Tag Archives: data mining

Processing live data feeds with RapidMiner

The Open File operator has been introduced in the 5.2 version of RapidMiner. It returns a file object for reading content either from a local file, from an URL or from a repository blob entry. Many data import operators including Read CSV, Read Excel and Read XML has been extended to accept a file object as input. With this new feature, now you can process live data feeds directly in RapidMiner.

Many data import operators provide a wizard to guide users through the process of parameter setting. Unfortunately, wizards can not use file objects, they always present a file chooser dialog on start. When dealing with data from the web, you can make use of the wizards according to the following scenario: download the data file and pass your local copy to the wizard. After successful import you can even delete the local file. Data import operators ignore their file name parameter when they receive a file object as input.

In the following a simple use case is presented for demonstration purposes.

The United States Geological Survey’s (USGS) Earthquake Hazards Program provides real-time earthquake data. Real-time feeds are available here. Data is updated periodically and is available for download in multiple formats. For example, click here to get data in CSV format about all M2.5+ earthquakes of the past 30 days (the feed is updated every fifteen minutes).

Let’s see how to read this feed in a RapidMiner process. First, download the feed to your computer. The local copy is required only to set the parameters of the Read CSV operator by using the Import Configuration Wizard. For this purpose you can use a smaller data file, for example this one.

Import the local copy of the feed using the wizard. Select the following data types for the attributes:

  • Src (source network): polynomial
  • EqId: polynomial
  • Version: integer
  • Datetime: date_time
  • Lat: real
  • Lon: real
  • Magintude: real
  • NST (number of reporting stations): integer
  • Region: text

Important: the value of the date format parameter must be set to E, MMM d, yyyy H:mm:ss z to ensure correct handling of the Datetime attribute. For details about date and time pattern strings consult the API documentation of the SimpleDateFormat class (see section titled Date and Time Patterns). It is also important to set the value of the locale parameter to one of the English locales.

Once the local file is imported successfully, drag the Open file operator into the process and connect its output port the input port of the Read CSV operator. Set the parameters of the Open file operator according to the following: set the value of the resource type parameter to URL, and provide the URL of the feed with the parameter url.

A RapidMiner process that uses the Open file operator to read a data feed from the web

Now you can delete the local data file, the operator will read the feed from the URL when the process is run.

You can download the complete RapidMiner process here.

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Breaking the silence: a note about the Apriori algorithm

It’s been a long time since my last post, here I am back again.

Introduction to Data Mining by Pang-Ning Tan, Michael Steinbach and Vipin Kumar [1] is a good introductory textbook in Data Mining. The book has been translated into Hungarian and will hopefully be published in my country this year. Actually, I am one of the translators of the Hungarian edition.

Apriori is a classic algorithm for mining association rules. Chapter 6 of the book discusses the Apriori algorithm. Unfortunately, I found that the pseudocodes for the rule generation step (see Algorithm 6.2 and 6.3 on pages 351 and 352) do not work as expected. These two pseudocodes are the following:

Here \sigma(X) denotes the support count of the itemset X and the function apriori-gen generates the set of frequent (k + 1)-itemsets from the set of frequent k-itemsets.

The main problem is that Algorithm 6.2 and 6.3 above will never generate rules with 1-item consequents. In the original paper that introduces the Apriori algorithm [2] the set H_1 on line 2 of Algorithm 6.2 is defined as the set of consequents of rules derived from f_k with one item in the consequent. However, this implicitly assumes that rules with 1-item consequents are already available. [2] also states that a separate algorithm is required to generate these rules (see page 14):

The rules having one-item consequents in step 2 of this algorithm can be found by using a modified version of the preceding genrules function in which steps 8 and 9 are deleted to avoid the recursive call.

It should also be noted that line 2 of Algorithm 6.2 is simply equivalent to H_1 = f_k.

Finally, the formula on line 2 of Algorithm 6.3 is misleading, since vertical bars are traditionally used to denote cardinality. (In our case m is not the cardinality of set H_m.) I think that the first two lines of Algorithm 6.3 are unnecessary and can be omitted.

Since the book is widely used as a textbook the above problems should be corrected. I have reported the problems to the authors, I hope that they will update the errata of the book accordingly.

Algorithm 6.2 and 6.3 can be modified as follows:

These modified algorithms work as expected and will generate all rules including the ones with 1-item consequents.

References

  1. Pang-Ning Tan, Michael Steinbach and Vipin Kumar. Introduction to Data Mining. Addison-Wesley, 2005.
  2. Rakesh Agrawal and Ramakrishnan Srikant. Fast Algorithms for Mining Association Rules. Proceedings of the 20th International Conference on Very Large Data Bases, Santiago, Chile, September 1994.
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Cross-validation in RapidMiner

Cross-validation is a standard statistical method to estimate the generalization error of a predictive model. In k-fold cross-validation a training set is divided into k equal-sized subsets. Then the following procedure is repeated for each subset: a model is built using the other (k - 1) subsets as the training set and its performance is evaluated on the current subset. This means that each subset is used for testing exactly once. The result of the cross-validation is the average of the performances obtained from the k rounds.

