Orange Visual Programming

Documentation
Release 3

Orange Data Mining

May 08, 2020

 Contents

1 Getting Started 1

2 Widgets 13

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 CHAPTER 1

Getting Started

Here we need to copy the getting started guide.

1.1 Loading your Data

Orange comes with its own data format, but can also handle native Excel, comma- or tab-delimited data files. The
input data set is usually a table, with data instances (samples) in rows and data attributes in columns. Attributes can
be of different types (numeric, categorical, datetime, and text) and have assigned roles (input features, meta attributes,
and class). Data attribute type and role can be provided in the data table header. They can also be changed in the File
widget, while data role can also be modified with Select Columns widget.

1.1.1 In a Nutshell

• Orange can import any comma- or tab-delimited data file, or Excel’s native files or Google Sheets document.
Use File widget to load the data and, if needed, define the class and meta attributes.
• Types and roles can be set in the File widget.
• Attribute names in the column header can be preceded with a label followed by a hash. Use c for class and m
for meta attribute, i to ignore a column, w for weights column, and C, D, T, S for continuous, discrete, time, and
string attribute types. Examples: C#mph, mS#name, i#dummy.
• An alternative to the hash notation is Orange’s native format with three header rows: the first with attribute
names, the second specifying the type (continuous, discrete, time, or string), and the third proving information
on the attribute role (class, meta, weight or ignore).

1.1.2 Data from Excel

Here is an example dataset (sample.xlsx) as entered in Excel:

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The file contains a header row, eight data instances (rows) and seven data attributes (columns). Empty cells in the table
denote missing data entries. Rows represent genes; their function (class) is provided in the first column and their name
in the second. The remaining columns store measurements that characterize each gene. With this data, we could, say,
develop a classifier that would predict gene function from its characteristic measurements.
Let us start with a simple workflow that reads the data and displays it in a table:

To load the data, open the File widget (double click on the icon of the widget), click on the file browser icon (“. . . ”)
and locate the downloaded file (called sample.xlsx) on your disk:

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File Widget: Setting the Attribute Type and Role

The File widget sends the data to the Data Table. Double click the Data Table to see its contents:

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Orange correctly assumed that a column with gene names is meta information, which is displayed in the Data Table
in columns shaded with light-brown. It has not guessed that function, the first non-meta column in our data file, is
a class column. To correct this in Orange, we can adjust attribute role in the column display of File widget (below).
Double-click the feature label in the function row and select target instead. This will set function attribute as our target
(class) variable.

You can also change attribute type from nominal to numeric, from string to datetime, and so on. Naturally, data values
have to suit the specified attribute type. Datetime accepts only values in ISO 8601 format, e.g. 2016-01-01 16:16:01.
Orange would also assume the attribute is numeric if it has several different values, else it would be considered
nominal. All other types are considered strings and are as such automatically categorized as meta attributes.
Change of attribute roles and types should be confirmed by clicking the Apply button.

Select Columns: Setting the Attribute Role

Another way to set the data role is to feed the data to the Select Columns widget:

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Opening Select Columns reveals Orange’s classification of attributes. We would like all of our continuous attributes to
be data features, gene function to be our target variable and gene names considered as meta attributes. We can obtain
this by dragging the attribute names around the boxes in Select Columns:

To correctly reassign attribute types, drag attribute named function to a Class box, and attribute named gene to a Meta
Attribute box. The Select Columns widget should now look like this:

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Change of attribute types in Select Columns widget should be confirmed by clicking the Apply button. The data from
this widget is fed into Data Table that now renders the data just the way we intended:

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We could also define the domain for this dataset in a different way. Say, we could make the dataset ready for regression,
and use heat 0 as a continuous class variable, keep gene function and name as meta variables, and remove heat 10 and
heat 20 from the dataset:

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By setting the attributes as above, the rendering of the data in the Data Table widget gives the following output:

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1.1.3 Header with Attribute Type Information

Consider again the sample.xlsx dataset. This time we will augment the names of the attributes with prefixes that define
attribute type (continuous, discrete, time, string) and role (class or meta attribute). Prefixes are separated from the
attribute name with a hash sign (“#”). Prefixes for attribute roles are:
• c: class attribute
• m: meta attribute
• i: ignore the attribute
• w: instance weights
and for the type:
• C: Continuous
• D: Discrete
• T: Time
• S: String
This is how the header with augmented attribute names looks like in Excel (sample-head.xlsx):

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We can again use a File widget to load this dataset and then render it in the Data Table:

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Notice that the attributes we have ignored (label “i” in the attribute name) are not present in the dataset.

1.1.4 Three-Row Header Format

Orange’s legacy native data format is a tab-delimited text file with three header rows. The first row lists the attribute
names, the second row defines their type (continuous, discrete, time and string, or abbreviated c, d, t, and s), and the
third row an optional role (class, meta, weight, or ignore). Here is an example:

1.1.5 Data from Google Sheets

Orange can read data from Google Sheets, as long as it conforms to the data presentation rules we have presented
above. In Google Sheets, copy the shareable link (Share button, then Get shareable link) and paste it in the Data File /
URL box of the File widget. For a taste, here’s one such link you can use: http://bit.ly/1J12Tdp, and the way we have
entered it in the File widget:

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1.1.6 Data from LibreOffice

If you are using LibreOffice, simply save your files in Excel (.xlsx) format (available from the drop-down menu under
Save As Type).

1.1.7 Datetime Format

To avoid ambiguity, Orange supports date and/or time formatted in one of the ISO 8601 formats. For example, the
following values are all valid:

2016
2016-12-27
2016-12-27 14:20:51
16:20

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 CHAPTER 2

Widgets

2.1 Data

2.1.1 File

Reads attribute-value data from an input file.

Outputs
• Data: dataset from the file
The File widget reads the input data file (data table with data instances) and sends the dataset to its output channel.
The history of most recently opened files is maintained in the widget. The widget also includes a directory with sample
datasets that come pre-installed with Orange.
The widget reads data from Excel (.xlsx), simple tab-delimited (.txt), comma-separated files (.csv) or URLs. For other
formats see Other Formats section below.

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1. Browse through previously opened data files, or load any of the sample ones.
2. Browse for a data file.
3. Reloads currently selected data file.
4. Insert data from URL addresses, including data from Google Sheets.
5. Information on the loaded dataset: dataset size, number and types of data features.
6. Additional information on the features in the dataset. Features can be edited by double-clicking on them. The
user can change the attribute names, select the type of variable per each attribute (Continuous, Nominal, String,
Datetime), and choose how to further define the attributes (as Features, Targets or Meta). The user can also
decide to ignore an attribute.
7. Browse documentation datasets.
8. Produce a report.

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Example

Most Orange workflows would probably start with the File widget. In the schema below, the widget is used to read
the data that is sent to both the Data Table and the Box Plot widget.

Loading your data

• Orange can import any comma, .xlsx or tab-delimited data file or URL. Use the File widget and then, if needed,
select class and meta attributes.
• To specify the domain and the type of the attribute, attribute names can be preceded with a label followed by a
hash. Use c for class and m for meta attribute, i to ignore a column, and C, D, S for continuous, discrete and
string attribute types. Examples: C#mpg, mS#name, i#dummy.
• Orange’s native format is a tab-delimited text file with three header rows. The first row contains attribute names,
the second the type (continuous, discrete or string), and the third the optional element (class, meta or time).

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Read more on loading your data here.

Other Formats

Supported formats and the widgets to load them:

• distance matrix: Distance File
• predictive model: Load Model
• network: Network File from Network add-on
• images: Import Images from Image Analytics add-on
• text/corpus: Corpus or Import Documents from Text add-on
• single cell data: Load Data from Single Cell add-on
• several spectroscopy files: Multifile from Spectroscopy add-on

2.1.2 CSV File Import

Import a data table from a CSV formatted file.

Outputs
• Data: dataset from the .csv file
• Data Frame: pandas DataFrame object

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The CSV File Import widget reads comma-separated files and sends the dataset to its output channel. File separators
can be commas, semicolons, spaces, tabs or manually-defined delimiters. The history of most recently opened files is
maintained in the widget.
Data Frame output can be used in the Python Script widget by connecting it to the in_object input (e.g. df =
in_object). Then it can be used a regular DataFrame.

Import Options

The import window where the user sets the import parameters. Can be re-opened by pressing Import Options in the
widget.
Right click on the column name to set the column type. Right click on the row index (on the left) to mark a row as a
header, skipped or a normal data row.

1. File encoding. Default is UTF-8. See Encoding subchapter for details.

2. Import settings:
• Cell delimiter:
– Tab
– Comma
– Semicolon
– Space
– Other (set the delimiter in the field to the right)
• Quote character: either “ or ‘. Defines what is considered a text.

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• Number separators:
– Grouping: delimiters for thousands, e.g. 1,000
– Decimal: delimiters for decimals, e.g. 1.234
3. Column type: select the column in the preview and set its type. Column type can be set also by right-clicking
on the selected column.
• Auto: Orange will automatically try to determine column type. (default)
• Numeric: for continuous data types, e.g. (1.23, 1.32, 1.42, 1.32)
• Categorical: for discrete data types, e.g. (brown, green, blue)
• Text: for string data types, e.g. (John, Olivia, Mike, Jane)
• Datetime: for time variables, e.g. (1970-01-01)
• Ignore: do not output the column.
4. Pressing Reset will return the settings to the previously set state (saved by pressing OK in the Import Options
dialogue). Restore Defaults will set the settings to their default values. Cancel aborts the import, while OK
imports the data and saves the settings.

Widget

The widget once the data is successfully imported.

1. The folder icon opens the dialogue for import the local .csv file. It can be used to either load the first file or
change the existing file (load new data). The File dropdown stores paths to previously loaded data sets.
2. Information on the imported data set. Reports on the number of instances (rows), variables (features or columns)
and meta variables (special columns).
3. Import Options re-opens the import dialogue where the user can set delimiters, encodings, text fields and so
on. Cancel aborts data import. Reload imports the file once again, adding to the data any changes made in the
original file.

Encoding

The dialogue for settings custom encodings list in the Import Options - Encoding dropdown. Select Customize Encod-
ings List. . . to change which encodings appear in the list. To save the changes, simply close the dialogue. Closing and
reopening Orange (even with Reset widget settings) will not re-set the list. To do this, press Restore Defaults. To have
all the available encodings in the list, press Select all.

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Example

CSV File Import works almost exactly like the File widget, with the added options for importing different types of
.csv files. In this workflow, the widget read the data from the file and sends it to the Data Table for inspection.

2.1.3 Datasets

Load a dataset from an online repository.

Outputs
• Data: output dataset
Datasets widget retrieves selected dataset from the server and sends it to the output. File is downloaded to the local
memory and thus instantly available even without the internet connection. Each dataset is provided with a description
and information on the data size, number of instances, number of variables, target and tags.

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1. Information on the number of datasets available and the number of them downloaded to the local memory.
2. Content of available datasets. Each dataset is described with the size, number of instances and variables, type
of the target variable and tags.
3. Formal description of the selected dataset.
4. If Send Data Automatically is ticked, selected dataset is communicated automatically. Alternatively, press Send
Data.

Example

Orange workflows can start with Datasets widget instead of File widget. In the example below, the widget retrieves
a dataset from an online repository (Kickstarter data), which is subsequently sent to both the Data Table and the
Distributions.

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2.1.4 SQL Table

Reads data from an SQL database.

Outputs
• Data: dataset from the database
The SQL widget accesses data stored in an SQL database. It can connect to PostgreSQL (requires psycopg2 module)
or SQL Server (requires pymssql module).
To handle large databases, Orange attempts to execute a part of the computation in the database itself without down-
loading the data. This only works with PostgreSQL database and requires quantile and tsm_system_time extensions
installed on server. If these extensions are not installed, the data will be downloaded locally.

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1. Database type (can be either PostgreSQL or MSSQL).

2. Host name.
3. Database name.
4. Username.
5. Password.
6. Press the blue button to connect to the database. Then select the table in the dropdown.
7. Auto-discover categorical variables will cast INT and CHAR columns with less than 20 distinct values as
categorical variables (finding all distinct values can be slow on large tables). When not selected, INT will be
treated as numeric and CHAR as text. Download to local memory downloads the selected table to your local
machine.
##Installation Instructions
###PostgreSQL
Install the backend.

pip install psycopg2

Alternatively, you can follow these instructions for installing the backend.
Install the extensions. [optional]
###MSSQL
Install the backend.

pip install pymssql

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If you are encountering issues, follow these instructions.

##Example
Here is a simple example on how to use the SQL Table widget. Place the widget on the canvas, enter your database
credentials and connect to your database. Then select the table you wish to analyse.
Connect SQL Table to Data Table widget to inspect the output. If the table is populated, your data has transferred
correctly. Now, you can use the SQL Table widget in the same way as the File widget.

2.1.5 Save Data

Saves data to a file.

Inputs
• Data: input dataset
The Save Data widget considers a dataset provided in the input channel and saves it to a data file with a specified
name. It can save the data as a tab-delimited or a comma-separated file.

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The widget does not save the data every time it receives a new signal in the input as this would constantly (and, mostly,
inadvertently) overwrite the file. Instead, the data is saved only after a new file name is set or the user pushes the Save
button.
If the file is saved to the same directory as the workflow or in the subtree of that directory, the widget remembers the
relative path. Otherwise it will store an absolute path, but disable auto save for security reasons.

1. Save by overwriting the existing file.

2. Save as to create a new file.

Example

In the workflow below, we used the Zoo dataset. We loaded the data into the Scatter Plot widget, with which we
selected a subset of data instances and pushed them to the Save Data widget to store them in a file.

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2.1.6 Data Info

Displays information on a selected dataset.

Inputs
• Data: input dataset
A simple widget that presents information on dataset size, features, targets, meta attributes, and location.

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1. Information on dataset size

2. Information on discrete and continuous features
3. Information on targets
4. Information on meta attributes
5. Information on where the data is stored
6. Produce a report.

Example

Below, we compare the basic statistics of two Data Info widgets - one with information on the entire dataset and the
other with information on the (manually) selected subset from the Scatter Plot widget. We used the Iris dataset.

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2.1.7 Data Table

Displays attribute-value data in a spreadsheet.

Inputs
• Data: input dataset
Outputs
• Selected Data: instances selected from the table
The Data Table widget receives one or more datasets in its input and presents them as a spreadsheet. Data instances
may be sorted by attribute values. The widget also supports manual selection of data instances.

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1. The name of the dataset (usually the input data file). Data instances are in rows and their attribute values in
columns. In this example, the dataset is sorted by the attribute “sepal length”.
2. Info on current dataset size and number and types of attributes
3. Values of continuous attributes can be visualized with bars; colors can be attributed to different classes.
4. Data instances (rows) can be selected and sent to the widget’s output channel.
5. Use the Restore Original Order button to reorder data instances after attribute-based sorting.
6. Produce a report.
7. While auto-send is on, all changes will be automatically communicated to other widgets. Otherwise, press Send
Selected Rows.

Example

We used two File widgets to read the Iris and Glass dataset (provided in Orange distribution), and send them to the
Data Table widget.

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Selected data instances in the first Data Table are passed to the second Data Table. Notice that we can select which
dataset to view (iris or glass). Changing from one dataset to another alters the communicated selection of data instances
if Commit on any change is selected.

2.1.8 Select Columns

Manual selection of data attributes and composition of data domain.

Inputs
• Data: input dataset

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Outputs
• Data: dataset with columns as set in the widget
The Select Columns widget is used to manually compose your data domain. The user can decide which attributes will
be used and how. Orange distinguishes between ordinary attributes, (optional) class attributes and meta attributes. For
instance, for building a classification model, the domain would be composed of a set of attributes and a discrete class
attribute. Meta attributes are not used in modeling, but several widgets can use them as instance labels.
Orange attributes have a type and are either discrete, continuous or a character string. The attribute type is marked
with a symbol appearing before the name of the attribute (D, C, S, respectively).

1. Left-out data attributes that will not be in the output data file
2. Data attributes in the new data file
3. Target variable. If none, the new dataset will be without a target variable.
4. Meta attributes of the new data file. These attributes are included in the dataset but are, for most methods, not
considered in the analysis.

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5. Produce a report.
6. Reset the domain composition to that of the input data file.
7. Tick if you wish to auto-apply changes of the data domain.
8. Apply changes of the data domain and send the new data file to the output channel of the widget.

Examples

In the workflow below, the Iris data from the File widget is fed into the Select Columns widget, where we select to
output only two attributes (namely petal width and petal length). We view both the original dataset and the dataset
with selected columns in the Data Table widget.

For a more complex use of the widget, we composed a workflow to redefine the classification problem in the heart-
disease dataset. Originally, the task was to predict if the patient has a coronary artery diameter narrowing. We changed
the problem to that of gender classification, based on age, chest pain and cholesterol level, and informatively kept the
diameter narrowing as a meta attribute.

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2.1.9 Select Rows

Selects data instances based on conditions over data features.

Inputs
• Data: input dataset
Outputs
• Matching Data: instances that match the conditions
• Non-Matching Data: instances that do not match the conditions
• Data: data with an additional column showing whether a instance is selected
This widget selects a subset from an input dataset, based on user-defined conditions. Instances that match the selection
rule are placed in the output Matching Data channel.
Criteria for data selection are presented as a collection of conjunct terms (i.e. selected items are those matching all the
terms in ‘Conditions’).
Condition terms are defined through selecting an attribute, selecting an operator from a list of operators, and, if needed,
defining the value to be used in the condition term. Operators are different for discrete, continuous and string attributes.

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1. Conditions you want to apply, their operators and related values

2. Add a new condition to the list of conditions.
3. Add all the possible variables at once.
4. Remove all the listed variables at once.
5. Information on the input dataset and information on instances that match the condition(s)
6. Purge the output data.
7. When the Send automatically box is ticked, all changes will be automatically communicated to other widgets.
8. Produce a report.
Any change in the composition of the condition will update the information pane (Data Out).
If Send automatically is selected, then the output is updated on any change in the composition of the condition or any
of its terms.

Example

In the workflow below, we used the Zoo data from the File widget and fed it into the Select Rows widget. In the
widget, we chose to output only two animal types, namely fish and reptiles. We can inspect both the original dataset
and the dataset with selected rows in the Data Table widget.

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In the next example, we used the data from the Titanic dataset and similarly fed it into the Box Plot widget. We first
observed the entire dataset based on survival. Then we selected only first class passengers in the Select Rows widget
and fed it again into the Box Plot. There we could see all the first class passengers listed by their survival rate and
grouped by gender.

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2.1.10 Data Sampler

Selects a subset of data instances from an input dataset.

Inputs
• Data: input dataset
Outputs
• Data Sample: sampled data instances
• Remaining Data: out-of-sample data
The Data Sampler widget implements several data sampling methods. It outputs a sampled and a complementary
dataset (with instances from the input set that are not included in the sampled dataset). The output is processed after
the input dataset is provided and Sample Data is pressed.

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1. Information on the input and output dataset.

2. The desired sampling method:
• Fixed proportion of data returns a selected percentage of the entire data (e.g. 70% of all the data)
• Fixed sample size returns a selected number of data instances with a chance to set Sample with replace-
ment, which always samples from the entire dataset (does not subtract instances already in the subset).
With replacement, you can generate more instances than available in the input dataset.

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• Cross Validation partitions data instances into complementary subsets, where you can select the number
of folds (subsets) and which fold you want to use as a sample.
• Bootstrap infers the sample from the population statistic.
3. Replicable sampling maintains sampling patterns that can be carried across users, while stratify sample mimics
the composition of the input dataset.
4. Press Sample Data to output the data sample.
If all data instances are selected (by setting the proportion to 100 % or setting the fixed sample size to the entire data
size), output instances are still shuffled.

