errors='strict')

After decoding, we have sometihng of type 'unicode'. If we try to print this and it is not simple English, it will probably give an error (UnicodeEncodeError: 'ascii' codec can't encode characters in position 63-66: ordinal not in range(128)). This is because Python will try to convert the characters to ASCII, which is not possible for characters that are not ASCII. So, to print out a Unicode text, we have to convert it to some encoding. Let’s say we want UTF-8 (there is no reason not to use UTF-8, so this is what you should always want):

lineUtf8 = lineUnicode.encode('utf-8')

Here again, there is a second parameter which defines how to handle characters that cannot be represented (which shouldn’t happen too often with UTF-8). Happy coding!

Further reading:
Unicode HOWTO in the Python documentation, Overcoming frustration: Correctly using unicode in python2 from the Python Kitchen project, The Absolute Minimum Every Software Developer Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!) by Joel Spolsky (not specific to Python, but gives a good background).

Learning to learn – What to look for in the evaluation of classification

Applying some machine learning algorithm to classify some data is made easy these days. There is a large amount of programming libraries, applications and online services available on the market. But how do we know whether the algorithm works? Or which of the methods to chose from is the best for our task? This post will give a very short introduction to the four most relevant issues in the evaluation of classification results. None of these points is restricted to a specific machine learning algorithm. In fact, none of them requires any understanding of the used classification method at all.

1. Good machine learning requires good data
The first and most obvious point is, that machine learning requires training data. Training data consists of a number of data items with associated labels assigned by humans. For example, we could train on a set of e-mails which have been labeled as spam or non-spam by the person receiving them. In order for a learning algorithm to learn something useful, a few conditions should be met by the training data. First, there should be enough data. Learning from only 100 e-mails will not work, as there are many types of spam mails. Second, the data should be as clean as possible. If half of the spam-labels are wrong, there is no way how an algorithm can learn what real spam is. And finally, the data should also be as close as possible to the real data that you want to classify later. Training a spam-recognition system on English and then apply it to German will probably not work well.

2. Don’t evaluate on your training data
After the machine learning algorithm has learned to distinguish the classes on the training data, it is ready to be applied to new data. Based on what it has learned from the training data, the algorithm will assign a class to each new data item. A common beginner’s mistake is to apply the algorithm to the training data again. This will lead to very good results, but these results are misleading. Imagine that the “learning algorithm” is just memorizing complete e-mails. If the exact same e-mail is shown to the algorithm again, it will confidently assign the correct class. 100% of training set e-mails will be correct! But even changing one word will cause the algorithm to fail, so it is no use to us in reality. Of course real learning algorithms are more complex, but the issue is the same. It is very easy to be confident about what you already have seen. The hard part is to deal with new stuff. So in order to have a reliable evaluation, the algorithm should be trained on one data set and applied to another totally separate set.

3. Evaluate on data that is close to the data you want to classify later
As we have just discussed, we need to evaluate on data that is different from the training data. But, just like the training data, the evaluation data should be as close as possible to the real data that you want to classify later. If you want to classify German, it doesn’t help you to know that the spam-classifier works very well on English. A common procedure for a good evaluation is to create one data set with labeled data, and then split it up into training and test data (e.g., 80% training data, 20% test data). No item is allowed to be in both sets at the same time. Another common technique is called k-fold cross-validation. This method splits the data into k (often 10) folds and does k train-test runs. In each run, one of the folds is used as test data and the other folds are used as training data. The folds do not change between runs, so in the end every item in the data has been assigned a label, but at that point this item was not in the training set, so point 2 is not violated. For both technique it is worth thinking about whether to randomly shuffle the folds or to enforce a similar label-distribution in all the folds in order to avoid artificial inflation of the results.

4. Chose the right evaluation metric for your problem
After the machine learning system has assigned a class to every data item, we compare the assigned labels to the real labels. The larger the percentage of correct labels, the better the system. There are many ways of comparing the labels depending on the nature of the labels and their distribution. The simplest measure, called accuracy, is to count the number of correct assignments, e.g., how many real spam-mails have been classified as spam by the system and how many non-spam-mails have been classified as non-spam. But accuracy is not a good measure in some cases. Let’s assume that 90% of mails are non-spam. If a system always assigns the label non-spam, it will be 90% accurate – but not useful at all. The same thing happens with many classes if some are much bigger than the others. Accuracy is also not a good choice when labels are on a scale. In this case confusing 1 and 5 is much more serious than confusing 1 and 2 and accuracy does not reflect this. There are alternative metrics for such scenarios that should be used.