This post explains how to interpret cross-validation results in RapidMiner. For demonstration purposes, we consider the following simple RapidMiner process that is available here:

The Read URL operator reads the yellow-small+adult-stretch.data file, a subset of the Balloons Data Set available from the UCI Machine Learning Repository. Since this data set contains only 16 examples, it is very easy to perform all calculations in your head.

The Set Role operator marks the last attribute as the one that provides the class labels. The number of validations is set to 3 on the X-Validation operator, that will result a 5-5-6 partitioning of the examples in our case.

In the training subprocess of the cross-validation process a decision tree classifier is built on the current training set. In the testing subprocess the accuracy of the decision tree is computed on the test set.

The result of the process is the following PerformanceVector:

74.44 is obviously the arithmetic mean of the accuracies obtained from the three rounds and 10.30 is their standard deviation. However, it is not clear how to interpret the confusion matrix below and the value labelled with the word makro. You may ask how a single confusion matrix is returned if several models are built and evaluated in the cross-validation process.

The Write as Text operator in the inner testing subprocess writes the performance vectors to a text file that helps us to understand the results above. The file contains the confusion matrices obtained from each round together with the corresponding accuracy values as shown below:

13.04.2012 22:07:35 Results of ResultWriter 'Write as Text' [1]: 
13.04.2012 22:07:35 PerformanceVector:
accuracy: 60.00%
ConfusionMatrix:
True:	T	F
T:	0	0
F:	2	3

13.04.2012 22:07:35 Results of ResultWriter 'Write as Text' [2]: 
13.04.2012 22:07:35 PerformanceVector:
accuracy: 83.33%
ConfusionMatrix:
True:	T	F
T:	2	0
F:	1	3

13.04.2012 22:07:35 Results of ResultWriter 'Write as Text' [3]: 
13.04.2012 22:07:35 PerformanceVector:
accuracy: 80.00%
ConfusionMatrix:
True:	T	F
T:	2	1
F:	0	2

Notice that the confusion matrix on the PerformanceVector (Performance) tab is simply the sum the three confusion matrices. The value labelled with the word mikro (75) is actually the accuracy computed from this aggregated confusion matrix. A performance calculated this way is called mikro average, while the mean of the averages is called makro average. Note that the confusion matrix behind the mikro average is constructed by evaluating different models on different test sets.

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Using Web Services in RapidMiner

The Enrich Data by Webservice operator of the RapidMiner Web Mining Extension allows you to interact with web services in your RapidMiner process.

A web service can be invoked for each example of an example set. (Note that this may be time-consuming.) All strings of the form <%attribute%> in a request will be automatically replaced with the corresponding attribute value of the current example. The operator provides several different methods to parse the response, including the use of regular expressions and XPath location paths. Parsing the result you can add new attributes to your example set.

For demonstration purposes we will use the Google Geocoding API. This web service also offers reverse geocoding functionality, i.e. provides a human-readable address for a geographical location. To see how it works, click on the following link: http://maps.googleapis.com/maps/api/geocode/xml?latlng=47.555214,21.621423&sensor=false. Notice that latitude and longitude values are passed to the service in the latlng query string parameter.

We will use this data file for our experiment. The file contains earthquake data that originates from the Earthquake Search service provided by the United States Geological Survey (USGS). Consider the following RapidMiner process that is available from here:

A RapidMiner process that uses the Enrich Data by Webservice operator to interact with a web service

A RapidMiner process that uses the Enrich Data by Webservice operator to interact with a web service

First, the data file is read by the Read CSV operator. Then the Sort and Filter Example Range operators are used to filter the 50 highest magnitude earthquakes. Finally, the Enrich Data by Webservice operator invokes the web service to retrieve country names for the geographical locations of these 50 earthquakes. (Only a small subset of the entire data is used to prevent excessive network traffic.)

The parameters of the Enrich Data by Webservice operator should be set as follows (see the figure below):

  • Set the value of the query type parameter to XPath
  • Set the value of the attribute type parameter to Nominal
  • Uncheck the checkbox of the assume html parameter
  • Set the value of the request method parameter to GET
  • Set the value of the url parameter to http://maps.googleapis.com/maps/api/geocode/xml?latlng=<%Latitude%&gt;,<%Longitude%>&sensor=false
Parameters of the Enrich Data by Webservice operator

Parameters of the Enrich Data by Webservice operator

Finally, click on the Edit List button next to the xpath queries parameter that will bring up an Edit Parameter List window. Enter the string Country into the attribute name field and the string //result[type = 'country']/formatted_address/text() into the query expression field.

Setting of the xpath queries parameter

Setting of the xpath queries parameter

That’s all! Unfortunately, running the process results in the following error:

Process Failed

Process Failed


Well, this is a bug that I have already reported to the developers. (See the bug report here.) The following trick solves the problem: set the request method parameter of the Enrich Data by Webservice operator to POST, enter some arbitrary text into the parameter service method, then set the request method parameter to GET again.

The figure below shows the enhanced example set that contains country names provided by the web service (see the Country attribute).

Enhanced example set with country names

Enhanced example set with country names

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