Examples

First, let’s see how the Data Sampler works. We will use the iris data from the File widget. We see there are 150
instances in the data. We sampled the data with the Data Sampler widget and we chose to go with a fixed sample
size of 5 instances for simplicity. We can observe the sampled data in the Data Table widget (Data Table (in-sample)).
The second Data Table (Data Table (out-of-sample)) shows the remaining 145 instances that weren’t in the sample. To
output the out-of-sample data, double-click the connection between the widgets and rewire the output to Remaining
Data –> Data.

Now, we will use the Data Sampler to split the data into training and testing part. We are using the iris data, which
we loaded with the File widget. In Data Sampler, we split the data with Fixed proportion of data, keeping 70% of
data instances in the sample.
Then we connected two outputs to the Test & Score widget, Data Sample –> Data and Remaining Data –> Test Data.
Finally, we added Logistic Regression as the learner. This runs logistic regression on the Data input and evaluates the
results on the Test Data.

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Over/Undersampling

Data Sampler can also be used to oversample a minority class or undersample majority class in the data. Let us show
an example for oversampling. First, separate the minority class using a Select Rows widget. We are using the iris data
from the File widget. The data set has 150 data instances, 50 of each class. Let us oversample, say, iris-setosa.
In Select Rows, set the condition to iris is iris-setosa. This will output 50 instances of the iris-setosa class. Now,
connect Matching Data into the Data Sampler, select Fixed sample size, set it to, say, 100 and select Sample with
replacement. Upon pressing Sample Data, the widget will output 100 instances of iris-setosa class, some of which
will be duplicated (because we used Sample with replacement).
Finally, use Concatenate to join the oversampled instances and the Unmatched Data output of the Select Rows widget.
This outputs a data set with 200 instances. We can observe the final results in the Distributions.

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2.1.11 Transpose

Transposes a data table.

Inputs
• Data: input dataset
Outputs
• Data: transposed dataset
Transpose widget transposes data table.

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Example

This is a simple workflow showing how to use Transpose. Connect the widget to File widget. The output of Transpose
is a transposed data table with rows as columns and columns as rows. You can observe the result in a Data Table.

2.1.12 Discretize

Discretizes continuous attributes from an input dataset.

Inputs
• Data: input dataset
Outputs
• Data: dataset with discretized values
The Discretize widget discretizes continuous attributes with a selected method.

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1. The basic version of the widget is rather simple. It allows choosing between three different discretizations.
• Entropy-MDL, invented by Fayyad and Irani is a top-down discretization, which recursively splits the
attribute at a cut maximizing information gain, until the gain is lower than the minimal description length
of the cut. This discretization can result in an arbitrary number of intervals, including a single interval, in
which case the attribute is discarded as useless (removed).
• Equal-frequency splits the attribute into a given number of intervals, so that they each contain approxi-
mately the same number of instances.
• Equal-width evenly splits the range between the smallest and the largest observed value. The Number of
intervals can be set manually.
• The widget can also be set to leave the attributes continuous or to remove them.
2. To treat attributes individually, go to Individual Attribute Settings. They show a specific discretization of each
attribute and allow changes. First, the top left list shows the cut-off points for each attribute. In the snapshot, we
used the entropy-MDL discretization, which determines the optimal number of intervals automatically; we can
see it discretized the age into seven intervals with cut-offs at 21.50, 23.50, 27.50, 35.50, 43.50, 54.50 and 61.50,

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respectively, while the capital-gain got split into many intervals with several cut-offs. The final weight (fnlwgt),
for instance, was left with a single interval and thus removed. On the right, we can select a specific discretization
method for each attribute. Attribute “fnlwgt” would be removed by the MDL-based discretization, so to prevent
its removal, we select the attribute and choose, for instance, Equal-frequency discretization. We could also
choose to leave the attribute continuous.
3. Produce a report.
4. Tick Apply automatically for the widget to automatically commit changes. Alternatively, press Apply.

Example

In the schema below, we show the Iris dataset with continuous attributes (as in the original data file) and with dis-
cretized attributes.

2.1.13 Continuize

Turns discrete variables (attributes) into numeric (“continuous”) dummy variables.

Inputs
• Data: input data set
Outputs
• Data: transformed data set

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The Continuize widget receives a data set in the input and outputs the same data set in which the discrete variables
(including binary variables) are replaced with continuous ones.

1. Define the treatment of non-binary categorical variables.

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Examples in this section will assume that we have a discrete attribute status with the values low, middle and
high, listed in that order. Options for their transformation are:
• First value as base: a N-valued categorical variable will be transformed into N-1 numeric variables, each
serving as an indicator for one of the original values except for the base value. The base value is the first
value in the list. By default, the values are ordered alphabetically; their order can be changed in Edit
Domain.
In the above case, the three-valued variable status is transformed into two numeric variables, status=middle
with values 0 or 1 indicating whether the original variable had value middle on a particular example, and
similarly, status=high.
• Most frequent value as base: similar to the above, except that the most frequent value is used as a base.
So, if the most frequent value in the above example is middle, then middle is considered as the base and
the two newly constructed variables are status=low and status=high.
• One attribute per value: this option constructs one numeric variable per each value of the original vari-
able. In the above case, we would get variables status=low, status=middle and status=high.
• Ignore multinomial attributes: removes non-binary categorical variables from the data.
• Treat as ordinal: converts the variable into a single numeric variable enumerating the original values. In
the above case, the new variable would have the value of 0 for low, 1 for middle and 2 for high. Again note
that the order of values can be set in Edit Domain.
• Divide by number of values: same as above, except that values are normalized into range 0-1. In our
example, the values of the new variable would be 0, 0.5 and 1.
2. Define the treatment of continuous attributes. Besised the option to Leave them as they are, we can Normalize
by span, which will subtract the lowest value found in the data and divide by the span, so all values will fit into
[0, 1]. Option Normalize by standard deviation subtracts the average and divides by the standard deviation.
3. Define the treatment of class attributes (outcomes, targets). Besides leaving it as it is, the available options
mirror those for multinomial attributes, except for those that would split the outcome into multiple outcome
variables.
4. This option defines the ranges of new variables. In the above text, we supposed the range from 0 to 1.
5. Produce a report.
6. If Apply automatically is ticked, changes are committed automatically. Otherwise, you have to press Apply after
each change.

Examples

First, let’s see what is the output of the Continuize widget. We feed the original data (the Heart disease data set) into
the Data Table and see how they look like. Then we continuize the discrete values and observe them in another Data
Table.

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In the second example, we show a typical use of this widget - in order to properly plot the linear projection of the
data, discrete attributes need to be converted to continuous ones and that is why we put the data through the Con-
tinuize widget before drawing it. The attribute “chest pain” originally had four values and was transformed into three
continuous attributes; similar happened to gender, which was transformed into a single attribute “gender=female”.

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2.1.14 Create Class

Create class attribute from a string attribute.

Inputs
• Data: input dataset
Outputs
• Data: dataset with a new class variable
Create Class creates a new class attribute from an existing discrete or string attribute. The widget matches the string
value of the selected attribute and constructs a new user-defined value for matching instances.

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1. The attribute the new class is constructed from.

2. Matching:
• Name: the name of the new class value
• Substring: regex-defined substring that will match the values from the above-defined attribute
• Instances: the number of instances matching the substring
• Press ‘+’ to add a new class value
3. Name of the new class column.
4. Match only at the beginning will begin matching from the beginning of the string. Case sensitive will match by
case, too.
5. Produce a report.
6. Press Apply to commit the results.

Example

Here is a simple example with the auto-mpg dataset. Pass the data to Create Class. Select car_name as a column to
create the new class from. Here, we wish to create new values that match the car brand. First, we type ford as the new
value for the matching strings. Then we define the substring that will match the data instances. This means that all
instances containing ford in their car_name, will now have a value ford in the new class column. Next, we define the
same for honda and fiat. The widget will tell us how many instance are yet unmatched (remaining instances). We will
name them other, but you can continue creating new values by adding a condition with ‘+’.

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We named our new class column car_brand and we matched at the beginning of the string.

Finally, we can observe the new column in a Data Table or use the value as color in the Scatter Plot.

2.1.15 Randomize

Shuffles classes, attributes and/or metas of an input dataset.

Inputs
• Data: input dataset
Outputs
• Data: randomized dataset
The Randomize widget receives a dataset in the input and outputs the same dataset in which the classes, attributes
or/and metas are shuffled.

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1. Select group of columns of the dataset you want to shuffle.

2. Select proportion of the dataset you want to shuffle.
3. Produce replicable output.
4. If Apply automatically is ticked, changes are committed automatically. Otherwise, you have to press Apply after
each change.
5. Produce a report.

Example

The Randomize widget is usually placed right after (e.g. File widget. The basic usage is shown in the following
workflow, where values of class variable of Iris dataset are randomly shuffled.

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In the next example we show how shuffling class values influences model performance on the same dataset as above.

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2.1.16 Concatenate

Concatenates data from multiple sources.

Inputs
• Primary Data: data set that defines the attribute set
• Additional Data: additional data set
Outputs
• Data: concatenated data
The widget concatenates multiple sets of instances (data sets). The merge is “vertical”, in a sense that two sets of 10
and 5 instances yield a new set of 15 instances.

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1. Set the attribute merging method.

2. Add the identification of source data sets to the output data set.
3. Produce a report.
4. If Apply automatically is ticked, changes are communicated automatically. Otherwise, click Apply.
If one of the tables is connected to the widget as the primary table, the resulting table will contain its own attributes.
If there is no primary table, the attributes can be either a union of all attributes that appear in the tables specified as
Additional Tables, or their intersection, that is, a list of attributes common to all the connected tables.

Example

As shown below, the widget can be used for merging data from two separate files. Let’s say we have two data sets
with the same attributes, one containing instances from the first experiment and the other instances from the second
experiment and we wish to join the two data tables together. We use the Concatenate widget to merge the data sets
by attributes (appending new rows under existing attributes).
Below, we used a modified Zoo data set. In the first File widget, we loaded only the animals beginning with the letters
A and B and in the second one only the animals beginning with the letter C. Upon concatenation, we observe the new
data in the Data Table widget, where we see the complete table with animals from A to C.

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2.1.17 Select by Data Index

Match instances by index from data subset.

Inputs
• Data: reference data set
• Data Subset: subset to match
Outputs
• Matching data: subset from reference data set that matches indices from subset data
• Unmatched data: subset from reference data set that does not match indices from subset data
• Annotated data: reference data set with an additional column defining matches
Select by Data Index enables matching the data by indices. Each row in a data set has an index and given a subset,
this widget can match these indices to indices from the reference data. Most often it is used to retrieve the original
data from the transformed data (say, from PCA space).

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1. Information on the reference data set. This data is used as index reference.
2. Information on the data subset. The indices of this data set are used to find matching data in the reference data
set. Matching data are on the output by default.

Example

A typical use of Select by Data Index is to retrieve the original data after a transformation. We will load iris.tab data
in the File widget. Then we will transform this data with PCA. We can project the transformed data in a Scatter Plot,
where we can only see PCA components and not the original features.
Now we will select an interesting subset (we could also select the entire data set). If we observe it in a Data Table, we
can see that the data is transformed. If we would like to see this data with the original features, we will have to retrieve
them with Select by Data Index.
Connect the original data and the subset from Scatter Plot to Select by Data Index. The widget will match the indices
of the subset with the indices of the reference (original) data and output the matching reference data. A final inspection
in another Data Table confirms the data on the output is from the original data space.

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2.1.18 Paint Data

Paints data on a 2D plane. You can place individual data points or use a brush to paint larger datasets.
Outputs
• Data: dataset as painted in the plot
The widget supports the creation of a new dataset by visually placing data points on a two-dimension plane. Data
points can be placed on the plane individually (Put) or in a larger number by brushing (Brush). Data points can belong
to classes if the data is intended to be used in supervised learning.

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1. Name the axes and select a class to paint data instances. You can add or remove classes. Use only one class to
create classless, unsupervised datasets.
2. Drawing tools. Paint data points with Brush (multiple data instances) or Put (individual data instance). Select
data points with Select and remove them with the Delete/Backspace key. Reposition data points with Jitter
(spread) and Magnet (focus). Use Zoom and scroll to zoom in or out. Below, set the radius and intensity for
Brush, Put, Jitter and Magnet tools.
3. Reset to Input Data.
4. Save Image saves the image to your computer in a .svg or .png format.
5. Produce a report.
6. Tick the box on the left to automatically commit changes to other widgets. Alternatively, press Send to apply
them.

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Example

In the example below, we have painted a dataset with 4 classes. Such dataset is great for demonstrating k-means
and hierarchical clustering methods. In the screenshot, we see that k-Means, overall, recognizes clusters better than
Hierarchical Clustering. It returns a score rank, where the best score (the one with the highest value) means the most
likely number of clusters. Hierarchical clustering, however, doesn’t group the right classes together. This is a great
tool for learning and exploring statistical concepts.

2.1.19 Pivot Table

Reshape data table based on column values.

Inputs
• Data: input data set
Outputs
• Pivot Table: contingency matrix as shown in the widget
• Filtered Data: subset selected from the plot
• Grouped Data: aggregates over groups defined by row values
Pivot Table summarizes the data of a more extensive table into a table of statistics. The statistics can include sums,
averages, counts, etc. The widget also allows selecting a subset from the table and grouping by row values, which
have to be a discrete variable. Data with only numeric variables cannot be displayed in the table.

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1. Discrete or numeric variable used for row values. Numeric variables are considered as integers.
2. Discrete variable used for column values. Variable values will appear as columns in the table.
3. Values used for aggregation. Aggregated values will appear as cells in the table.
4. Aggregation methods:
• For any variable type:
– Count: number of instances with the given row and column value.
– Count defined: number of instances where the aggregation value is defined.
• For numeric variables:
– Sum: sum of values.
– Mean: average of values.
– Mode: most frequent value of the subset.
– Min: smallest value.
– Max: highest value.
– Median: middle value.
– Var: variance of the subset.
• For discrete variables:
– Majority: most frequent value of the subset.
5. Tick the box on the left to automatically output any changes. Alternatively, press Apply .

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Discrete variables

Example of a pivot table with only discrete variables selected. We are using heart-disease data set for this example.
Rows correspond to values of diameter narrowing variable. Our columns are values of gender, namely female and
male. We are using thal as values in our cells.
We have selected Count and Majority as aggregation methods. In the pivot table, we can see the number of instances
that do not have diameter narrowing and are female. There are 72 such patients. Concurrently, there are 92 male
patients that don’t have diameter narrowing. Thal values don’t have any effect here, we are just counting occurrences
in the data.
The second row shows majority. This means most female patients that don’t have diameter narrowing have normal
thal results. Conversely, female patients that have diameter narrowing most often have reversable defect.

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Numeric variables

Example of a pivot table with numeric variables. We are using heart-disease data set for this example. Rows corre-
spond to values of diameter narrowing variable. Our columns are values of gender, namely female and male. We are
using rest SBP as values in our cells.
We have selected Count, Sum and Median as aggregation methods. Under Count, we see there are 72 female patients
that don’t have diameter narrowing, same as before for discrete values. What is different are the sum and median
aggregations. We see that the sum of resting systolic blood pressure for female patients that don’t have diameter
narrowing is 9269 and the median value is 130.

Example

We are using Forest Fires for this example. The data is loaded in the Datasets widget and passed to Pivot Table.
Forest Fires datasets reports forest fires by the month and day they happened. We can aggregate all occurrences of
forest fires by selecting Count as aggregation method and using month as row and day as column values. Since we are
using Count, Values variable will have no effect.
We can plot the counts in Line Plot. But first, let us organize our data a bit. With Edit Domain, we will reorder rows
values so that months will appear in the correct order, namely from January to December. To do the same for columns,
we will use Select Columns and reorder day to go from Monday to Sunday.
Finally, our data is ready. Let us pass it to Line Plot. We can see that forest fires are most common in August and
September, while their frequency is higher during the weekend than during weekdays.

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2.1.20 Python Script

Extends functionalities through Python scripting.

Inputs
• Data (Orange.data.Table): input dataset bound to in_data variable
• Learner (Orange.classification.Learner): input learner bound to in_learner variable
• Classifier (Orange.classification.Learner): input classifier bound to in_classifier variable
• Object: input Python object bound to in_object variable
Outputs
• Data (Orange.data.Table): dataset retrieved from out_data variable
• Learner (Orange.classification.Learner): learner retrieved from out_learner variable
• Classifier (Orange.classification.Learner): classifier retrieved from out_classifier variable
• Object: Python object retrieved from out_object variable
Python Script widget can be used to run a python script in the input, when a suitable functionality is not imple-
mented in an existing widget. The script has in_data, in_distance, in_learner, in_classifier and
in_object variables (from input signals) in its local namespace. If a signal is not connected or it did not yet receive
any data, those variables contain None.
After the script is executed variables from the script’s local namespace are extracted and used as outputs of the widget.
The widget can be further connected to other widgets for visualizing the output.
For instance the following script would simply pass on all signals it receives:

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out_data = in_data
out_distance = in_distance
out_learner = in_learner
out_classifier = in_classifier
out_object = in_object

Note: You should not modify the input objects in place.

1. Info box contains names of basic operators for Orange Python script.
2. The Library control can be used to manage multiple scripts. Pressing “+” will add a new entry and open it
in the Python script editor. When the script is modified, its entry in the Library will change to indicate it has
unsaved changes. Pressing Update will save the script (keyboard shortcut “Ctrl+S”). A script can be removed
by selecting it and pressing the “-“ button.
3. Pressing Execute in the Run box executes the script (keyboard shortcut “Ctrl+R”). Any script output (from
print) is captured and displayed in the Console below the script.
4. The Python script editor on the left can be used to edit a script (it supports some rudimentary syntax highlight-
ing).
5. Console displays the output of the script.

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Examples

Python Script widget is intended to extend functionalities for advanced users. Classes from Orange library are de-
scribed in the documentation. To find further information about orange Table class see Table, Domain, and Variable
documentation.
One can, for example, do batch filtering by attributes. We used zoo.tab for the example and we filtered out all the
attributes that have more than 5 discrete values. This in our case removed only ‘leg’ attribute, but imagine an example
where one would have many such attributes.

from Orange.data import Domain, Table

domain = Domain([attr for attr in in_data.domain.attributes
if attr.is_continuous or len(attr.values) <= 5],
in_data.domain.class_vars)
out_data = Table(domain, in_data)

The second example shows how to round all the values in a few lines of code. This time we used wine.tab and rounded
all the values to whole numbers.

import numpy as np
(continues on next page)

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(continued from previous page)

out_data = in_data.copy()
#copy, otherwise input data will be overwritten
np.round(out_data.X, 0, out_data.X)

The third example introduces some Gaussian noise to the data. Again we make a copy of the input data, then walk
through all the values with a double for loop and add random noise.

import random
from Orange.data import Domain, Table
new_data = in_data.copy()
for inst in new_data:
for f in inst.domain.attributes:
inst[f] += random.gauss(0, 0.02)
out_data = new_data

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The final example uses Orange3-Text add-on. Python Script is very useful for custom preprocessing in text mining,
extracting new features from strings, or utilizing advanced nltk or gensim functions. Below, we simply tokenized our
input data from deerwester.tab by splitting them by whitespace.

print('Running Preprocessing ...')

tokens = [doc.split(' ') for doc in in_data.documents]
print('Tokens:', tokens)
out_object = in_data
out_object.store_tokens(tokens)

You can add a lot of other preprocessing steps to further adjust the output. The output of Python Script can be used
with any widget that accepts the type of output your script produces. In this case, connection is green, which signalizes
the right type of input for Word Cloud widget.