I will stop here, although there is more much to be said. I encourage everybody to investigate the topic in more detail. Good evaluation is at least as important as good machine learning algorithms. If evaluation numbers do not reflect the expected real performance of a system, how can they be the basis of any decision?

This post has first appeared at 5analytics.com

Encoding question mark in TikZ

I’m trying to draw the question mark that is sometimes displayed when there are encoding issues: �

T-shirt Sch... Encoding

This is my solution:

\node[fill=black,rotate=45,inner sep=.1ex,text height=1.8ex,text width=1.8ex] {};
\node[font=\color{white}] (wi) {?};

Accessing JVM arguments from inside Java

Whenever I get a ClassNotFoundException error in Java, I think to myself “but it is there!” and then I correct the typo in the classpath or get angry at Eclipse for messing up my classpath. Lately I have programmed in more complex settings where it was not always clear to me where the application gets the classpath from, so I wanted to check which of my libraries actually end up on the classpath. Turns out it is not very complicated. Here is code to print a number of useful things:

System.out.println("Working directory: " 
      + Paths.get(".").toAbsolutePath().normalize().toString());
System.out.println("Classpath: " 
      + System.getProperty("java.class.path"));
System.out.println("Library path: " 
      + System.getProperty("java.library.path"));
System.out.println("java.ext.dirs: " 
      + System.getProperty("java.ext.dirs"));

The current working directory is the starting point for all relative paths, e.g., for reading and writing files. The normalization of the path makes it a bit more readable, but is not necessary. The class Paths is from the package java.nio.file.Paths. The classpath is the place where Java looks for (bytecode for) classes. The entries should be folders or jar-files. The Java library path is where Java looks for native libraries, e.g., platform dependent things. You can of course access other environment variables with the same method, but I cannot at the moment think of a useful example.

Related (at least related enough to put it into the same post), this is how you can print the space used and available on the JVM heap:

int mbfactor = 1024*1024;
System.out.println("Memory free/used/total/max " 
      + Runtime.getRuntime().freeMemory()/mbfactor + "/"
      + (Runtime.getRuntime().totalMemory()-Runtime.getRuntime().freeMemory())/mbfactor + "/"
      + Runtime.getRuntime().totalMemory()/mbfactor + "/"
      + Runtime.getRuntime().maxMemory()/mbfactor + " MB"

Positionng rests in the middle of a two-voice line

In choir scores, you often have the score for two voices (e.g., soprano and alto) in one line:

      \new Staff  = "Frauen"<<
         \new Voice = "Sopran" { \voiceOne \global  \soprano }
         \new Voice = "Alt" { \voiceTwo \global  \alto }

When they both have a pause at the same time with the same length, lilypond will still print two rests in different positions. If you (like me) think this looks weird, here is how you can change it:

soprano = \relative c' { a2 \oneVoice r4 \voiceOne } a4 }
alto = \relative c' { a2 s4 } a4 }

In one voice, change to only one voice with \oneVoice for the rest and then back to the usual voice, here /voiceOne. If you do the same in the other voice, you will get warnings about clashing notes, so instead of using a rest, use an invisible rest (spacer) with s.

An alternative is the following command which causes all rests to appear in the middle of the line. It should be used inside the \layout block:

   \override Voice.Rest #'staff-position = #0

Precision, Recall and F-measure

In the last post we discussed accuracy, a straightforward method of calculating the performance of a classification system. Using accuracy is fine when the classes are of equal size, but this is often not the case in real world tasks. In such cases the very large number of true negatives outweighs the number of true positives in the evaluation so that accuracy will always be artificially high.