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2.1.21 Feature Constructor

Add new features to your dataset.

Inputs
• Data: input dataset
Outputs
• Data: dataset with additional features
The Feature Constructor allows you to manually add features (columns) into your dataset. The new feature can be a
computation of an existing one or a combination of several (addition, subtraction, etc.). You can choose what type of
feature it will be (discrete, continuous or string) and what its parameters are (name, value, expression). For continuous
variables you only have to construct an expression in Python.

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1. List of constructed variables

2. Add or remove variables
3. New feature name
4. Expression in Python
5. Select a feature
6. Select a function
7. Produce a report
8. Press Send to communicate changes
For discrete variables, however, there’s a bit more work. First add or remove the values you want for the new feature.
Then select the base value and the expression. In the example below, we have constructed an expression with ‘if lower
than’ and defined three conditions; the program ascribes 0 (which we renamed to lower) if the original value is lower
than 6, 1 (mid) if it is lower than 7 and 2 (higher) for all the other values. Notice that we use an underscore for the
feature name (e.g. petal_length).

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1. List of variable definitions

2. Add or remove variables
3. New feature name
4. Expression in Python
5. Select a feature
6. Select a function
7. Assign values
8. Produce a report
9. Press Send to communicate changes

Example

With the Feature Constructor you can easily adjust or combine existing features into new ones. Below, we added
one new discrete feature to the Titanic dataset. We created a new attribute called Financial status and set the values
to be rich if the person belongs to the first class (status = first) and not rich for everybody else. We can see the new
dataset with Data Table widget.

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Hints

If you are unfamiliar with Python math language, here’s a quick introduction.
• +, - to add, subtract
• * to multiply
• / to divide
• % to divide and return the remainder
• ** for exponent (for square root square by 0.5)
• // for floor division
• <, >, <=, >= less than, greater than, less or equal, greater or equal
• == for equal
• != for not equal
As in the example: (value) if (feature name) < (value), else (value) if (feature name) < (value), else (value)
[Use value 1 if feature is less than specified value, else use value 2 if feature is less than specified value 2, else use
value 3.]
See more here.

2.1.22 Edit Domain

Rename features and their values.

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Inputs
• Data: input dataset
Outputs
• Data: dataset with edited domain
This widget can be used to edit/change a dataset’s domain.

1. All features (including meta attributes) from the input dataset are listed in the Variables list. Selecting one
feature displays an editor on the right.
2. Change the name of the feature.
3. Change the value names for discrete features in the Values list box. Double-click to edit the name. To reorder
the values (for example to display them in Distributions, use the up and down keys at the bottom of the box. To
add or remove a value, use + and - buttons.
4. Additional feature annotations can be added, removed or edited in the Labels box. Add a new label with the
+ button and add the Key and Value for the new entry. Key will be displayed in the top left corner of the Data
Table, while values will appear below the specified column. Remove an existing label with the - button.
5. To revert the changes made to the selected feature, press the Reset Selected button while the feature is selected
in the Variables list. Pressing Reset All will remove all the changes to the domain.
6. Press Apply to send the new domain to the output.

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Example

Below, we demonstrate how to simply edit an existing domain. We selected the heart_disease.tab dataset and edited
the gender attribute. Where in the original we had the values female and male, we changed it into F for female and M
for male. Then we used the down key to switch the order of the variables. Finally, we added a label to mark that the
attribute is binary. We can observe the edited data in the Data Table widget.

2.1.23 Impute

Replaces unknown values in the data.

Inputs
• Data: input dataset
• Learner: learning algorithm for imputation
Outputs
• Data: dataset with imputed values
Some Orange’s algorithms and visualizations cannot handle unknown values in the data. This widget does what
statisticians call imputation: it substitutes missing values by values either computed from the data or set by the user.
The default imputation is (1-NN).

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1. In the top-most box, Default method, the user can specify a general imputation technique for all attributes.
• Don’t Impute does nothing with the missing values.
• Average/Most-frequent uses the average value (for continuous attributes) or the most common value (for
discrete attributes).
• As a distinct value creates new values to substitute the missing ones.
• Model-based imputer constructs a model for predicting the missing value, based on values of other at-
tributes; a separate model is constructed for each attribute. The default model is 1-NN learner, which
takes the value from the most similar example (this is sometimes referred to as hot deck imputation). This
algorithm can be substituted by one that the user connects to the input signal Learner for Imputation. Note,
however, that if there are discrete and continuous attributes in the data, the algorithm needs to be capable
of handling them both; at the moment only 1-NN learner can do that. (In the future, when Orange has
more regressors, the Impute widget may have separate input signals for discrete and continuous models.)

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• Random values computes the distributions of values for each attribute and then imputes by picking random
values from them.
• Remove examples with missing values removes the example containing missing values. This check also
applies to the class attribute if Impute class values is checked.
2. It is possible to specify individual treatment for each attribute, which overrides the default treatment set. One can
also specify a manually defined value used for imputation. In the screenshot, we decided not to impute the values
of “normalized-losses” and “make”, the missing values of “aspiration” will be replaced by random values, while
the missing values of “body-style” and “drive-wheels” are replaced by “hatchback” and “fwd”,respectively. If
the values of “length”, “width” or “height” are missing, the example is discarded. Values of all other attributes
use the default method set above (model-based imputer, in our case).
3. The imputation methods for individual attributes are the same as default methods.
4. Restore All to Default resets the individual attribute treatments to default.
5. Produce a report.
6. All changes are committed immediately if Apply automatically is checked. Otherwise, Apply needs to be ticked
to apply any new settings.

Example

To demonstrate how the Impute widget works, we played around with the Iris dataset and deleted some of the data.
We used the Impute widget and selected the Model-based imputer to impute the missing values. In another Data
Table, we see how the question marks turned into distinct values (“Iris-setosa, “Iris-versicolor”).

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2.1.24 Merge Data

Merges two datasets, based on values of selected attributes.

Inputs
• Data: input dataset
• Extra Data: additional dataset
Outputs
• Data: dataset with features added from extra data
The Merge Data widget is used to horizontally merge two datasets, based on the values of selected attributes
(columns). In the input, two datasets are required, data and extra data. Rows from the two data sets are matched
by the values of pairs of attributes, chosen by the user. The widget produces one output. It corresponds to the in-
stances from the input data to which attributes (columns) from input extra data are appended.
If the selected attribute pair does not contain unique values (in other words, the attributes have duplicate values), the
widget will give a warning. Instead, one can match by more than one attribute. Click on the plus icon to add the
attribute to merge on. The final result has to be a unique combination for each individual row.

1. Information on main data.

2. Information on data to append.
3. Merging type:
• Append columns from Extra Data outputs all rows from the Data, augmented by the columns in the
Extra Data. Rows without matches are retained, even where the data in the extra columns are missing.
• Find matching pairs of rows outputs rows from the Data, augmented by the columns in the Extra Data.
Rows without matches are removed from the output.
• Concatenate tables treats both data sources symmetrically. The output is similar to the first option, except
that non-matched values from Extra Data are appended at the end.
4. List of attributes from Data input.
5. List of attributes from Extra Data input.
6. Produce a report.

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Merging Types

#####Append Columns from Extra Data (left join)

Columns from the Extra Data are added to the Data. Instances with no matching rows will have missing values added.
For example, the first table may contain city names and the second would be a list of cities and their coordinates.
Columns with coordinates would then be appended to the data with city names. Where city names cannot be matched,
missing values will appear.
In our example, the first Data input contained 6 cities, but the Extra Data did not provide Lat and Lon values for
Bratislava, so the fields will be empty.

#####Find matching pairs of rows (inner join)

Only those rows that are matched will be present on the output, with the Extra Data columns appended. Rows without
matches are removed.
In our example, Bratislava from the Data input did not have Lat and Lon values, while Belgrade from the Extra Data
could not be found in the City column we were merging on. Hence both instances are remove - only the intersection
of instances is sent to the output.

#####Concatenate tables (outer join)

The rows from both the Data and the Extra Data will be present on the output. Where rows cannot be matched, missing
values will appear.
In our example, both Bratislava and Belgrade are now present. Bratislava will have missing Lat and Lon values, while
Belgrade will have a missing Population value.

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#####Row index
Data will be merged in the same order as they appear in the table. Row number 1 from the Data input will be joined
with row number 1 from the Extra Data input. Row numbers are assigned by Orange based on the original order of
the data instances.
#####Instance ID
This is a more complex option. Sometimes, data in transformed in the analysis and the domain is no longer the same.
Nevertheless, the original row indices are still present in the background (Orange remembers them). In this case one
can merge on instance ID. For example if you transformed the data with PCA, visualized it in the Scatter Plot, selected
some data instances and now you wish to see the original information of the selected subset. Connect the output of
Scatter Plot to Merge Data, add the original data set as Extra Data and merge by Instance ID.

#####Merge by two or more attributes

Sometimes our data instances are unique with respect to a combination of columns, not a single column. To merge
by more than a single column, add the Row matching condition by pressing plus next to the matching condition. To
remove it, press the x.
In the below example, we are merging by student column and class column.

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Say we have two data sets with student names and the class they’re in. The first data set has students’ grades and the
second on the elective course they have chosen. Unfortunately, there are two Jacks in our data, one from class A and
the other from class B. Same for Jane.
To distinguish between the two, we can match rows on both, the student’s name and her class.

Examples

Merging two datasets results in appending new attributes to the original file, based on a selected common attribute.
In the example below, we wanted to merge the zoo.tab file containing only factual data with zoo-with-images.tab
containing images. Both files share a common string attribute names. Now, we create a workflow connecting the two
files. The zoo.tab data is connected to Data input of the Merge Data widget, and the zoo-with-images.tab data to the
Extra Data input. Outputs of the Merge Data widget is then connected to the Data Table widget. In the latter, the
Merged Data channels are shown, where image attributes are added to the original data.

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The case where we want to include all instances in the output, even those where no match by attribute names was
found, is shown in the following workflow.

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The third type of merging is shown in the next workflow. The output consists of both inputs, with unknown values
assigned where no match was found.

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2.1.25 Outliers

Outlier detection widget.

Inputs
• Data: input dataset
Outputs
• Outliers: instances scored as outliers
• Inliers: instances not scored as outliers
• Data: input dataset appended Outlier variable
The Outliers widget applies one of the four methods for outlier detection. All methods apply classification to the
dataset. One-class SVM with non-linear kernels (RBF) performs well with non-Gaussian distributions, while Covari-
ance estimator works only for data with Gaussian distribution. One efficient way to perform outlier detection on
moderately high dimensional datasets is to use the Local Outlier Factor algorithm. The algorithm computes a score
reflecting the degree of abnormality of the observations. It measures the local density deviation of a given data point
with respect to its neighbors. Another efficient way of performing outlier detection in high-dimensional datasets is to
use random forests (Isolation Forest).

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1. Method for outlier detection:

• One Class SVM
• Covariance Estimator
• Local Outlier Factor
• Isolation Forest
2. Set parameters for the method:
• One class SVM with non-linear kernel (RBF): classifies data as similar or different from the core class:
– Nu is a parameter for the upper bound on the fraction of training errors and a lower bound of the
fraction of support vectors
– Kernel coefficient is a gamma parameter, which specifies how much influence a single data instance
has
• Covariance estimator: fits ellipsis to central points with Mahalanobis distance metric:
– Contamination is the proportion of outliers in the dataset
– Support fraction specifies the proportion of points included in the estimate
• Local Outlier Factor: obtains local density from the k-nearest neighbors:
– Contamination is the proportion of outliers in the dataset
– Neighbors represents number of neighbors
– Metric is the distance measure

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• Isolation Forest: isolates observations by randomly selecting a feature and then randomly selecting a split
value between the maximum and minimum values of the selected feature:
– Contamination is the proportion of outliers in the dataset
– Replicabe training fixes random seed
3. If Apply automatically is ticked, changes will be propagated automatically. Alternatively, click Apply.
4. Produce a report.
5. Number of instances on the input, followed by number of instances scored as inliers.

Example

Below is an example of how to use this widget. We used subset (versicolor and virginica instances) of the Iris dataset
to detect the outliers. We chose the Local Outlier Factor method, with Euclidean distance. Then we observed the
annotated instances in the Scatter Plot widget. In the next step we used the setosa instances to demonstrate novelty
detection using Apply Domain widget. After concatenating both outputs we examined the outliers in the Scatter Plot
(1).

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2.1.26 Preprocess

Preprocesses data with selected methods.

Inputs
• Data: input dataset
Outputs
• Preprocessor: preprocessing method
• Preprocessed Data: data preprocessed with selected methods
Preprocessing is crucial for achieving better-quality analysis results. The Preprocess widget offers several preprocess-
ing methods that can be combined in a single preprocessing pipeline. Some methods are available as separate widgets,
which offer advanced techniques and greater parameter tuning.

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1. List of preprocessors. Double click the preprocessors you wish to use and shuffle their order by dragging them
up or down. You can also add preprocessors by dragging them from the left menu to the right.
2. Preprocessing pipeline.
3. When the box is ticked (Send Automatically), the widget will communicate changes automatically. Alternatively,
click Send.

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Preprocessors

1. Discretization of continuous values:

• Entropy-MDL discretization by Fayyad and Irani that uses expected information to determine bins.
• Equal frequency discretization splits by frequency (same number of instances in each bin.

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• Equal width discretization creates bins of equal width (span of each bin is the same).
• Remove numeric features altogether.
2. Continuization of discrete values:
• Most frequent as base treats the most frequent discrete value as 0 and others as 1. The discrete attributes
with more than 2 values, the most frequent will be considered as a base and contrasted with remaining
values in corresponding columns.
• One feature per value creates columns for each value, place 1 where an instance has that value and 0 where
it doesn’t. Essentially One Hot Encoding.
• Remove non-binary features retains only categorical features that have values of either 0 or 1 and trans-
forms them into continuous.
• Remove categorical features removes categorical features altogether.
• Treat as ordinal takes discrete values and treats them as numbers. If discrete values are categories, each
category will be assigned a number as they appear in the data.
• Divide by number of values is similar to treat as ordinal, but the final values will be divided by the total
number of values and hence the range of the new continuous variable will be [0, 1].
3. Impute missing values:
• Average/Most frequent replaces missing values (NaN) with the average (for continuous) or most frequent
(for discrete) value.
• Replace with random value replaces missing values with random ones within the range of each variable.
• Remove rows with missing values.
4. Select relevant features:
• Similar to Rank, this preprocessor outputs only the most informative features. Score can be determined
by information gain, gain ratio, gini index, ReliefF, fast correlation based filter, ANOVA, Chi2, RReliefF,
and Univariate Linear Regression.
• Strategy refers to how many variables should be on the output. Fixed returns a fixed number of top scored
variables, while Percentile return the selected top percent of the features.

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1. Select random features outputs either a fixed number of features from the original data or a percentage. This is
mainly used for advanced testing and educational purposes.
2. Normalize adjusts values to a common scale. Center values by mean or median or omit centering altogether.
Similar for scaling, one can scale by SD (standard deviation), by span or not at all.
3. Randomize instances. Randomize classes shuffles class values and destroys connection between instances and
class. Similarly, one can randomize features or meta data. If replicable shuffling is on, randomization results
can be shared and repeated with a saved workflow. This is mainly used for advanced testing and educational
purposes.
4. Remove sparse features retains features that have more than user-defined threshold percentage of non-zero val-
ues. The rest are discarded.
5. Principal component analysis outputs results of a PCA transformation. Similar to the PCA widget.

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6. CUR matrix decomposition is a dimensionality reduction method, similar to SVD.

Examples

In the first example, we have used the heart_disease.tab dataset available in the dropdown menu of the File widget.
then we used Preprocess to impute missing values and normalize features. We can observe the changes in the Data
Table and compare it to the non-processed data.

In the second example, we show how to use Preprocess for predictive modeling.
This time we are using the heart_disease.tab data from the File widget. You can access the data through the dropdown
menu. This is a dataset with 303 patients that came to the doctor suffering from a chest pain. After the tests were done,
some patients were found to have diameter narrowing and others did not (this is our class variable).
The heart disease data have some missing values and we wish to account for that. First, we will split the data set into
train and test data with Data Sampler.
Then we will send the Data Sample into Preprocess. We will use Impute Missing Values, but you can try any combina-
tion of preprocessors on your data. We will send preprocessed data to Logistic Regression and the constructed model
to Predictions.
Finally, Predictions also needs the data to predict on. We will use the output of Data Sampler for prediction, but this
time not the Data Sample, but the Remaining Data, this is the data that wasn’t used for training the model.
Notice how we send the remaining data directly to Predictions without applying any preprocessing. This is because
Orange handles preprocessing on new data internally to prevent any errors in the model construction. The exact same
preprocessor that was used on the training data will be used for predictions. The same process applies to Test & Score.

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2.1.27 Apply Domain

Given dataset and template transforms the dataset.

Inputs
• Data: input dataset
• Template Data: template for transforming the dataset
Outputs
• Transformed Data: transformed dataset
Apply Domain maps new data into a transformed space. For example, if we transform some data with PCA and wish
to observe new data in the same space, we can use Apply Domain to map the new data into the PCA space created
from the original data.

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The widget receives a dataset and a template dataset used to transform the dataset.

Example

We will use iris data from the File widget for this example. To create two separate data sets, we will use Select Rows
and set the condition to iris is one of iris-setosa, iris-versicolor. This will output a data set with a 100 rows, half of
them belonging to iris-setosa class and the other half to iris-versicolor.
We will transform the data with PCA and select the first two components, which explain 96% of variance. Now, we
would like to apply the same preprocessing on the ‘new’ data, that is the remaining 50 iris virginicas. Send the unused
data from Select Rows to Apply Domain. Make sure to use the Unmatched Data output from Select Rows widget.
Then add the Transformed data output from PCA.
Apply Domain will apply the preprocessor to the new data and output it. To add the new data to the old data, use
Concatenate. Use Transformed Data output from PCA as Primary Data and Transformed Data from Apply Domain
as Additional Data.
Observe the results in a Data Table or in a Scatter Plot to see the new data in relation to the old one.

2.1.28 Purge Domain

Removes unused attribute values and useless attributes, sorts the remaining values.
Inputs
• Data: input dataset
Outputs

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• Data: filtered dataset

Definitions of nominal attributes sometimes contain values which don’t appear in the data. Even if this does not happen
in the original data, filtering the data, selecting exemplary subsets and alike can remove all examples for which the
attribute has some particular value. Such values clutter data presentation, especially various visualizations, and should
be removed.
After purging an attribute, it may become single-valued or, in extreme case, have no values at all (if the value of this
attribute was undefined for all examples). In such cases, the attribute can be removed.
A different issue is the order of attribute values: if the data is read from a file in a format in which values are not
declared in advance, they are sorted “in order of appearance”. Sometimes we would prefer to have them sorted
alphabetically.

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1. Purge attributes.
2. Purge classes.
3. Purge meta attributes.
4. Information on the filtering process.
5. Produce a report.
6. If Apply automatically is ticked, the widget will output data at each change of widget settings.
Such purification is done by the widget Purge Domain. Ordinary attributes and class attributes are treated separately.
For each, we can decide if we want the values sorted or not. Next, we may allow the widget to remove attributes with
less than two values or remove the class attribute if there are less than two classes. Finally, we can instruct the widget
to check which values of attributes actually appear in the data and remove the unused values. The widget cannot
remove values if it is not allowed to remove the attributes, since having attributes without values makes no sense.
The new, reduced attributes get the prefix “R”, which distinguishes them from the original ones. The values of new
attributes can be computed from the old ones, but not the other way around. This means that if you construct a
classifier from the new attributes, you can use it to classify the examples described by the original attributes. But not
the opposite: constructing a classifier from the old attributes and using it on examples described by the reduced ones
won’t work. Fortunately, the latter is seldom the case. In a typical setup, one would explore the data, visualize it, filter
it, purify it. . . and then test the final model on the original data.

Example

The Purge Domain widget would typically appear after data filtering, for instance when selecting a subset of visual-
ized examples.
In the above schema, we play with the adult.tab dataset: we visualize it and select a portion of the data, which contains
only four out of the five original classes. To get rid of the empty class, we put the data through Purge Domain before
going on to the Box Plot widget. The latter shows only the four classes which are in the Purge Data output. To see the
effect of data purification, uncheck Remove unused class variable values and observe the effect this has on Box Plot.

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2.1.29 Rank

Ranking of attributes in classification or regression datasets.

Inputs
• Data: input dataset
• Scorer: models for feature scoring
Outputs
• Reduced Data: dataset with selected attributes
The Rank widget considers class-labeled datasets (classification or regression) and scores the attributes according to
their correlation with the class. Rank accepts also models for scoring, such as linear regression, logistic regression,
random forest, SGD, etc.

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1. Select attributes from the data table.

2. Data table with attributes (rows) and their scores by different scoring methods (columns)
3. Produce a report.
4. If ‘Send Automatically’ is ticked, the widget automatically communicates changes to other widgets.

Scoring methods

1. Information Gain: the expected amount of information (reduction of entropy)

2. Gain Ratio: a ratio of the information gain and the attribute’s intrinsic information, which reduces the bias
towards multivalued features that occurs in information gain
3. Gini: the inequality among values of a frequency distribution
4. ANOVA: the difference between average vaules of the feature in different classes
5. Chi2: dependence between the feature and the class as measure by the chi-square statistic
6. ReliefF: the ability of an attribute to distinguish between classes on similar data instances
7. FCBF (Fast Correlation Based Filter): entropy-based measure, which also identifies redundancy due to pairwise
correlations between features
Additionally, you can connect certain learners that enable scoring the features according to how important they are in
models that the learners build (e.g. Linear Regression / Logistic Regression, Random Forest, SGD).

Example: Attribute Ranking and Selection

Below, we have used the Rank widget immediately after the File widget to reduce the set of data attributes and include
only the most informative ones:

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Notice how the widget outputs a dataset that includes only the best-scored attributes:

Example: Feature Subset Selection for Machine Learning

What follows is a bit more complicated example. In the workflow below, we first split the data into a training set and a
test set. In the upper branch, the training data passes through the Rank widget to select the most informative attributes,
while in the lower branch there is no feature selection. Both feature selected and original datasets are passed to their
own Test & Score widgets, which develop a Naive Bayes classifier and score it on a test set.

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For datasets with many features, a naive Bayesian classifier feature selection, as shown above, would often yield a
better predictive accuracy.

2.1.30 Correlations

Compute all pairwise attribute correlations.

Inputs
• Data: input dataset
Outputs
• Data: input dataset
• Features: selected pair of features
• Correlations: data table with correlation scores
Correlations computes Pearson or Spearman correlation scores for all pairs of features in a dataset. These methods
can only detect monotonic relationship.

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1. Correlation measure:
• Pairwise Pearson correlation.
• Pairwise Spearman correlation.
2. Filter for finding attribute pairs.
3. A list of attribute pairs with correlation coefficient. Press Finished to stop computation for large datasets.
4. Access widget help and produce report.

Example

Correlations can be computed only for numeric (continuous) features, so we will use housing as an example data set.
Load it in the File widget and connect it to Correlations. Positively correlated feature pairs will be at the top of the
list and negatively correlated will be at the bottom.

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Go to the most negatively correlated pair, DIS-NOX. Now connect Scatter Plot to Correlations and set two outputs,
Data to Data and Features to Features. Observe how the feature pair is immediately set in the scatter plot. Looks like
the two features are indeed negatively correlated.

2.1.31 Color

Set color legend for variables.

Inputs
• Data: input data set

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Outputs
• Data: data set with a new color legend
The Color widget sets the color legend for visualizations.

1. A list of discrete variables. Set the color of each variable by double-clicking on it. The widget also enables
renaming variables by clicking on their names.
2. A list of continuous variables. Click on the color strip to choose a different palette. To use the same palette for
all variables, change it for one variable and click Copy to all that appears on the right. The widget also enables
renaming variables by clicking on their names.
3. Produce a report.
4. Apply changes. If Apply automatically is ticked, changes will be communicated automatically. Alternatively,
just click Apply.

Palettes for numeric variables are grouped and tagged by their properties.

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• Diverging palettes have two colors on its ends and a central color (white or black) in the middle. Such palettes
are particularly useful when the the values can be positive or negative, as some widgets (for instance the Heat
map) will put the 0 at the middle point in the palette.
• Linear palettes are constructed so that human perception of the color change is linear with the change of the
value.
• Color blind palettes cover different types of color blindness, and can also be linear or diverging.
• In isoluminant palettes, all colors have equal brightness.
• Rainbow palettes are particularly nice in widgets that bin numeric values in visualizations.

Example

We chose to work with the heart_disease data set. We opened the color palette and selected two new colors for
diameter narrowing variable. Then we opened the Scatter Plot widget and viewed the changes made to the scatter plot.

To see the effect of color palettes for numeric variables, we color the points in the scatter plot by cholesterol and
change the palette for this attribute in the Color widget.

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2.1.32 Feature Statistics

Show basic statistics for data features.

Inputs
• Data: input data
Outputs
• Reduced data: table containing only selected features
• Statistics: table containing statistics of the selected features
The Feature Statistics widget provides a quick way to inspect and find interesting features in a given data set.

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The Feature Statistics widget on the heart-disease data set. The feature exerc ind ang was manually changed to a meta
variable for illustration purposes.
1. Info on the current data set size and number and types of features
2. The histograms on the right can be colored by any feature. If the selected feature is categorical, a discrete color
palette is used (as shown in the example). If the selected feature is numerical, a continuous color palette is used.
The table on the right contains statistics about each feature in the data set. The features can be sorted by each
statistic, which we now describe.
3. The feature type - can be one of categorical, numeric, time and string.
4. The name of the feature.
5. A histogram of feature values. If the feature is numeric, we appropriately discretize the values into bins. If the
feature is categorical, each value is assigned its own bar in the histogram.
6. The central tendency of the feature values. For categorical features, this is the mode. For numeric features, this
is mean value.
7. The dispersion of the feature values. For categorical features, this is the entropy of the value distribution. For
numeric features, this is the coefficient of variation.
8. The minimum value. This is computed for numerical and ordinal categorical features.
9. The maximum value. This is computed for numerical and ordinal categorical features.
10. The number of missing values in the data.
Notice also that some rows are colored differently. White rows indicate regular features, gray rows indicate class
variables and the lighter gray indicates meta variables.

Example

The Feature Statistics widget is most often used after the File widget to inspect and find potentially interesting features
in the given data set. In the following examples, we use the heart-disease data set.

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Once we have found a subset of potentially interesting features, or we have found features that we would like to
exclude, we can simply select the features we want to keep. The widget outputs a new data set with only these
features.

Alternatively, if we want to store feature statistics, we can use the Statistics output and manipulate those values as
needed. In this example, we simply select all the features and display the statistics in a table.

2.1.33 Neighbors

Compute nearest neighbors in data according to reference.

Inputs
• Data: An input data set.

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• Reference: A reference data for neighbor computation.

Outputs
• Neighbors: A data table of nearest neighbors according to reference.
The Neighbors widget computes nearest neighbors for a given reference and for a given distance measure. The
reference can be either one instance or more instances. In the case with one reference widget outputs closest n
instances from data where n is set by the Number of neighbors option in the widget. When reference contains more
instances widget computes the combined distance for each data instance as a minimum of distances to each reference.
Widget outputs n data instances with lowest combined distance.

1. Distance measure for computing neighbors. Supported measures are: Euclidean, Manhattan, Mahalanobis,
Cosine, Jaccard, Spearman, absolute Spearman, Pearson, absolute Pearson.
2. Number of neighbors on the output.
3. If Exclude rows (equal to) references is ticked, data instances that are highly similar to the reference (distance <
1e-5), will be excluded.
4. Click Apply to commit the changes. To communicate changes automatically tick Apply Automatically.
5. Status bar with access to widget help and information on the input and output data.

Examples

In the first example, we used iris data and passed it to Neighbors and to Data Table. In Data Table, we selected an
instance of iris, that will serve as our reference, meaning we wish to retrieve 10 closest examples to the select data
instance. We connect Data Table to Neighbors as well.
We can observe the results of neighbor computation in Data Table (1), where we can see 10 closest images to our
selected iris flower.

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Now change the selection Data Table to multiple examples. As a result, we get instances with closest combined
distances to the references. The method computes the combined distance as a minimum of distances to each reference.

Another example requires the installation of Image Analytics add-on. We loaded 15 paintings from famous painters
with Import Images widget and passed them to Image Embedding, where we selected Painters embedder.
Then the procedure is the same as above. We passed embedded images to Image Viewer and selected a painting from
Monet to serve as our reference image. We passed the image to Neighbors, where we set the distance measure to
cosine, ticked off Exclude reference and set the neighbors to 2. This allows us to find the actual closest neighbor to a
reference painting and observe them side by side in Image Viewer (1).

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2.2 Visualize

2.2.1 Box Plot

Shows distribution of attribute values.

Inputs
• Data: input dataset
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
The Box Plot widget shows the distributions of attribute values. It is a good practice to check any new data with this
widget to quickly discover any anomalies, such as duplicated values (e.g. gray and grey), outliers, and alike.

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1. Select the variable you want to plot. Tick Order by relevance to order variables by Chi2 or ANOVA over the
selected subgroup.
2. Choose Subgroups to see box plots displayed by a discrete subgroup.
3. When instances are grouped by a subgroup, you can change the display mode. Annotated boxes will display the
end values, the mean and the median, while compare medians and compare means will, naturally, compare the

selected value between subgroups. continuous

4. The mean (the dark blue vertical line). The thin blue line represents the standard deviation.
5. Values of the first (25%) and the third (75%) quantile. The blue highlighted area represents the values between
the first and the third quartile.
6. The median (yellow vertical line).
7. If Send automatically is ticked, changes are communicated automatically. Alternatively, press Send.
8. Access help, save image or produce a report.
For discrete attributes, the bars represent the number of instances with each particular attribute value. The plot shows
the number of different animal types in the Zoo dataset: there are 41 mammals, 13 fish, 20 birds and so on.

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Example

The Box Plot widget is most commonly used immediately after the File widget to observe the statistical properties of
a dataset. In the first example, we have used heart-disease data to inspect our variables.

Box Plot is also useful for finding the properties of a specific dataset, for instance a set of instances manually defined
in another widget (e.g. Scatter Plot or instances belonging to some cluster or a classification tree node. Let us now use
zoo data and create a typical clustering workflow with Distances and Hierarchical Clustering.
Now define the threshold for cluster selection (click on the ruler at the top). Connect Box Plot to Hierarchical
Clustering, tick Order by relevance and select Cluster as a subgroup. This will order attributes by how well they
define the selected subgroup, in our case a cluster. Seems like our clusters indeed correspond very well with the
animal type!

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2.2.2 Distributions

Displays value distributions for a single attribute.

Inputs
• Data: input dataset
The Distributions widget displays the value distribution of discrete or continuous attributes. If the data contains a
class variable, distributions may be conditioned on the class.
For discrete attributes, the graph displayed by the widget shows how many times (e.g., in how many instances) each
attribute value appears in the data. If the data contains a class variable, class distributions for each of the attribute
values will be displayed as well (like in the snapshot below). In order to create this graph, we used the Zoo dataset.

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1. A list of variables for distributions display

2. If Bin continuous variables is ticked, the widget will discretize continuous variables by assigning them to inter-
vals. The number of intervals is set by precision scale. Alternatively, you can set smoothness for the distribution
curves of continuous variables.
3. The widget may be requested to display value distributions only for instances of certain class (Group by). Show
relative frequencies will scale the data by percentage of the dataset.
4. Show probabilities.
5. Save image saves the graph to your computer in a .svg or .png format.
6. Produce a report.
For continuous attributes, the attribute values are displayed as a function graph. Class probabilities for continuous
attributes are obtained with Gaussian kernel density estimation, while the appearance of the curve is set with the
Precision bar (smooth or precise).
For the purpose of this example, we used the Iris dataset.

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In class-less domains, the bars are displayed in gray. Here we set Bin continuous variables into 10 bins, which
distributes variables into 10 intervals and displays averages of these intervals as histograms (see 2. above). We used
the Housing dataset.

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2.2.3 Heat Map

Plots a heat map for a pair of attributes.

Inputs
• Data: input dataset
Outputs
• Selected Data: instances selected from the plot
Heat map is a graphical method for visualizing attribute values by class in a two-way matrix. It only works on datasets
containing continuous variables. The values are represented by color: the higher a certain value is, the darker the
represented color. By combining class and attributes on x and y axes, we see where the attribute values are the
strongest and where the weakest, thus enabling us to find typical features (discrete) or value range (continuous) for
each class.

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1. The color scheme legend. Low and High are thresholds for the color palette (low for attributes with low values
and high for attributes with high values).
2. Merge data.
3. Sort columns and rows:

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• No Sorting (lists attributes as found in the dataset)

• Clustering (clusters data by similarity)
• Clustering with ordered leaves (maximizes the sum of similarities of adjacent elements)
4. Set what is displayed in the plot in Annotation & Legend.
• If Show legend is ticked, a color chart will be displayed above the map.
• If Stripes with averages is ticked, a new line with attribute averages will be displayed on the left.
• Row Annotations adds annotations to each instance on the right.
• Column Label Positions places column labels in a selected place (None, Top, Bottom, Top and Bottom).
5. If Keep aspect ratio is ticked, each value will be displayed with a square (proportionate to the map).
6. If Send Automatically is ticked, changes are communicated automatically. Alternatively, click Send.
7. Save image saves the image to your computer in a .svg or .png format.
8. Produce a report.

Example

The Heat Map below displays attribute values for the Housing dataset. The aforementioned dataset concerns the
housing values in the suburbs of Boston.
The first thing we see in the map are the ‘B’ and ‘Tax’ attributes, which are the only two colored in dark orange. The
‘B’ attribute provides information on the proportion of blacks by town and the ‘Tax’ attribute informs us about the
full-value property-tax rate per $10,000. In order to get a clearer heat map, we then use the Select Columns widget
and remove the two attributes from the dataset. Then we again feed the data to the Heat map. The new projection
offers additional information.
By removing ‘B’ and ‘Tax’, we can see other deciding factors, namely ‘Age’ and ‘ZN’. The ‘Age’ attribute provides
information on the proportion of owner-occupied units built prior to 1940 and the ‘ZN’ attribute informs us about the
proportion of non-retail business acres per town.

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The Heat Map widget is a nice tool for discovering relevant features in the data. By removing some of the more
pronounced features, we came across new information, which was hiding in the background.

References

Housing Dataset

2.2.4 Scatter Plot

Scatter plot visualization with explorative analysis and intelligent data visualization enhancements.
Inputs
• Data: input dataset
• Data Subset: subset of instances
• Features: list of attributes
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected

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The Scatter Plot widget provides a 2-dimensional scatter plot visualization for continuous attributes. The data is
displayed as a collection of points, each having the value of the x-axis attribute determining the position on the
horizontal axis and the value of the y-axis attribute determining the position on the vertical axis. Various properties of
the graph, like color, size and shape of the points, axis titles, maximum point size and jittering can be adjusted on the
left side of the widget. A snapshot below shows the scatter plot of the Iris dataset with the coloring matching of the
class attribute.

1. Select the x and y attribute. Optimize your projection by using Rank Projections. This feature scores attribute
pairs by average classification accuracy and returns the top scoring pair with a simultaneous visualization update.
Set jittering to prevent the dots overlapping. If Jitter continuous values is ticked, continuous instances will be
dispersed.
2. Set the color of the displayed points (you will get colors for discrete values and grey-scale points for continuous).
Set label, shape and size to differentiate between points. Set symbol size and opacity for all data points. Set the
desired colors scale.
3. Adjust plot properties:
• Show legend displays a legend on the right. Click and drag the legend to move it.
• Show gridlines displays the grid behind the plot.
• Show all data on mouse hover enables information bubbles if the cursor is placed on a dot.

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• Show class density colors the graph by class (see the screenshot below).
• Show regression line draws the regression line for pair of continuous attributes.
• Label only selected points allows you to select individual data instances and label them.
4. Select, zoom, pan and zoom to fit are the options for exploring the graph. The manual selection of data instances
works as an angular/square selection tool. Double click to move the projection. Scroll in or out for zoom.
5. If Send automatically is ticked, changes are communicated automatically. Alternatively, press Send.
6. Save Image saves the created image to your computer in a .svg or .png format.
7. Produce a report.
Here is an example of the Scatter Plot widget if the Show class density and Show regression line boxes are ticked.

Intelligent Data Visualization

If a dataset has many attributes, it is impossible to manually scan through all the pairs to find interesting or useful
scatter plots. Orange implements intelligent data visualization with the Find Informative Projections option in the
widget.

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If a categorical variable is selected in the Color section, the score is computed as follows. For each data instance,
the method finds 10 nearest neighbors in the projected 2D space, that is, on the combination of attribute pairs. It
then checks how many of them have the same color. The total score of the projection is then the average number of
same-colored neighbors.
Computation for continuous colors is similar, except that the coefficient of determination is used for measuring the
local homogeneity of the projection.
To use this method, go to the Find Informative Projections option in the widget, open the subwindow and press Start
Evaluation. The feature will return a list of attribute pairs by average classification accuracy score.
Below, there is an example demonstrating the utility of ranking. The first scatter plot projection was set as the default
sepal width to sepal length plot (we used the Iris dataset for simplicity). Upon running Find Informative Projections
optimization, the scatter plot converted to a much better projection of petal width to petal length plot.

Selection

Selection can be used to manually defined subgroups in the data. Use Shift modifier when selecting data instances to
put them into a new group. Shift + Ctrl (or Shift + Cmd on macOs) appends instances to the last group.
Signal data outputs a data table with an additional column that contains group indices.

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Explorative Data Analysis

The Scatter Plot, as the rest of Orange widgets, supports zooming-in and out of part of the plot and a manual selection
of data instances. These functions are available in the lower left corner of the widget.
The default tool is Select, which selects data instances within the chosen rectangular area. Pan enables you to move
the scatter plot around the pane. With Zoom you can zoom in and out of the pane with a mouse scroll, while Reset
zoom resets the visualization to its optimal size. An example of a simple schema, where we selected data instances
from a rectangular region and sent them to the Data Table widget, is shown below. Notice that the scatter plot doesn’t
show all 52 data instances, because some data instances overlap (they have the same values for both attributes used).

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Example

The Scatter Plot can be combined with any widget that outputs a list of selected data instances. In the example below,
we combine Tree and Scatter Plot to display instances taken from a chosen decision tree node (clicking on any node
of the tree will send a set of selected data instances to the scatter plot and mark selected instances with filled symbols).

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References

Gregor Leban and Blaz Zupan and Gaj Vidmar and Ivan Bratko (2006) VizRank: Data Visualization Guided by
Machine Learning. Data Mining and Knowledge Discovery, 13 (2). pp. 119-136. Available here.

2.2.5 Line Plot

Visualization of data profiles (e.g., time series).

Inputs
• Data: input dataset
• Data Subset: subset of instances
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
Line plot a type of plot which displays the data as a series of points, connected by straight line segments. It only works
for numerical data, while categorical can be used for grouping of the data points.

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1. Information on the input data.