Luckily there are performance measures that ignore the number of true negatives. Two frequently used measures are precision and recall. Precision P indicates how many of the items that we have identified as positives are really positives. In other words, how precise have we been in our identification. How many of those that we think are X, really are X. Formally, this means that we divide the number of true positives by the number of all identified positives (true and false):
P = TP/(TP+FP)

Recall R indicates how many of the real positives we have found. So from all of the positive items that are there, how many did we manage to identify. In other words, how exhaustive we were. Formally, this means that we divide the number of true positives by the number of all existing positives (true positives and false negatives):
R = TP/(TP+FN)

For our example from the last post, precision and recall are as follows:
P = 1/(1+3) = 1/4 = 0.25
R = 1/(1+2) = 1/3 = 0.33

It is easy to get a recall of 100%. We just say for everything that it is a positive. But as this will probably not the case (or else we have a really easy dataset to classify!), this approach will give us a really low precision. On the other hand, we can usually get a high precision if we only classify as positive one single item that we are really, really sure about. But if we do that, recall will be low, as there will be more than one item in the dataset to be classified (or else it is not a very meaningful set).

So recall and precision are in a sort of balance. The F1 score or F1 measure is a way of putting the two of them together to produce one single number. Formally it calculates the harmonic mean of the two numbers and weights the two of them with the same importance (there are other variants that put more importance on one of them):
F_1 = (2 \cdot P \cdot R)/(P + R)

Using the values for precision and recall for our example, F1 is:
F_1 = (2 \cdot 0.25 \cdot 0.33)/(0.25 + 0.33) = 0.165 / 0.58 = 0.28

Intuitively, F1 is between the two values of precision and recall, but closer to the lower of the two. In other words, it penalizes if we concentrate only on one of the values and rewards systems where precision and recall are closer together.

Link for a second explanation: Explanation from an Information Retrieval perspective


We are still trying to figure out how good our system for determining whether e-mails are spam or not is. In the last post we ended up with a confusion matrix like this:

Actual label
Spam NonSpam
Predicted label Spam 1 (true positives, TP) 3 (false positives, FP)
NonSpam 2 (false negatives, FN) 4 (true negatives, TN)

Now we want to calculate numbers from this table to describe the performance of our system. One easy way of doing this is to use accuracy A. Accuracy basically describes which percentage of decisions we got right. So we would take the diagonal entries in the matrix (the true positives and true negatives) and divide by the total number of entries. Formally:

In our example the accuracy is:
A = (1+4)/(1+4+2+3) = 5/10 = 0.5

Using accuracy is fine in examples like the above when both classes occur more or less with the same frequency. But frequently the number of true negatives is larger than the number of true positives by many orders of magnitudes. So let’s assume 994 for true negatives and when we calculate accuracy again, we get this:
A = (1+994)/(1+994+2+3) = 995/1000 = 0.995

It doesn’t really matter if we correctly identify any spam mails. Even if we always say NonSpam, so we get zero Spam-Mails right, we still get more nearly the same accuracy as above. So accuracy is not a good indicator of performance for our system in this situation. In the next post we will look at other measures we can use instead.

Link for a second explanation: Explanation from an Information Retrieval perspective

Confusion matrix

Let’s say we want to analyze e-mails to determine whether they are spam or not. We have a set of mails and for each of them we have a label that says either "Spam" or "NotSpam" (for example we could get these labels from users who mark mails as spam). On this set of documents (the training data) we can train a machine learning system which given an e-mail can predict the label. So now we want to know how the system that we have trained is performing, whether it really recognizes spam or not.

So how can we find out? We take another set of mails that have been marked as "Spam" or "NotSpam" (the test data), apply our machine learning system and get predicted labels for these documents. So we end up with a list like this:

Actual label Predicted label
Mail 1 Spam NonSpam
Mail 2 NonSpam NonSpam
Mail 3 NonSpam NonSpam
Mail 4 Spam Spam
Mail 5 NonSpam NonSpam
Mail 6 NonSpam NonSpam
Mail 7 Spam NonSpam
Mail 8 NonSpam Spam
Mail 9 NonSpam Spam
Mail 10 NonSpam Spam

We can now compare the predicted labels from our system to the actual labels to find out how many of them we got right. When we have two classes, there are four possible outcomes for the comparison of a predicted label and an actual label. We could have predicted "Spam" and the actual label is also "Spam". Or we predicted "NonSpam" and the label is actually "NonSpam". In both of these cases we were right, so these are the true predictions. But, we could also have predicted "Spam" when the actual label is "NonSpam". Or "NonSpam" when we should have predicted "Spam". So these are the false predictions, the cases where we have been wrong. Let’s assume that we are interested in how well we can predict "Spam". Every mail for which we have predicted the class "Spam" is a positive prediction, a prediction for the class we are interested in. Every mail where we have predicted "NonSpam" is a negative prediction, a prediction of not the class we are interested in. So we can summarize the possible outcomes and their names in this table:

Actual label
Spam NonSpam
Predicted label Spam true positives (TP) false positives (FP)
NonSpam false negatives (FN) true negatives (TN)

The true positives are the mails where we have predicted "Spam", the class we are interested in, so it is a positive prediction, and the actual label was also "Spam", so the prediction was true. The false positives are the mails where we have predicted "Spam" (a positive prediction), but the actual label is "NonSpam", so the prediction is false. Correspondingly the false negatives, the mails we should have labeled as "Spam" but didn’t. And the true negatives that we correctly recognized as "NonSpam". This matrix is called a confusion matrix.

Let’s create the confusion matrix for the table with the ten mails that we classified above. Mail 1 is "Spam", but we predicted "NonSpam", so this is a false negative. Mail 2 is "NonSpam" and we predicted "NonSpam", so this is a true negative. And so on. We end up with this table:

Actual label
Spam NonSpam
Predicted label Spam 1 3
NonSpam 2 4

In the next post we will take a loo at how we can calculate performance measures from this table.

Link for a second explanation: Explanation from an Information Retrieval perspective

Histograms of category frequencies in R

I am learning R, so this is my first attempt to create histograms in R. The data that I have is a vector of one category for each data point. For this example we will use a vector of a random sample of letters. The important thing is that we want a histogram of the frequencies of texts, not numbers. And the texts are longer than just one letter. So let’s start with this:

labels <- sample(letters[1:20],100,replace=TRUE)
labels <- vapply(seq_along(labels), 
                 function(x) paste(rep(labels[x],10), collapse = ""),
                 character(1L)) # Repeat each letter 10 times
library(plyr) # for the function 'count'
distribution <- count(labels)
distribution_sorted <- 
   distribution[order(distribution[,"freq"], decreasing=TRUE),]

I use the function count from the package plyr to get a matrix distribution with the different categories in column one (called "x") and the number of times this label occurs in column two (called "freq"). As I would like the histogram to display the categories from the most frequent to the least frequent one, I then sort this matrix by frequency with the function order. The function gives back a vector of indices in the correct order, so I need to plug this into the original matrix as row numbers.

Now let's do the histogram:

mp <- barplot(distribution_sorted[,"freq"],
         names.arg=distribution_sorted[,1], # X-axis names
         las=2,  # turn labels by 90 degrees
         col=c("blue"), # blue bars (just for fun)
         xlab="Kategorie", ylab="Häufigkeit", # Axis labels

There are many more settings to adapt, e.g., you can use cex to increase the font size for the numerical y-axis values (cex.axis), the categorical x-axis names (cex.names), and axis labels (cex.lab).

In my plot there is one problem. My categorie names are much longer than the values on the y-axis and so the axis labels are positioned incorrectly. This is the point to give up and do the plot in Excel (ahem, LaTeX!) - or take input from fellow bloggers. They explain the issues way better than me, so I will just post my final solution. I took the x-axis label out of the plot and inserted it separately with mtext. I then wanted a line for the x-axis as well and in the end I took out the x-axis names from the plot again and put them into a separate axis at the bottom (side=1) with zero-length ticks (tcl=0) intersecting the y-axis at pos=-0.3.

# mai = space around the plot: bottom - left - top - right
# mgp = spacing for axis title - axis labels - axis line
par(mai=c(2.5,1,0.3,0.15), mgp=c(2.5,0.75,0))
mp <- barplot(distribution_sorted[,"freq"],
         #names.arg=distribution_sorted[,1], # X-axis names/labels
         las=2,  # turn labels by 90 degrees
         col=c("blue"), # blue bars (just for fun)
         ylab="Häufigkeit", # Axis title
axis(side=1, at=mp, pos=-0.3, 
     tick=TRUE, tcl=0, 
     labels=distribution_sorted[,1], las=2, 
mtext("Kategorie", side=1, line=8.5) # x-axis label

There has to be an easier way !?