2. Select what you wish to display:
• Lines show individual data instances in a plot.
• Range shows the range of data points between 10th and 90th percentile.
• Mean adds the line for mean value. If group by is selected, means will be displayed per each group value.
• Error bars show the standard deviation of each attribute.
3. Select a categorical attribute to use for grouping of data instances. Use None to show ungrouped data.
4. Select, zoom, pan and zoom to fit are the options for exploring the graph. The manual selection of data instances
works as a line selection, meaning the data under the selected line plots will be sent on the output. Scroll in or
out for zoom.
5. If Send Automatically is ticked, changes are communicated automatically. Alternatively, click Send.

Example

Line Plot is a standard visualization widget, which displays data profiles, normally of ordered numerical data. In this
simple example, we will display the iris data in a line plot, grouped by the iris attribute. The plot shows how petal
length nicely separates between class values.
If we observe this in a Scatter Plot, we can confirm this is indeed so. Petal length is an interesting attribute for
separation of classes, especially when enhanced with petal width, which is also nicely separated in the line plot.

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2.2.6 Venn Diagram

Plots a Venn diagram for two or more data subsets.

Inputs
• Data: input dataset
Outputs
• Selected Data: instances selected from the plot
• Data: entire data with a column indicating whether an instance was selected or not
The Venn Diagram widget displays logical relations between datasets by showing the number of common data in-
stances (rows) or the number of shared features (columns). Selecting a part of the visualization outputs the corre-
sponding instances or features.

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1. Select whether to count common features or instances.

2. Select whether to include duplicates or to output only unique rows (applicable only when matching by instances).
If Auto commit is on, changes are automatically communicated to other widgets.
Rows can be matched by their identity, e.g. rows from different data sets match if they came from the same row in a
file. Instead of using identities, we can choose a string variable to match the rows by. A warning is shown if data sets
have no common string variable.

Examples

The easiest way to use the Venn Diagram is to select data subsets and find matching instances in the visualization. We
use the breast-cancer dataset to select two subsets with Select Rows widget - the first subset is that of breast cancer
patients aged between 40 and 49 and the second is that of patients with a tumor size between 20 and 29. The Venn
Diagram helps us find instances that correspond to both criteria, which can be found in the intersection of the two
circles.

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The Venn Diagram widget can be also used for exploring different prediction models. In the following example,
we analysed 3 prediction methods, namely Naive Bayes, SVM and Random Forest, according to their misclassified
instances.
By selecting misclassifications in the three Confusion Matrix widgets and sending them to Venn diagram, we can see
all the misclassification instances visualized per method used. Then we open Venn Diagram and select, for example,
the misclassified instances that were identified by all three methods. This is represented as an intersection of all three
circles. Click on the intersection to see this two instances marked in the Scatter Plot widget. Try selecting different
diagram sections to see how the scatter plot visualization changes.

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2.2.7 Linear Projection

A linear projection method with explorative data analysis.

Inputs
• Data: input dataset
• Data Subset: subset of instances
• Projection: custom projection vectors
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
• Components: projection vectors
This widget displays linear projections of class-labeled data. It supports various types of projections such as circular,
linear discriminant analysis, principal component analysis, and custom projection.
Consider, for a start, a projection of the Iris dataset shown below. Notice that it is the sepal width and sepal length that
already separate Iris setosa from the other two, while the petal length is the attribute best separating Iris versicolor
from Iris virginica.

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1. Axes in the projection that are displayed and other available axes.
2. Optimize your projection by using Suggest Features. This feature scores attributes by average classification
accuracy and returns the top scoring attributes with a simultaneous visualization update.
3. Choose the type of projection.
4. Axes inside a circle are hidden. Circle radius can be be changed using a slider.
5. Adjust plot properties:
• Set jittering to prevent the dots from overlapping (especially for discrete attributes).
• Show legend displays a legend on the right. Click and drag the legend to move it.
• Show class density colors the graph by class (see the screenshot below).
• Label only selected points allows you to select individual data instances and label them.
6. Select, zoom, pan and zoom to fit are the options for exploring the graph. Manual selection of data instances
works as an angular/square selection tool. Double click to move the projection. Scroll in or out for zoom.
7. If Send automatically is ticked, changes are communicated automatically. Alternatively, press Send.
8. Save Image saves the created image to your computer in a .svg or .png format. Produce a report.

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Example

The Linear Projection widget works just like other visualization widgets. Below, we connected it to the File widget
to see the set projected on a 2-D plane. Then we selected the data for further analysis and connected it to the Data
Table widget to see the details of the selected subset.

References

Koren Y., Carmel L. (2003). Visualization of labeled data using linear transformations. In Proceedings of IEEE
Information Visualization 2003, (InfoVis’03). Available here.
Boulesteix A.-L., Strimmer K. (2006). Partial least squares: a versatile tool for the analysis of high-dimensional
genomic data. Briefings in Bioinformatics, 8(1), 32-44. Abstract here.

2.2.8 Sieve Diagram

Plots a sieve diagram for a pair of attributes.

Inputs
• Data: input dataset
A Sieve Diagram is a graphical method for visualizing frequencies in a two-way contingency table and comparing
them to expected frequencies under assumption of independence. It was proposed by Riedwyl and Schüpbach in a
technical report in 1983 and later called a parquet diagram (Riedwyl and Schüpbach 1994). In this display, the area
of each rectangle is proportional to the expected frequency, while the observed frequency is shown by the number
of squares in each rectangle. The difference between observed and expected frequency (proportional to the standard
Pearson residual) appears as the density of shading, using color to indicate whether the deviation from independence
is positive (blue) or negative (red).

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1. Select the attributes you want to display in the sieve plot.

2. Score combinations enables you to fin the best possible combination of attributes.
3. Save Image saves the created image to your computer in a .svg or .png format.

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4. Produce a report.
The snapshot below shows a sieve diagram for the Titanic dataset and has the attributes sex and survived (the latter is
a class attribute in this dataset). The plot shows that the two variables are highly associated, as there are substantial
differences between observed and expected frequencies in all of the four quadrants. For example, and as highlighted
in the balloon, the chance for surviving the accident was much higher for female passengers than expected (0.06 vs.
0.15).

Pairs of attributes with interesting associations have a strong shading, such as the diagram shown in the above snapshot.
For contrast, a sieve diagram of the least interesting pair (age vs. survival) is shown below.

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Example

Below, we see a simple schema using the Titanic dataset, where we use the Rank widget to select the best attributes
(the ones with the highest information gain, gain ratio or Gini index) and feed them into the Sieve Diagram. This
displays the sieve plot for the two best attributes, which in our case are sex and status. We see that the survival rate on
the Titanic was very high for women of the first class and very low for female crew members.

The Sieve Diagram also features the Score Combinations option, which makes the ranking of attributes even easier.

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References

Riedwyl, H., and Schüpbach, M. (1994). Parquet diagram to plot contingency tables. In Softstat ‘93: Advances in
Statistical Software, F. Faulbaum (Ed.). New York: Gustav Fischer, 293-299.

2.2.9 Pythagorean Tree

Pythagorean tree visualization for classification or regression trees.

Inputs
• Tree: tree model
• Selected Data: instances selected from the tree
Pythagorean Trees are plane fractals that can be used to depict general tree hierarchies as presented in an article by
Fabian Beck and co-authors. In our case, they are used for visualizing and exploring tree models, such as Tree.

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1. Information on the input tree model.

2. Visualization parameters:
• Depth: set the depth of displayed trees.
• Target class (for classification trees): the intensity of the color for nodes of the tree will correspond to the
probability of the target class. If None is selected, the color of the node will denote the most probable
class.
• Node color (for regression trees): node colors can correspond to mean or standard deviation of class value
of the training data instances in the node.
• Size: define a method to compute the size of the square representing the node. Normal will keep node sizes
correspond to the size of training data subset in the node. Square root and Logarithmic are the respective
transformations of the node size.
• Log scale factor is only enabled when logarithmic transformation is selected. You can set the log factor
between 1 and 10.
3. Plot properties:
• Enable tooltips: display node information upon hovering.
• Show legend: shows color legend for the plot.
4. Reporting:
• Save Image: save the visualization to a SVG or PNG file.
• Report: add visualization to the report.

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Pythagorean Tree can visualize both classification and regression trees. Below is an example for regression tree. The
only difference between the two is that regression tree doesn’t enable coloring by class, but can color by class mean or
standard deviation.

Example

The workflow from the screenshot below demonstrates the difference between Tree Viewer and Pythagorean Tree.
They can both visualize Tree, but Pythagorean visualization takes less space and is more compact, even for a small Iris
flower dataset. For both visualization widgets, we have hidden the control area on the left by clicking on the splitter
between control and visualization area.

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Pythagorean Tree is interactive: click on any of the nodes (squares) to select training data instances that were associated
with that node. The following workflow explores these feature.

The selected data instances are shown as a subset in the Scatter Plot, sent to the Data Table and examined in the Box

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Plot. We have used brown-selected dataset in this example. The tree and scatter plot are shown below; the selected
node in the tree has a black outline.

References

Beck, F., Burch, M., Munz, T., Di Silvestro, L. and Weiskopf, D. (2014). Generalized Pythagoras Trees for Visualizing
Hierarchies. In IVAPP ‘14 Proceedings of the 5th International Conference on Information Visualization Theory and
Applications, 17-28.

2.2.10 Pythagorean Forest

Pythagorean forest for visualizing random forests.

Inputs
• Random Forest: tree models from random forest
Outputs
• Tree: selected tree model
Pythagorean Forest shows all learned decision tree models from Random Forest widget. It displays them as
Pythagorean trees, each visualization pertaining to one randomly constructed tree. In the visualization, you can select
a tree and display it in Pythagorean Tree widget. The best tree is the one with the shortest and most strongly colored
branches. This means few attributes split the branches well.
Widget displays both classification and regression results. Classification requires discrete target variable in the dataset,
while regression requires a continuous target variable. Still, they both should be fed a Tree on the input.

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1. Information on the input random forest model.

2. Display parameters:
• Depth: set the depth to which the trees are grown.
• Target class: set the target class for coloring the trees. If None is selected, the tree will be white. If the input
is a classification tree, you can color the nodes by their respective class. If the input is a regression tree,
the options are Class mean, which will color tree nodes by the class mean value and Standard deviation,
which will color them by the standard deviation value of the node.
• Size: set the size of the nodes. Normal will keep the nodes the size of the subset in the node. Square root
and Logarithmic are the respective transformations of the node size.
• Zoom: allows you to see the size of the tree visualizations.
3. Save Image: save the visualization to your computer as a .svg or .png file. Report: produce a report.

Example

Pythagorean Forest is great for visualizing several built trees at once. In the example below, we’ve used housing
dataset and plotted all 10 trees we’ve grown with Random Forest. When changing the parameters in Random Forest,
visualization in Pythagorean Forest will change as well.
Then we’ve selected a tree in the visualization and inspected it further with Pythagorean Tree widget.

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References

Beck, F., Burch, M., Munz, T., Di Silvestro, L. and Weiskopf, D. (2014). Generalized Pythagoras Trees for Visualizing
Hierarchies. In IVAPP ‘14 Proceedings of the 5th International Conference on Information Visualization Theory and
Applications, 17-28.

2.2.11 CN2 Rule Viewer

CN2 Rule Viewer

Inputs
• Data: dataset to filter
• CN2 Rule Classifier: CN2 Rule Classifier, including a list of induced rules
Outputs
• Filtered Data: data instances covered by all selected rules
A widget that displays CN2 classification rules. If data is also connected, upon rule selection, one can analyze which
instances abide to the conditions.

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1. Original order of induced rules can be restored.

2. When rules are many and complex, the view can appear packed. For this reason, compact view was implemented,
which allows a flat presentation and a cleaner inspection of rules.
3. Click Report to bring up a detailed description of the rule induction algorithm and its parameters, the data
domain, and induced rules.
Additionally, upon selection, rules can be copied to clipboard by pressing the default system shortcut (ctrl+C, cmd+C).

Examples

In the schema below, the most common use of the widget is presented. First, the data is read and a CN2 rule classifier
is trained. We are using titanic dataset for the rule construction. The rules are then viewed using the Rule Viewer.
To explore different CN2 algorithms and understand how adjusting parameters influences the learning process, Rule
Viewer should be kept open and in sight, while setting the CN2 learning algorithm (the presentation will be updated
promptly).

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Selecting a rule outputs filtered data instances. These can be viewed in a Data Table.

2.2.12 Mosaic Display

Display data in a mosaic plot.

Inputs
• Data: input dataset
• Data subset: subset of instances
Outputs
• Selected data: instances selected from the plot
The Mosaic plot is a graphical representation of a two-way frequency table or a contingency table. It is used for
visualizing data from two or more qualitative variables and was introduced in 1981 by Hartigan and Kleiner and ex-
panded and refined by Friendly in 1994. It provides the user with the means to more efficiently recognize relationships
between different variables. If you wish to read up on the history of Mosaic Display, additional reading is available
here.

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1. Select the variables you wish to see plotted.

2. Select interior coloring. You can color the interior according to class or you can use the Pearson residual, which
is the difference between observed and fitted values, divided by an estimate of the standard deviation of the
observed value. If Compare to total is clicked, a comparison is made to all instances.
3. Save image saves the created image to your computer in a .svg or .png format.
4. Produce a report.

Example

We loaded the titanic dataset and connected it to the Mosaic Display widget. We decided to focus on two variables,
namely status, sex and survival. We colored the interiors according to Pearson residuals in order to demonstrate the
difference between observed and fitted values.

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We can see that the survival rates for men and women clearly deviate from the fitted value.

2.2.13 Silhouette Plot

A graphical representation of consistency within clusters of data.

Inputs
• Data: input dataset
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected

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The Silhouette Plot widget offers a graphical representation of consistency within clusters of data and provides the
user with the means to visually assess cluster quality. The silhouette score is a measure of how similar an object is to
its own cluster in comparison to other clusters and is crucial in the creation of a silhouette plot. The silhouette score
close to 1 indicates that the data instance is close to the center of the cluster and instances possessing the silhouette
scores close to 0 are on the border between two clusters.

1. Choose the distance metric. You can choose between:

• Euclidean (“straight line” distance between two points)
• Manhattan (the sum of absolute differences for all attributes)
• Cosine (1 - cosine of the angle between two vectors)
2. Select the cluster label. You can decide whether to group the instances by cluster or not.
3. Display options:
• Choose bar width.

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• Annotations: annotate the silhouette plot.

4. Save Image saves the created silhouette plot to your computer in a .png or .svg format.
5. Produce a report.
6. Output:
• Add silhouette scores (good clusters have higher silhouette scores)
• By clicking Commit, changes are communicated to the output of the widget. Alternatively, tick the box on
the left and changes will be communicated automatically.
7. The created silhouette plot.

Example

In the snapshot below, we have decided to use the Silhouette Plot on the iris dataset. We selected data instances with
low silhouette scores and passed them on as a subset to the Scatter Plot widget. This visualization only confirms the
accuracy of the Silhouette Plot widget, as you can clearly see that the subset lies in the border between two clusters.

If you are interested in other uses of the Silhouette Plot widget, feel free to explore our blog post.

2.2.14 Tree Viewer

A visualization of classification and regression trees.

Inputs
• Tree: decision tree

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Outputs
• Selected Data: instances selected from the tree node
• Data: data with an additional column showing whether a point is selected
This is a versatile widget with 2-D visualization of classification and regression trees. The user can select a node,
instructing the widget to output the data associated with the node, thus enabling explorative data analysis.

1. Information on the input.

2. Display options:
• Zoom in and zoom out
• Select the tree width. The nodes display information bubbles when hovering over them.
• Select the depth of your tree.
• Select edge width. The edges between the nodes in the tree graph are drawn based on the selected edge
width.
– All the edges will be of equal width if Fixed is chosen.
– When Relative to root is selected, the width of the edge will correspond to the proportion of instances
in the corresponding node with respect to all the instances in the training data. Under this selection,
the edge will get thinner and thinner when traversing toward the bottom of the tree.
– Relative to parent makes the edge width correspond to the proportion of instances in the nodes with
respect to the instances in their parent node.
• Define the target class, which you can change based on classes in the data.
3. Press Save image to save the created tree graph to your computer as a .svg or .png file.
4. Produce a report.

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Examples

Below, is a simple classification schema, where we have read the data, constructed the decision tree and viewed it in
our Tree Viewer. If both the viewer and Tree are open, any re-run of the tree induction algorithm will immediately
affect the visualization. You can thus use this combination to explore how the parameters of the induction algorithm
influence the structure of the resulting tree.

Clicking on any node will output the related data instances. This is explored in the schema below that shows the subset
in the data table and in the Scatter Plot. Make sure that the tree data is passed as a data subset; this can be done by
connecting the Scatter Plot to the File widget first, and connecting it to the Tree Viewer widget next. Selected data
will be displayed as bold dots.
Tree Viewer can also export labeled data. Connect Data Table to Tree Viewer and set the link between widgets to
Data instead of Selected Data. This will send the entire data to Data Table with an additional meta column labeling
selected data instances (Yes for selected and No for the remaining).

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Finally, Tree Viewer can be used also for visualizing regression trees. Connect Random Forest to File widget using
housing.tab dataset. Then connect Pythagorean Forest to Random Forest. In Pythagorean Forest select a regression
tree you wish to further analyze and pass it to the Tree Viewer. The widget will display the constructed tree. For
visualizing larger trees, especially for regression, Pythagorean Tree could be a better option.

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2.2.15 Nomogram

Nomograms for visualization of Naive Bayes and Logistic Regression classifiers.

Inputs
• Classifier: trained classifier
• Data: input dataset
Outputs
• Features: selected variables, 10 by default
The Nomogram enables some classifier’s (more precisely Naive Bayes classifier and Logistic Regression classifier)
visual representation. It offers an insight into the structure of the training data and effects of the attributes on the
class probabilities. Besides visualization of the classifier, the widget offers interactive support for prediction of class
probabilities. A snapshot below shows the nomogram of the Titanic dataset, that models the probability for a passenger
not to survive the disaster of the Titanic.
When there are too many attributes in the plotted dataset, only best ranked ones can be selected for display. It is
possible to choose from ‘No sorting’, ‘Name’, ‘Absolute importance’, ‘Positive influence’ and ‘Negative influence’
for Naive Bayes representation and from ‘No sorting’, ‘Name’ and ‘Absolute importance’ for Logistic Regression
representation.
The probability for the chosen target class is computed by ‘1-vs-all’ principle, which should be taken in consideration
when dealing with multiclass data (alternating probabilities do not sum to 1). To avoid this inconvenience, you can
choose to normalize probabilities.

1. Select the target class you want to model the probability for. Select, whether you want to normalize the proba-
bilities or not.
2. By default Scale is set to Log odds ration. For easier understanding and interpretation option Point scale can
be used. The unit is obtained by re-scaling the log odds so that the maximal absolute log odds ratio in the
nomogram represents 100 points.

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3. Display all attributes or only the best ranked ones. Sort them and set the projection type.
Continuous attributes can be plotted in 2D (only for Logistic Regression).

logreg

Examples

The Nomogram widget should be used immediately after trained classifier widget (e.g. Naive Bayes or Logistics
Regression). It can also be passed a data instance using any widget that enables selection (e.g. Data Table) as shown
in the workflow below.

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Referring to the Titanic dataset once again, 1490 (68%) passengers on Titanic out of 2201 died. To make a prediction,
the contribution of each attribute is measured as a point score and the individual point scores are summed to determine
the probability. When the value of the attribute is unknown, its contribution is 0 points. Therefore, not knowing
anything about the passenger, the total point score is 0 and the corresponding probability equals the unconditional
prior. The nomogram in the example shows the case when we know that the passenger is a male adult from the first
class. The points sum to -0.36, with a corresponding probability of not surviving of about 53%.

Features output

The second example shows how to use the Features output. Let us use heart_disease data for this exercise and load
it in the File widget. Now connect File to Naive Bayes (or Logistic Regression) and add Nomogram to Naive Bayes.
Finally, connect File to Select Columns.
Select Columns selects a subset of variables, while Nomogram shows the top scoring variables for the trained classifier.
To filter the data by the variables selected in the Nomogram, connect Nomogram to Select Columns as shown below.
Nomogram will pass a list of selected variables to Select Columns, which will retain only the variables from the list.
For this to work, you have to press Use input features in Select Columns (or tick it to always apply it).
We have selected the top 5 variables in Nomogram and used Select Columns to retain only those variables.

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2.2.16 FreeViz

Displays FreeViz projection.

Inputs
• Data: input dataset
• Data Subset: subset of instances
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
• Components: FreeViz vectors
FreeViz uses a paradigm borrowed from particle physics: points in the same class attract each other, those from
different class repel each other, and the resulting forces are exerted on the anchors of the attributes, that is, on unit
vectors of each of the dimensional axis. The points cannot move (are projected in the projection space), but the
attribute anchors can, so the optimization process is a hill-climbing optimization where at the end the anchors are
placed such that forces are in equilibrium. The button Optimize is used to invoke the optimization process. The result
of the optimization may depend on the initial placement of the anchors, which can be set in a circle, arbitrary or even
manually. The later also works at any stage of optimization, and we recommend to play with this option in order to
understand how a change of one anchor affects the positions of the data points. In any linear projection, projections of
unit vector that are very short compared to the others indicate that their associated attribute is not very informative for
particular classification task. Those vectors, that is, their corresponding anchors, may be hidden from the visualization
using Radius slider in Show anchors box.

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1. Two initial positions of anchors are possible: random and circular. Optimization moves anchors in an optimal
position.
2. Set the color of the displayed points (you will get colors for discrete values and grey-scale points for continuous).
Set label, shape and size to differentiate between points. Set symbol size and opacity for all data points.
3. Anchors inside a circle are hidden. Circle radius can be be changed using a slider.
4. Adjust plot properties:
• Set jittering to prevent the dots from overlapping (especially for discrete attributes).
• Show legend displays a legend on the right. Click and drag the legend to move it.
• Show class density colors the graph by class (see the screenshot below).
• Label only selected points allows you to select individual data instances and label them.

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5. Select, zoom, pan and zoom to fit are the options for exploring the graph. The manual selection of data instances
works as an angular/square selection tool. Double click to move the projection. Scroll in or out for zoom.
6. If Send automatically is ticked, changes are communicated automatically. Alternatively, press Send.
7. Save Image saves the created image to your computer in a .svg or .png format.
8. Produce a report.

Manually move anchors

One can manually move anchors. Use a mouse pointer and hover above the end of an anchor. Click the left button and
then you can move selected anchor where ever you want.

Selection

Selection can be used to manually defined subgroups in the data. Use Shift modifier when selecting data instances to
put them into a new group. Shift + Ctrl (or Shift + Cmd on macOs) appends instances to the last group.
Signal data outputs a data table with an additional column that contains group indices.

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Explorative Data Analysis

The FreeViz, as the rest of Orange widgets, supports zooming-in and out of part of the plot and a manual selection of
data instances. These functions are available in the lower left corner of the widget. The default tool is Select, which
selects data instances within the chosen rectangular area. Pan enables you to move the plot around the pane. With
Zoom you can zoom in and out of the pane with a mouse scroll, while Reset zoom resets the visualization to its optimal
size. An example of a simple schema, where we selected data instances from a rectangular region and sent them to the
Data Table widget, is shown below.

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2.2.17 Radviz

Radviz vizualization with explorative data analysis and intelligent data visualization enhancements.
Inputs
• Data: input dataset
• Data Subset: subset of instances
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
• Components: Radviz vectors
Radviz (Hoffman et al. 1997) is a non-linear multi-dimensional visualization technique that can display data defined
by three or more variables in a 2-dimensional projection. The visualized variables are presented as anchor points
equally spaced around the perimeter of a unit circle. Data instances are shown as points inside the circle, with their
positions determined by a metaphor from physics: each point is held in place with springs that are attached at the other
end to the variable anchors. The stiffness of each spring is proportional to the value of the corresponding variable and
the point ends up at the position where the spring forces are in equilibrium. Prior to visualization, variable values are
scaled to lie between 0 and 1. Data instances that are close to a set of variable anchors have higher values for these
variables than for the others.
The snapshot shown below shows a Radviz widget with a visualization of the dataset from functional genomics (Brown
et al. 2000). In this particular visualization the data instances are colored according to the corresponding class, and
the visualization space is colored according to the computed class probability. Notice that the particular visualization
very nicely separates data instances of different class, making the visualization interesting and potentially informative.

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Just like all point-based visualizations, this widget includes tools for intelligent data visualization (VizRank, see Leban
et al. 2006) and an interface for explorative data analysis - selection of data points in visualization. Just like the Scatter
Plot widget, it can be used to find a set of variables that would result in an interesting visualization. The Radviz graph
above is according to this definition an example of a very good visualization, while the one below - where we show an
VizRank’s interface (Suggest features button) with a list of 3-attribute visualizations and their scores - is not.

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References

Hoffman, P. E. et al. (1997) DNA visual and analytic data mining. In the Proceedings of the IEEE Visualization.
Phoenix, AZ, pp. 437-441.
Brown, M. P., W. N. Grundy et al. (2000). “Knowledge-based analysis of microarray gene expression data by using
support vector machines.” Proc Natl Acad Sci U S A 97(1): 262-7.
Leban, G., B. Zupan et al. (2006). “VizRank: Data Visualization Guided by Machine Learning.” Data Mining and
Knowledge Discovery 13(2): 119-136.
Mramor, M., G. Leban, J. Demsar, and B. Zupan. Visualization-based cancer microarray data classification analysis.
Bioinformatics 23(16): 2147-2154, 2007.

2.3 Model

2.3.1 Constant

Predict the most frequent class or mean value from the training set.
Inputs
• Data: input dataset

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• Preprocessor: preprocessing method(s)

Outputs
• Learner: majority/mean learning algorithm
• Model: trained model
This learner produces a model that always predicts themajority for classification tasks and mean value for regression
tasks.
For classification, when predicting the class value with Predictions, the widget will return relative frequencies of the
classes in the training set. When there are two or more majority classes, the classifier chooses the predicted class
randomly, but always returns the same class for a particular example.
For regression, it learns the mean of the class variable and returns a predictor with the same mean value.
The widget is typically used as a baseline for other models.

This widget provides the user with two options:

1. The name under which it will appear in other widgets. Default name is “Constant”.
2. Produce a report.
If you change the widget’s name, you need to click Apply. Alternatively, tick the box on the left side and changes will
be communicated automatically.

Examples

In a typical classification example, we would use this widget to compare the scores of other learning algorithms (such
as kNN) with the default scores. Use iris dataset and connect it to Test & Score. Then connect Constant and kNN to
Test & Score and observe how well kNN performs against a constant baseline.

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For regression, we use Constant to construct a predictor in Predictions. We used the housing dataset. In Predictions,
you can see that Mean Learner returns one (mean) value for all instances.

2.3.2 CN2 Rule Induction

Induce rules from data using CN2 algorithm.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)

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Outputs
• Learner: CN2 learning algorithm
• CN2 Rule Classifier: trained model
The CN2 algorithm is a classification technique designed for the efficient induction of simple, comprehensible rules
of form “if cond then predict class”, even in domains where noise may be present.
CN2 Rule Induction works only for classification.

1. Name under which the learner appears in other widgets. The default name is CN2 Rule Induction.

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2. Rule ordering:
• Ordered: induce ordered rules (decision list). Rule conditions are found and the majority class is assigned
in the rule head.
• Unordered: induce unordered rules (rule set). Learn rules for each class individually, in regard to the
original learning data.
3. Covering algorithm:
• Exclusive: after covering a learning instance, remove it from further consideration.
• Weighted: after covering a learning instance, decrease its weight (multiplication by gamma) and in-turn
decrease its impact on further iterations of the algorithm.
4. Rule search:
• Evaluation measure: select a heuristic to evaluate found hypotheses:
– Entropy (measure of unpredictability of content)
– Laplace Accuracy
– Weighted Relative Accuracy
• Beam width; remember the best rule found thus far and monitor a fixed number of alternatives (the beam).
5. Rule filtering:
• Minimum rule coverage: found rules must cover at least the minimum required number of covered
examples. Unordered rules must cover this many target class examples.
• Maximum rule length: found rules may combine at most the maximum allowed number of selectors
(conditions).
• Default alpha: significance testing to prune out most specialised (less frequently applicable) rules in
regard to the initial distribution of classes.
• Parent alpha: significance testing to prune out most specialised (less frequently applicable) rules in regard
to the parent class distribution.
6. Tick ‘Apply Automatically’ to auto-communicate changes to other widgets and to immediately train the classi-
fier if learning data is connected. Alternatively, press ‘Apply‘ after configuration.

Examples

For the example below, we have used zoo dataset and passed it to CN2 Rule Induction. We can review and interpret
the built model with CN2 Rule Viewer widget.

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The second workflow tests evaluates CN2 Rule Induction and Tree in Test & Score.

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References

1. Fürnkranz, Johannes. “Separate-and-Conquer Rule Learning”, Artificial Intelligence Review 13, 3-54, 1999.
2. Clark, Peter and Tim Niblett. “The CN2 Induction Algorithm”, Machine Learning Journal, 3 (4), 261-283,
1989.
3. Clark, Peter and Robin Boswell. “Rule Induction with CN2: Some Recent Improvements”, Machine Learning -
Proceedings of the 5th European Conference (EWSL-91),151-163, 1991.
4. Lavrač, Nada et al. “Subgroup Discovery with CN2-SD”,Journal of Machine Learning Research 5, 153-188,
2004

2.3.3 Calibrated Learner

Wraps another learner with probability calibration and decision threshold optimization.
Inputs
• Data: input dataset

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• Preprocessor: preprocessing method(s)

• Base Learner: learner to calibrate
Outputs
• Learner: calibrated learning algorithm
• Model: trained model using the calibrated learner
This learner produces a model that calibrates the distribution of class probabilities and optimizes decision threshold.
The widget works only for binary classification tasks.

1. The name under which it will appear in other widgets. Default name is composed of the learner, calibration and
optimization parameters.
2. Probability calibration:
• Sigmoid calibration
• Isotonic calibration
• No calibration
3. Decision threshold optimization:
• Optimize classification accuracy
• Optimize F1 score
• No threshold optimization
4. Press Apply to commit changes. If Apply Automatically is ticked, changes are committed automatically.

Example

A simple example with Calibrated Learner. We are using the titanic data set as the widget requires binary class
values (in this case they are ‘survived’ and ‘not survived’).
We will use Logistic Regression as the base learner which will we calibrate with the default settings, that is with
sigmoid optimization of distribution values and by optimizing the CA.
Comparing the results with the uncalibrated Logistic Regression model we see that the calibrated model performs
better.

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2.3.4 kNN

Predict according to the nearest training instances.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: kNN learning algorithm
• Model: trained model
The kNN widget uses the kNN algorithm that searches for k closest training examples in feature space and uses their
average as prediction.

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1. A name under which it will appear in other widgets. The default name is “kNN”.
2. Set the number of nearest neighbors, the distance parameter (metric) and weights as model criteria.
• Metric can be:
– Euclidean (“straight line”, distance between two points)
– Manhattan (sum of absolute differences of all attributes)
– Maximal (greatest of absolute differences between attributes)
– Mahalanobis (distance between point and distribution).
• The Weights you can use are:
– Uniform: all points in each neighborhood are weighted equally.
– Distance: closer neighbors of a query point have a greater influence than the neighbors further away.
3. Produce a report.
4. When you change one or more settings, you need to click Apply, which will put a new learner on the output and,
if the training examples are given, construct a new model and output it as well. Changes can also be applied
automatically by clicking the box on the left side of the Apply button.

Examples

The first example is a classification task on iris dataset. We compare the results of k-Nearest neighbors with the default
model Constant, which always predicts the majority class.

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The second example is a regression task. This workflow shows how to use the Learner output. For the purpose of this
example, we used the housing dataset. We input the kNN prediction model into Predictions and observe the predicted
values.

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2.3.5 Tree

A tree algorithm with forward pruning.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: decision tree learning algorithm
• Model: trained model
Tree is a simple algorithm that splits the data into nodes by class purity. It is a precursor to Random Forest. Tree in
Orange is designed in-house and can handle both discrete and continuous datasets.
It can also be used for both classification and regression tasks.

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1. The learner can be given a name under which it will appear in other widgets. The default name is “Tree”.
2. Tree parameters:
• Induce binary tree: build a binary tree (split into two child nodes)
• Min. number of instances in leaves: if checked, the algorithm will never construct a split which would
put less than the specified number of training examples into any of the branches.
• Do not split subsets smaller than: forbids the algorithm to split the nodes with less than the given number
of instances.
• Limit the maximal tree depth: limits the depth of the classification tree to the specified number of node
levels.
3. Stop when majority reaches [%]: stop splitting the nodes after a specified majority threshold is reached
4. Produce a report. After changing the settings, you need to click Apply, which will put the new learner on the
output and, if the training examples are given, construct a new classifier and output it as well. Alternatively, tick
the box on the left and changes will be communicated automatically.

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Examples

There are two typical uses for this widget. First, you may want to induce a model and check what it looks like in Tree
Viewer.

The second schema trains a model and evaluates its performance against Logistic Regression.

We used the iris dataset in both examples. However, Tree works for regression tasks as well. Use housing dataset

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and pass it to Tree. The selected tree node from Tree Viewer is presented in the Scatter Plot and we can see that the
selected examples exhibit the same features.

2.3.6 Random Forest

Predict using an ensemble of decision trees.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: random forest learning algorithm
• Model: trained model
Random forest is an ensemble learning method used for classification, regression and other tasks. It was first proposed
by Tin Kam Ho and further developed by Leo Breiman (Breiman, 2001) and Adele Cutler.
Random Forest builds a set of decision trees. Each tree is developed from a bootstrap sample from the training data.
When developing individual trees, an arbitrary subset of attributes is drawn (hence the term “Random”), from which
the best attribute for the split is selected. The final model is based on the majority vote from individually developed
trees in the forest.
Random Forest works for both classification and regression tasks.

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1. Specify the name of the model. The default name is “Random Forest”.
2. Specify how many decision trees will be included in the forest (Number of trees in the forest), and how many
attributes will be arbitrarily drawn for consideration at each node. If the latter is not specified (option Number of
attributes. . . left unchecked), this number is equal to the square root of the number of attributes in the data. You
can also choose to fix the seed for tree generation (Fixed seed for random generator), which enables replicability
of the results.
3. Original Breiman’s proposal is to grow the trees without any pre-pruning, but since pre-pruning often works
quite well and is faster, the user can set the depth to which the trees will be grown (Limit depth of individual
trees). Another pre-pruning option is to select the smallest subset that can be split (Do not split subsets smaller
than).
4. Produce a report.
5. Click Apply to communicate the changes to other widgets. Alternatively, tick the box on the left side of the
Apply button and changes will be communicated automatically.

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Examples

For classification tasks, we use iris dataset. Connect it to Predictions. Then, connect File to Random Forest and Tree
and connect them further to Predictions. Finally, observe the predictions for the two models.

For regressions tasks, we will use housing data. Here, we will compare different models, namely Random Forest,
Linear Regression and Constant, in the Test & Score widget.

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References

Breiman, L. (2001). Random Forests. In Machine Learning, 45(1), 5-32. Available here.

2.3.7 SVM

Support Vector Machines map inputs to higher-dimensional feature spaces.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: linear regression learning algorithm
• Model: trained model
• Support Vectors: instances used as support vectors
Support vector machine (SVM) is a machine learning technique that separates the attribute space with a hyperplane,
thus maximizing the margin between the instances of different classes or class values. The technique often yields
supreme predictive performance results. Orange embeds a popular implementation of SVM from the LIBSVM pack-
age. This widget is its graphical user interface.
For regression tasks, SVM performs linear regression in a high dimension feature space using an 𝜖-insensitive loss.
Its estimation accuracy depends on a good setting of C, 𝜖 and kernel parameters. The widget outputs class predictions
based on a SVM Regression.

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The widget works for both classification and regression tasks.

1. The learner can be given a name under which it will appear in other widgets. The default name is “SVM”.
2. SVM type with test error settings. SVM and 𝜈-SVM are based on different minimization of the error function.
On the right side, you can set test error bounds:
• SVM:

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– Cost: penalty term for loss and applies for classification and regression tasks.
– 𝜖: a parameter to the epsilon-SVR model, applies to regression tasks. Defines the distance from true
values within which no penalty is associated with predicted values.
• 𝜈-SVM:
– Cost: penalty term for loss and applies only to regression tasks
– 𝜈: a parameter to the 𝜈-SVR model, applies to classification and regression tasks. An upper bound on
the fraction of training errors and a lower bound of the fraction of support vectors.
3. Kernel is a function that transforms attribute space to a new feature space to fit the maximum-margin hyperplane,
thus allowing the algorithm to create the model with Linear, Polynomial, RBF and Sigmoid kernels. Functions
that specify the kernel are presented upon selecting them, and the constants involved are:
• g for the gamma constant in kernel function (the recommended value is 1/k, where k is the number of the
attributes, but since there may be no training set given to the widget the default is 0 and the user has to set
this option manually),
• c for the constant c0 in the kernel function (default 0), and
• d for the degree of the kernel (default 3).
4. Set permitted deviation from the expected value in Numerical Tolerance. Tick the box next to Iteration Limit to
set the maximum number of iterations permitted.
5. Produce a report.
6. Click Apply to commit changes. If you tick the box on the left side of the Apply button, changes will be
communicated automatically.

Examples

In the first (regression) example, we have used housing dataset and split the data into two data subsets (Data Sample
and Remaining Data) with Data Sampler. The sample was sent to SVM which produced a Model, which was then
used in Predictions to predict the values in Remaining Data. A similar schema can be used if the data is already in two
separate files; in this case, two File widgets would be used instead of the File - Data Sampler combination.

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The second example shows how to use SVM in combination with Scatter Plot. The following workflow trains a SVM
model on iris data and outputs support vectors, which are those data instances that were used as support vectors in
the learning phase. We can observe which are these data instances in a scatter plot visualization. Note that for the
workflow to work correctly, you must set the links between widgets as demonstrated in the screenshot below.

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References

Introduction to SVM on StatSoft.

2.3.8 Linear Regression

A linear regression algorithm with optional L1 (LASSO), L2 (ridge) or L1L2 (elastic net) regularization.
Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: linear regression learning algorithm
• Model: trained model
• Coefficients: linear regression coefficients
The Linear Regression widget constructs a learner/predictor that learns a linear function from its input data. The
model can identify the relationship between a predictor xi and the response variable y. Additionally, Lasso and Ridge
regularization parameters can be specified. Lasso regression minimizes a penalized version of the least squares loss
function with L1-norm penalty and Ridge regularization with L2-norm penalty.
Linear regression works only on regression tasks.

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1. The learner/predictor name

2. Choose a model to train:
• no regularization
• a Ridge regularization (L2-norm penalty)
• a Lasso bound (L1-norm penalty)
• an Elastic net regularization
3. Produce a report.
4. Press Apply to commit changes. If Apply Automatically is ticked, changes are committed automatically.

Example

Below, is a simple workflow with housing dataset. We trained Linear Regression and Random Forest and evaluated
their performance in Test & Score.

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2.3.9 Logistic Regression

The logistic regression classification algorithm with LASSO (L1) or ridge (L2) regularization.
Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: logistic regression learning algorithm
• Model: trained model
• Coefficients: logistic regression coefficients
Logistic Regression learns a Logistic Regression model from the data. It only works for classification tasks.

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1. A name under which the learner appears in other widgets. The default name is “Logistic Regression”.
2. Regularization type (either L1 or L2). Set the cost strength (default is C=1).
3. Press Apply to commit changes. If Apply Automatically is ticked, changes will be communicated automatically.

Example

The widget is used just as any other widget for inducing a classifier. This is an example demonstrating prediction
results with logistic regression on the hayes-roth dataset. We first load hayes-roth_learn in the File widget and pass
the data to Logistic Regression. Then we pass the trained model to Predictions.
Now we want to predict class value on a new dataset. We load hayes-roth_test in the second File widget and connect
it to Predictions. We can now observe class values predicted with Logistic Regression directly in Predictions.

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2.3.10 Naive Bayes

A fast and simple probabilistic classifier based on Bayes’ theorem with the assumption of feature independence.
Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: naive bayes learning algorithm
• Model: trained model
Naive Bayes learns a Naive Bayesian model from the data. It only works for classification tasks.

This widget has two options: the name under which it will appear in other widgets and producing a report. The default
name is Naive Bayes. When you change it, you need to press Apply.

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Examples

Here, we present two uses of this widget. First, we compare the results of the Naive Bayes with another model, the
Random Forest. We connect iris data from File to Test & Score. We also connect Naive Bayes and Random Forest to
Test & Score and observe their prediction scores.

The second schema shows the quality of predictions made with Naive Bayes. We feed the Test & Score widget a
Naive Bayes learner and then send the data to the Confusion Matrix. We also connect Scatter Plot with File. Then we
select the misclassified instances in the Confusion Matrix and show feed them to Scatter Plot. The bold dots in the
scatterplot are the misclassified instances from Naive Bayes.

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2.3.11 AdaBoost

An ensemble meta-algorithm that combines weak learners and adapts to the ‘hardness’ of each training sample.
Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
• Learner: learning algorithm
Outputs
• Learner: AdaBoost learning algorithm
• Model: trained model
The AdaBoost (short for “Adaptive boosting”) widget is a machine-learning algorithm, formulated by Yoav Freund
and Robert Schapire. It can be used with other learning algorithms to boost their performance. It does so by tweaking
the weak learners.
AdaBoost works for both classification and regression.

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1. The learner can be given a name under which it will appear in other widgets. The default name is “AdaBoost”.
2. Set the parameters. The base estimator is a tree and you can set:
• Number of estimators
• Learning rate: it determines to what extent the newly acquired information will override the old informa-
tion (0 = the agent will not learn anything, 1 = the agent considers only the most recent information)
• Fixed seed for random generator: set a fixed seed to enable reproducing the results.
3. Boosting method.
• Classification algorithm (if classification on input): SAMME (updates base estimator’s weights with clas-
sification results) or SAMME.R (updates base estimator’s weight with probability estimates).
• Regression loss function (if regression on input): Linear (), Square (), Exponential ().
4. Produce a report.
5. Click Apply after changing the settings. That will put the new learner in the output and, if the training examples
are given, construct a new model and output it as well. To communicate changes automatically tick Apply
Automatically.

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Examples

For classification, we loaded the iris dataset. We used AdaBoost, Tree and Logistic Regression and evaluated the
models’ performance in Test & Score.

For regression, we loaded the housing dataset, sent the data instances to two different models (AdaBoost and Tree)
and output them to the Predictions widget.

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2.3.12 Neural Network

A multi-layer perceptron (MLP) algorithm with backpropagation.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: multi-layer perceptron learning algorithm
• Model: trained model
The Neural Network widget uses sklearn’s Multi-layer Perceptron algorithm that can learn non-linear models as well
as linear.

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1. A name under which it will appear in other widgets. The default name is “Neural Network”.
2. Set model parameters:
• Neurons per hidden layer: defined as the ith element represents the number of neurons in the ith hidden
layer. E.g. a neural network with 3 layers can be defined as 2, 3, 2.
• Activation function for the hidden layer:
– Identity: no-op activation, useful to implement linear bottleneck
– Logistic: the logistic sigmoid function
– tanh: the hyperbolic tan function
– ReLu: the rectified linear unit function
• Solver for weight optimization:
– L-BFGS-B: an optimizer in the family of quasi-Newton methods
– SGD: stochastic gradient descent
– Adam: stochastic gradient-based optimizer
• Alpha: L2 penalty (regularization term) parameter
• Max iterations: maximum number of iterations
Other parameters are set to sklearn’s defaults.

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3. Produce a report.
4. When the box is ticked (Apply Automatically), the widget will communicate changes automatically. Alterna-
tively, click Apply.

Examples

The first example is a classification task on iris dataset. We compare the results of Neural Network with the Logistic
Regression.

The second example is a prediction task, still using the iris data. This workflow shows how to use the Learner output.
We input the Neural Network prediction model into Predictions and observe the predicted values.

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2.3.13 Stochastic Gradient Descent

Minimize an objective function using a stochastic approximation of gradient descent.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
Outputs
• Learner: stochastic gradient descent learning algorithm
• Model: trained model
The Stochastic Gradient Descent widget uses stochastic gradient descent that minimizes a chosen loss function with
a linear function. The algorithm approximates a true gradient by considering one sample at a time, and simultaneously
updates the model based on the gradient of the loss function. For regression, it returns predictors as minimizers of the
sum, i.e. M-estimators, and is especially useful for large-scale and sparse datasets.

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1. Specify the name of the model. The default name is “SGD”.

2. Algorithm parameters:
• Classification loss function:
– Hinge (linear SVM)
– Logistic Regression (logistic regression SGD)
– Modified Huber (smooth loss that brings tolerance to outliers as well as probability estimates)
– Squared Hinge (quadratically penalized hinge)
– Perceptron (linear loss used by the perceptron algorithm)
– Squared Loss (fitted to ordinary least-squares)
– Huber (switches to linear loss beyond 𝜖)
– Epsilon insensitive (ignores errors within 𝜖, linear beyond it)
– Squared epsilon insensitive (loss is squared beyond 𝜖-region).
• Regression loss function:
– Squared Loss (fitted to ordinary least-squares)
– Huber (switches to linear loss beyond 𝜖)
– Epsilon insensitive (ignores errors within 𝜖, linear beyond it)
– Squared epsilon insensitive (loss is squared beyond 𝜖-region).
3. Regularization norms to prevent overfitting:
• None.
• Lasso (L1) (L1 leading to sparse solutions)
• Ridge (L2) (L2, standard regularizer)
• Elastic net (mixing both penalty norms).
Regularization strength defines how much regularization will be applied (the less we regularize, the more we
allow the model to fit the data) and the mixing parameter what the ratio between L1 and L2 loss will be (if set
to 0 then the loss is L2, if set to 1 then it is L1).
4. Learning parameters.
• Learning rate:
– Constant: learning rate stays the same through all epochs (passes)
– Optimal: a heuristic proposed by Leon Bottou
– Inverse scaling: earning rate is inversely related to the number of iterations
• Initial learning rate.
• Inverse scaling exponent: learning rate decay.
• Number of iterations: the number of passes through the training data.
• If Shuffle data after each iteration is on, the order of data instances is mixed after each pass.
• If Fixed seed for random shuffling is on, the algorithm will use a fixed random seed and enable replicating
the results.
5. Produce a report.

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6. Press Apply to commit changes. Alternatively, tick the box on the left side of the Apply button and changes will
be communicated automatically.

Examples

For the classification task, we will use iris dataset and test two models on it. We connected Stochastic Gradient Descent
and Tree to Test & Score. We also connected File to Test & Score and observed model performance in the widget.

For the regression task, we will compare three different models to see which predict what kind of results. For the
purpose of this example, the housing dataset is used. We connect the File widget to Stochastic Gradient Descent,
Linear Regression and kNN widget and all four to the Predictions widget.

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2.3.14 Stacking

Stack multiple models.

Inputs
• Data: input dataset
• Preprocessor: preprocessing method(s)
• Learners: learning algorithm
• Aggregate: model aggregation method
Outputs
• Learner: aggregated (stacked) learning algorithm
• Model: trained model
Stacking is an ensemble method that computes a meta model from several base models. The Stacking widget has
the Aggregate input, which provides a method for aggregating the input models. If no aggregation input is given
the default methods are used. Those are Logistic Regression for classification and Ridge Regression for regression
problems.

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1. The meta learner can be given a name under which it will appear in other widgets. The default name is “Stack”.
2. Click Apply to commit the aggregated model. That will put the new learner in the output and, if the training
examples are given, construct a new model and output it as well. To communicate changes automatically tick
Apply Automatically.
3. Access help and produce a report.

Example

We will use Paint Data to demonstrate how the widget is used. We painted a complex dataset with 4 class labels and
sent it to Test & Score. We also provided three kNN learners, each with a different parameters (number of neighbors
is 5, 10 or 15). Evaluation results are good, but can we do better?
Let’s use Stacking. Stacking requires several learners on the input and an aggregation method. In our case, this is
Logistic Regression. A constructed meta learner is then sent to Test & Score. Results have improved, even if only
marginally. Stacking normally works well on complex data sets.

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2.3.15 Load Model

Load a model from an input file.

Outputs
• Model: trained model

1. Choose from a list of previously used models.

2. Browse for saved models.
3. Reload the selected model.

Example

When you want to use a custom-set model that you’ve saved before, open the Load Model widget and select the
desired file with the Browse icon. This widget loads the existing model into Predictions widget. Datasets used with
Load Model have to contain compatible attributes!

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2.3.16 Save Model

Save a trained model to an output file.

If the file is saved to the same directory as the workflow or in the subtree of that directory, the widget remembers the
relative path. Otherwise it will store an absolute path, but disable auto save for security reasons.
Inputs
• Model: trained model

1. Choose from previously saved models.

2. Save the created model with the Browse icon. Click on the icon and en-
ter the name of the file. The model will be saved to a pickled file.

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3. Save the model.

Example

When you want to save a custom-set model, feed the data to the model (e.g. Logistic Regression) and connect it to
Save Model. Name the model; load it later into workflows with Load Model. Datasets used with Load Model have
to contain compatible attributes.

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2.4 Evaluate

2.4.1 Calibration Plot

Shows the match between classifiers’ probability predictions and actual class probabilities.
Inputs
• Evaluation Results: results of testing classification algorithms
The Calibration Plotplots class probabilities against those predicted by the classifier(s).

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1. Select the desired target class from the drop down menu.
2. Choose which classifiers to plot. The diagonal represents optimal behavior; the closer the classifier’s curve gets,
the more accurate its prediction probabilities are. Thus we would use this widget to see whether a classifier is
overly optimistic (gives predominantly positive results) or pessimistic (gives predominantly negative results).
3. If Show rug is enabled, ticks are displayed at the bottom and the top of the graph, which represent negative and
positive examples respectively. Their position corresponds to the classifier’s probability prediction and the color
shows the classifier. At the bottom of the graph, the points to the left are those which are (correctly) assigned a
low probability of the target class, and those to the right are incorrectly assigned high probabilities. At the top
of the graph, the instances to the right are correctly assigned high probabilities and vice versa.
4. Press Save Image if you want to save the created image to your computer in a .svg or .png format.
5. Produce a report.

Example

At the moment, the only widget which gives the right type of signal needed by the Calibration Plot is Test & Score.
The Calibration Plot will hence always follow Test & Score and, since it has no outputs, no other widgets follow it.
Here is a typical example, where we compare three classifiers (namely Naive Bayes, Tree and Constant) and input
them into Test & Score. We used the Titanic dataset. Test & Score then displays evaluation results for each classifier.
Then we draw Calibration Plot and ROC Analysis widgets from Test & Score to further analyze the performance of
classifiers. Calibration Plot enables you to see prediction accuracy of class probabilities in a plot.

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2.4.2 Confusion Matrix

Shows proportions between the predicted and actual class.

Inputs
• Evaluation results: results of testing classification algorithms
Outputs
• Selected Data: data subset selected from confusion matrix
• Data: data with the additional information on whether a data instance was selected
The Confusion Matrix gives the number/proportion of instances between the predicted and actual class. The selection
of the elements in the matrix feeds the corresponding instances into the output signal. This way, one can observe
which specific instances were misclassified and how.
The widget usually gets the evaluation results from Test & Score; an example of the schema is shown below.

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1. When evaluation results contain data on multiple learning algorithms, we have to choose one in the Learners
box. The snapshot shows the confusion matrix for Tree and Naive Bayesian models trained and tested on the
iris data. The right-hand side of the widget contains the matrix for the naive Bayesian model (since this model
is selected on the left). Each row corresponds to a correct class, while columns represent the predicted classes.
For instance, four instances of Iris-versicolor were misclassified as Iris-virginica. The rightmost column gives
the number of instances from each class (there are 50 irises of each of the three classes) and the bottom row
gives the number of instances classified into each class (e.g., 48 instances were classified into virginica).
2. In Show, we select what data we would like to see in the matrix.
• Number of instances shows correctly and incorrectly classified instances numerically.
• Proportions of predicted shows how many instances classified as, say, Iris-versicolor are in which true
class; in the table we can read the 0% of them are actually setosae, 88.5% of those classified as versicolor
are versicolors, and 7.7% are virginicae.
• Proportions of actual shows the opposite relation: of all true versicolors, 92% were classified as versicol-

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ors and 8% as virginicae.

3. In Select, you can choose the desired output.
• Correct sends all correctly classified instances to the output by selecting the diagonal of the matrix.
• Misclassified selects the misclassified instances.
• None annuls the selection. As mentioned before, one can also select individual cells of the table to select
specific kinds of misclassified instances (e.g. the versicolors classified as virginicae).
4. When sending selected instances, the widget can add new attributes, such as predicted classes or their probabil-
ities, if the corresponding options Predictions and/or Probabilities are checked.
5. The widget outputs every change if Send Automatically is ticked. If not, the user will need to click Send Selected
to commit the changes.
6. Produce a report.

Example

The following workflow demonstrates what this widget can be used for.

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Test & Score gets the data from File and two learning algorithms from Naive Bayes and Tree. It performs cross-
validation or some other train-and-test procedures to get class predictions by both algorithms for all (or some) data
instances. The test results are fed into the Confusion Matrix, where we can observe how many instances were
misclassified and in which way.
In the output, we used Data Table to show the instances we selected in the confusion matrix. If we, for instance, click
Misclassified, the table will contain all instances which were misclassified by the selected method.
The Scatter Plot gets two sets of data. From the File widget it gets the complete data, while the confusion matrix
sends only the selected data, misclassifications for instance. The scatter plot will show all the data, with bold symbols
representing the selected data.

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2.4.3 Lift Curve

Measures the performance of a chosen classifier against a random classifier.

Inputs
• Evaluation Results: results of testing classification algorithms
The Lift curve shows the relation between the number of instances which were predicted positive and those that are
indeed positive and thus measures the performance of a chosen classifier against a random classifier. The graph is
constructed with the cumulative number of cases (in descending order of probability) on the x-axis and the cumulative
number of true positives on the y-axis. Lift curve is often used in segmenting the population, e.g., plotting the number
of responding customers against the number of all customers contacted. You can also determine the optimal classifier
and its threshold from the graph.

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1. Choose the desired Target class. The default class is chosen alphabetically.
2. If test results contain more than one classifier, the user can choose which curves she or he wants to see plotted.
Click on a classifier to select or deselect the curve.
3. Show lift convex hull plots a convex hull over lift curves for all classifiers (yellow curve). The curve shows the
optimal classifier (or combination thereof) for each desired TP/P rate.
4. Press Save Image if you want to save the created image to your computer in a .svg or .png format.
5. Produce a report.
6. 2-D pane with P rate (population) as x-axis and TP rate (true positives) as a y-axis. The diagonal line represents
the behavior of a random classifier. Click and drag to move the pane and scroll in or out to zoom. Click on the
“A” sign at the bottom left corner to realign the pane.
Note! The perfect classifier would have a steep slope towards 1 until all classes are guessed correctly and then run
straight along 1 on y-axis to (1,1).

Example

At the moment, the only widget which gives the right type of the signal needed by the Lift Curve is Test & Score.
In the example below, we try to see the prediction quality for the class ‘survived’ on the Titanic dataset. We compared
three different classifiers in the Test Learners widget and sent them to Lift Curve to see their performance against a
random model. We see the Tree classifier is the best out of the three, since it best aligns with lift convex hull. We also
see that its performance is the best for the first 30% of the population (in order of descending probability), which we
can set as the threshold for optimal classification.

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References

Handouts of the University of Notre Dame on Data Mining - Lift Curve. Available here.

2.4.4 Predictions

Shows models’ predictions on the data.

Inputs
• Data: input dataset
• Predictors: predictors to be used on the data
Outputs
• Predictions: data with added predictions
• Evaluation Results: results of testing classification algorithms

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The widget receives a dataset and one or more predictors (predictive models, not learning algorithms - see the example
below). It outputs the data and the predictions.

1. Information on the input, namely the number of instances to predict, the number of predictors and the task
(classification or regression). If you have sorted the data table by attribute and you wish to see the original view,
press Restore Original Order.
2. You can select the options for classification. If Predicted class is ticked, the view provides information on
predicted class. If Predicted probabilities for is ticked, the view provides information on probabilities predicted
by the classifier(s). You can also select the predicted class displayed in the view. The option Draw distribution
bars provides a visualization of probabilities.
3. By ticking the Show full dataset, you can view the entire data table (otherwise only class variable will be shown).
4. Select the desired output.
5. Predictions.
The widget show the probabilities and final decisions of predictive models. The output of the widget is another dataset,
where predictions are appended as new meta attributes. You can select which features you wish to output (original
data, predictions, probabilities). The result can be observed in a Data Table. If the predicted data includes true class
values, the result of prediction can also be observed in a Confusion Matrix.

Examples

In the first example, we will use Attrition - Train data from the Datasets widget. This is a data on attrition of employees.
In other words, we wish to know whether a certain employee will resign from the job or not. We will construct a
predictive model with the Tree widget and observe probabilities in Predictions.

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For predictions we need both the training data, which we have loaded in the first Datasets widget and the data to
predict, which we will load in another Datasets widget. We will use Attrition - Predict data this time. Connect the
second data set to Predictions. Now we can see predictions for the three data instances from the second data set.
The Tree model predicts none of the employees will leave the company. You can try other model and see if predictions
change. Or test the predictive scores first in the Test & Score widget.

In the second example, we will see how to properly use Preprocess with Predictions or Test & Score.
This time we are using the heart disease.tab data from the File widget. You can access the data through the dropdown
menu. This is a dataset with 303 patients that came to the doctor suffering from a chest pain. After the tests were done,
some patients were found to have diameter narrowing and others did not (this is our class variable).
The heart disease data have some missing values and we wish to account for that. First, we will split the data set into
train and test data with Data Sampler.
Then we will send the Data Sample into Preprocess. We will use Impute Missing Values, but you can try any combina-
tion of preprocessors on your data. We will send preprocessed data to Logistic Regression and the constructed model
to Predictions.
Finally, Predictions also needs the data to predict on. We will use the output of Data Sampler for prediction, but this
time not the Data Sample, but the Remaining Data, this is the data that wasn’t used for training the model.
Notice how we send the remaining data directly to Predictions without applying any preprocessing. This is because
Orange handles preprocessing on new data internally to prevent any errors in the model construction. The exact same
preprocessor that was used on the training data will be used for predictions. The same process applies to Test & Score.

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2.4.5 ROC Analysis

Plots a true positive rate against a false positive rate of a test.

Inputs
• Evaluation Results: results of testing classification algorithms
The widget shows ROC curves for the tested models and the corresponding convex hull. It serves as a mean of
comparison between classification models. The curve plots a false positive rate on an x-axis (1-specificity; probability
that target=1 when true value=0) against a true positive rate on a y-axis (sensitivity; probability that target=1 when
true value=1). The closer the curve follows the left-hand border and then the top border of the ROC space, the more
accurate the classifier. Given the costs of false positives and false negatives, the widget can also determine the optimal
classifier and threshold.

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1. Choose the desired Target Class. The default class is chosen alphabetically.
2. If test results contain more than one classifier, the user can choose which curves she or he wants to see plotted.
Click on a classifier to select or deselect it.
3. When the data comes from multiple iterations of training and testing, such
as k-fold cross validation, the results can be (and usually are) averaged.

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The averaging options are:

• Merge predictions from folds (top left), which treats all the test data as if they came from a single iteration
• Mean TP rate (top right) averages the curves vertically, showing the corresponding confidence intervals
• Mean TP and FP at threshold (bottom left) traverses over threshold, averages the positions of curves and
shows horizontal and vertical confidence intervals
• Show individual curves (bottom right) does not average but prints all the curves instead
4. Option Show convex ROC curves refers to convex curves over each individual classifier (the thin lines positioned
over curves). Show ROC convex hull plots a convex hull combining all classifiers (the gray area below the
curves). Plotting both types of convex curves makes sense since selecting a threshold in a concave part of the
curve cannot yield optimal results, disregarding the cost matrix. Besides, it is possible to reach any point on
the convex curve by combining the classifiers represented by the points on the border of the concave region.

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The diagonal dotted line represents the behavior of a random classifier. The full diagonal line represents iso-
performance. A black “A” symbol at the bottom of the graph proportionally readjusts the graph.
5. The final box is dedicated to the analysis of the curve. The user can specify the cost of false positives (FP) and
false negatives (FN), and the prior target class probability.
• Default threshold (0.5) point shows the point on the ROC curve achieved by the classifier if it predicts the
target class if its probability equals or exceeds 0.5.
• Show performance line shows iso-performance in the ROC space so that all the points on the line give the
same profit/loss. The line further to the upper left is better than the one down and right. The direction of the
line depends upon costs and probabilities. This gives a recipe for depicting the optimal threshold for the
given costs: this is the point where the tangent with the given inclination touches the curve and it is marked
in the plot. If we push the iso-performance higher or more to the left, the points on the iso-performance
line cannot be reached by the learner. Going down or to the right, decreases the performance.
• The widget allows setting the costs from 1 to 1000. Units are not important, as are not the magnitudes.
What matters is the relation between the two costs, so setting them to 100 and 200 will give the same
result as 400 and 800. Defaults: both costs equal (500), Prior target class probability 50%(from the data).

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False positive cost: 830, False negative cost 650, Prior target class probability 73%.

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6. Press Save Image if you want to save the created image to your computer in a .svg or .png format.
7. Produce a report.

Example

At the moment, the only widget which gives the right type of signal needed by the ROC Analysis is Test & Score.
Below, we compare two classifiers, namely Tree and Naive Bayes, in Test&Score and then compare their performance
in ROC Analysis, Life Curve and Calibration Plot.

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2.4.6 Test and Score

Tests learning algorithms on data.

Inputs
• Data: input dataset
• Test Data: separate data for testing
• Learner: learning algorithm(s)
Outputs
• Evaluation Results: results of testing classification algorithms
The widget tests learning algorithms. Different sampling schemes are available, including using separate test data. The
widget does two things. First, it shows a table with different classifier performance measures, such as classification
accuracy and area under the curve. Second, it outputs evaluation results, which can be used by other widgets for
analyzing the performance of classifiers, such as ROC Analysis or Confusion Matrix.
The Learner signal has an uncommon property: it can be connected to more than one widget to test multiple learners
with the same procedures.

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1. The widget supports various sampling methods.

• Cross-validation splits the data into a given number of folds (usually 5 or 10). The algorithm is tested by
holding out examples from one fold at a time; the model is induced from other folds and examples from
the held out fold are classified. This is repeated for all the folds.
• Cross validation by feature performs cross-validation but folds are defined by the selected categorical
feature from meta-features.
• Random sampling randomly splits the data into the training and testing set in the given proportion (e.g.
70:30); the whole procedure is repeated for a specified number of times.
• Leave-one-out is similar, but it holds out one instance at a time, inducing the model from all others and
then classifying the held out instances. This method is obviously very stable, reliable. . . and very slow.
• Test on train data uses the whole dataset for training and then for testing. This method practically always
gives wrong results.
• Test on test data: the above methods use the data from Data signal only. To input another dataset with test-
ing examples (for instance from another file or some data selected in another widget), we select Separate
Test Data signal in the communication channel and select Test on test data.
2. For classification, Target class can be selected at the bottom of the widget. When Target class is (Average over
classes), methods return scores that are weighted averages over all classes. For example, in case of the classifier
with 3 classes, scores are computed for class 1 as a target class, class 2 as a target class, and class 3 as a target

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class. Those scores are averaged with weights based on the class size to retrieve the final score.
3. The widget will compute a number of performance statistics. A few are shown by default. To see others,
right-click on the header and select the desired statistic.

• Classification
– Area under ROC is the area under the receiver-operating curve.
– Classification accuracy is the proportion of correctly classified examples.
– F-1 is a weighted harmonic mean of precision and recall (see below).
– Precision is the proportion of true positives among instances classified as positive, e.g. the proportion
of Iris virginica correctly identified as Iris virginica.
– Recall is the proportion of true positives among all positive instances in the data, e.g. the number of
sick among all diagnosed as sick.
– Specificity is the proportion of true negatives among all negative instances, e.g. the number of non-
sick among all diagnosed as non-sick.
– LogLoss or cross-entropy loss takes into account the uncertainty of your prediction based on how
much it varies from the actual label.
– Train time - cumulative time in seconds used for training models.
– Test time - cumulative time in seconds used for testing models.

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• Regression
– MSE measures the average of the squares of the errors or deviations (the difference between the
estimator and what is estimated).
– RMSE is the square root of the arithmetic mean of the squares of a set of numbers (a measure of
imperfection of the fit of the estimator to the data)
– MAE is used to measure how close forecasts or predictions are to eventual outcomes.
– R2 is interpreted as the proportion of the variance in the dependent variable that is predictable from
the independent variable.
– CVRMSE is RMSE normalized by the mean value of actual values.
– Train time - cumulative time in seconds used for training models.
– Test time - cumulative time in seconds used for testing models.
4. Choose the score for pairwise comparison of models and the region of practical equivalence (ROPE), in which
differences are considered negligible.
5. Pairwise comparison of models using the selected score (available only for cross-validation). The number in the
table gives the probability that the model corresponding to the row is better than the model corresponding to the
column. If negligible difference is enabled, the smaller number below shows the probability that the difference
between the pair is negligible. The test is based on the Bayesian interpretation of the t-test (shorter introduction).
6. Get help and produce a report.

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Example

In a typical use of the widget, we give it a dataset and a few learning algorithms and we observe their performance in
the table inside the Test & Score widget and in the ROC. The data is often preprocessed before testing; in this case
we did some manual feature selection (Select Columns widget) on Titanic dataset, where we want to know only the
sex and status of the survived and omit the age.
In the bottom table, we have a pairwise comparison of models. We selected that comparison is based on the area under
ROC curve statistic. The number in the table gives the probability that the model corresponding to the row is better
than the model corresponding to the column. We can, for example, see that probability for the tree to be better than
SVM is almost one, and the probability that tree is better than Naive Bayes is 0.001. Smaller numbers in the table are
probabilities that the difference between the pair is negligible based on the negligible threshold 0.1.

Another example of using this widget is presented in the documentation for the Confusion Matrix widget.

2.5 Unsupervised

2.5.1 PCA

PCA linear transformation of input data.

Inputs
• Data: input dataset

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Outputs
• Transformed Data: PCA transformed data
• Components: Eigenvectors.
Principal Component Analysis (PCA) computes the PCA linear transformation of the input data. It outputs either a
transformed dataset with weights of individual instances or weights of principal components.

1. Select how many principal components you wish in your output. It is best to choose as few as possible with
variance covered as high as possible. You can also set how much variance you wish to cover with your principal
components.
2. You can normalize data to adjust the values to common scale.
3. When Apply Automatically is ticked, the widget will automatically communicate all changes. Alternatively,
click Apply.
4. Press Save Image if you want to save the created image to your computer.
5. Produce a report.
6. Principal components graph, where the red (lower) line is the variance covered per component and the green
(upper) line is cumulative variance covered by components.
The number of components of the transformation can be selected either in the Components Selection input box or by
dragging the vertical cutoff line in the graph.

Examples

PCA can be used to simplify visualizations of large datasets. Below, we used the Iris dataset to show how we can
improve the visualization of the dataset with PCA. The transformed data in the Scatter Plot show a much clearer

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distinction between classes than the default settings.

The widget provides two outputs: transformed data and principal components. Transformed data are weights for
individual instances in the new coordinate system, while components are the system descriptors (weights for principal
components). When fed into the Data Table, we can see both outputs in numerical form. We used two data tables in
order to provide a more clean visualization of the workflow, but you can also choose to edit the links in such a way
that you display the data in just one data table. You only need to create two links and connect the Transformed data
and Components inputs to the Data output.

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2.5.2 Correspondence Analysis

Correspondence analysis for categorical multivariate data.

Inputs
• Data: input dataset
Outputs
• Coordinates: coordinates of all components
Correspondence Analysis (CA) computes the CA linear transformation of the input data. While it is similar to PCA,
CA computes linear transformation on discrete rather than on continuous data.

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1. Select the variables you want to see plotted.

2. Select the component for each axis.
3. Inertia values (percentage of independence from transformation, i.e. variables are in the same dimension).
4. Produce a report.

Example

Below, is a simple comparison between the Correspondence Analysis and Scatter Plot widgets on the Titanic dataset.
While the Scatter Plot shows fairly well which class and sex had a good survival rate and which one didn’t, Corre-
spondence Analysis can plot several variables in a 2-D graph, thus making it easy to see the relations between variable
values. It is clear from the graph that “no”, “male” and “crew” are related to each other. The same goes for “yes”,
“female” and “first”.

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2.5.3 Distance Map

Visualizes distances between items.

Inputs
• Distances: distance matrix
Outputs
• Data: instances selected from the matrix
• Features: attributes selected from the matrix
The Distance Map visualizes distances between objects. The visualization is the same as if we printed out a table of
numbers, except that the numbers are replaced by colored spots.
Distances are most often those between instances (“rows” in the Distances widget) or attributes (“columns” in Dis-
tances widget). The only suitable input for Distance Map is the Distances widget. For the output, the user can select
a region of the map and the widget will output the corresponding instances or attributes. Also note that the Distances
widget ignores discrete values and calculates distances only for continuous data, thus it can only display distance map
for discrete data if you Continuize them first.
The snapshot shows distances between columns in the heart disease data, where smaller distances are represented with
light and larger with dark orange. The matrix is symmetric and the diagonal is a light shade of orange - no attribute is
different from itself. Symmetricity is always assumed, while the diagonal may also be non-zero.

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1. Element sorting arranges elements in the map by

• None (lists instances as found in the dataset)
• Clustering (clusters data by similarity)
• Clustering with ordered leaves (maximizes the sum of similarities of adjacent elements)
2. Colors
• Colors (select the color palette for your distance map)
• Low and High are thresholds for the color palette (low for instances or attributes with low distances and
high for instances or attributes with high distances).
3. Select Annotations.
4. If Send Selected Automatically is on, the data subset is communicated automatically, otherwise you need to press
Send Selected.
5. Press Save Image if you want to save the created image to your computer.
6. Produce a report.
Normally, a color palette is used to visualize the entire range of distances appearing in the matrix. This can be changed
by setting the low and high threshold. In this way we ignore the differences in distances outside this interval and
visualize the interesting part of the distribution.

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Below, we visualized the most correlated attributes (distances by columns) in the heart disease dataset by setting the
color threshold for high distances to the minimum. We get a predominantly black square, where attributes with the
lowest distance scores are represented by a lighter shade of the selected color schema (in our case: orange). Beside
the diagonal line, we see that in our example ST by exercise and major vessels colored are the two attributes closest
together.

The user can select a region in the map with the usual click-and-drag of the cursor. When a part of the map is selected,
the widget outputs all items from the selected cells.

Examples

The first workflow shows a very standard use of the Distance Map widget. We select 70% of the original Iris data as
our sample and view the distances between rows in Distance Map.

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In the second example, we use the heart disease data again and select a subset of women only from the Scatter Plot.
Then, we visualize distances between columns in the Distance Map. Since the subset also contains some discrete data,
the Distances widget warns us it will ignore the discrete features, thus we will see only continuous instances/attributes
in the map.

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2.5.4 Distances

Computes distances between rows/columns in a dataset.

Inputs
• Data: input dataset
Outputs
• Distances: distance matrix
The Distances widget computes distances between rows or columns in a dataset. By default, the data will be normal-
ized to ensure equal treatment of individual features. Normalization is always done column-wise.
Sparse data can only be used with Euclidean, Manhattan and Cosine metric.
The resulting distance matrix can be fed further to Hierarchical Clustering for uncovering groups in the data, to
Distance Map or Distance Matrix for visualizing the distances (Distance Matrix can be quite slow for larger data
sets), to MDS for mapping the data instances using the distance matrix and finally, saved with Save Distance Matrix.
Distance file can be loaded with Distance File.
Distances work well with Orange add-ons, too. The distance matrix can be fed to Network from Distances (Network
add-on) to convert the matrix into a graph and to Duplicate Detection (Text add-on) to find duplicate documents in the
corpus.

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1. Choose whether to measure distances between rows or columns.

2. Choose the Distance Metric:
• Euclidean (“straight line”, distance between two points)
• Manhattan (the sum of absolute differences for all attributes)
• Cosine (the cosine of the angle between two vectors of an inner product space)
• Jaccard (the size of the intersection divided by the size of the union of the sample sets)
• Spearman(linear correlation between the rank of the values, remapped as a distance in a [0, 1] interval)
• Spearman absolute(linear correlation between the rank of the absolute values, remapped as a distance in a
[0, 1] interval)
• Pearson (linear correlation between the values, remapped as a distance in a [0, 1] interval)
• Pearson absolute (linear correlation between the absolute values, remapped as a distance in a [0, 1] interval)
• Hamming (the number of features at which the corresponding values are different)
• Bhattacharyya distance (Similarity between two probability distributions, not a real distance as it doesn’t
obey triangle inequality.)
Normalize the features. Normalization is always done column-wise. Values are zero centered and scaled. In
case of missing values, the widget automatically imputes the average value of the row or the column. The widget
works for both numeric and categorical data. In case of categorical data, the distance is 0 if the two values are
the same (‘green’ and ‘green’) and 1 if they are not (‘green’ and ‘blue’).
3. Tick Apply Automatically to automatically commit changes to other widgets. Alternatively, press ‘Apply’.

Examples

The first example shows a typical use of the Distances widget. We are using the iris.tab data from the File widget. We
compute distances between data instances (rows) and pass the result to the Hierarchical Clustering. This is a simple
workflow to find groups of data instances.

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Alternatively, we can compute distance between columns and find how similar our features are.

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The second example shows how to visualize the resulting distance matrix. A nice way to observe data similarity is in
a Distance Map or in MDS.

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2.5.5 Distance Matrix

Visualizes distance measures in a distance matrix.

Inputs
• Distances: distance matrix
Outputs
• Distances: distance matrix
• Table: distance measures in a distance matrix
The Distance Matrix widget creates a distance matrix, which is a two-dimensional array containing the distances,
taken pairwise, between the elements of a set. The number of elements in the dataset defines the size of the matrix.
Data matrices are essential for hierarchical clustering and they are extremely useful in bioinformatics as well, where
they are used to represent protein structures in a coordinate-independent manner.

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1. Elements in the dataset and the distances between them.

2. Label the table. The options are: none, enumeration, according to variables.
3. Produce a report.
4. Click Send to communicate changes to other widgets. Alternatively, tick the box in front of the Send button and
changes will be communicated automatically (Send Automatically).
The only two suitable inputs for Distance Matrix are the Distances widget and the Distance Transformation widget.
The output of the widget is a data table containing the distance matrix. The user can decide how to label the table and
the distance matrix (or instances in the distance matrix) can then be visualized or displayed in a separate data table.

Example

The example below displays a very standard use of the Distance Matrix widget. We compute the distances between
rows in the sample from the Iris dataset and output them in the Distance Matrix. It comes as no surprise that Iris
Virginica and Iris Setosa are the furthest apart.

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2.5.6 Distance Transformation

Transforms distances in a dataset.

Inputs
• Distances: distance matrix
Outputs
• Distances: transformed distance matrix
The Distances Transformation widget is used for the normalization and inversion of distance matrices. The normal-
ization of data is necessary to bring all the variables into proportion with one another.

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1. Choose the type of Normalization:

• No normalization
• To interval [0, 1]
• To interval [-1, 1]
• Sigmoid function: 1/(1+exp(-X))
2. Choose the type of Inversion:
• No inversion
• -X
• 1-X
• max(X) - X
• 1/X
3. Produce a report.
4. After changing the settings, you need to click Apply to commit changes to other widgets. Alternatively, tick
Apply automatically.

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Example

In the snapshot below, you can see how transformation affects the distance matrix. We loaded the Iris dataset and
calculated the distances between rows with the help of the Distances widget. In order to demonstrate how Distance
Transformation affects the Distance Matrix, we created the workflow below and compared the transformed distance
matrix with the “original” one.

2.5.7 Distance File

Loads an existing distance file.

Outputs
• Distance File: distance matrix

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1. Choose from a list of previously saved distance files.

2. Browse for saved distance files.
3. Reload the selected distance file.
4. Information about the distance file (number of points, labelled/unlabelled).
5. Browse documentation datasets.
6. Produce a report.

Example

When you want to use a custom-set distance file that you’ve saved before, open the Distance File widget and select
the desired file with the Browse icon. This widget loads the existing distance file. In the snapshot below, we loaded the
transformed Iris distance matrix from the Save Distance Matrix example. We displayed the transformed data matrix
in the Distance Map widget. We also decided to display a distance map of the original Iris dataset for comparison.

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2.5.8 Save Distance Matrix

Saves a distance matrix.

If the file is saved to the same directory as the workflow or in the subtree of that directory, the widget remembers the
relative path. Otherwise it will store an absolute path, but disable auto save for security reasons.
Inputs
• Distances: distance matrix

1. By clicking Save, you choose from previously saved distance matrices. Alternatively, tick the box on the left
side of the Save button and changes will be communicated automatically.
2. By clicking Save as, you save the distance matrix to your computer, you only need to enter the name of the file
and click Save. The distance matrix will be saved as type .dst.

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Example

In the snapshot below, we used the Distance Transformation widget to transform the distances in the Iris dataset. We
then chose to save the transformed version to our computer, so we could use it later on. We decided to output all data
instances. You can choose to output just a minor subset of the data matrix. Pairs are marked automatically. If you wish
to know what happened to our changed file, see Distance File.

2.5.9 Hierarchical Clustering

Groups items using a hierarchical clustering algorithm.

Inputs

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• Distances: distance matrix

Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether an instance is selected
The widget computes hierarchical clustering of arbitrary types of objects from a matrix of distances and shows a
corresponding dendrogram.

1. The widget supports four ways of measuring distances between clusters:

• Single linkage computes the distance between the closest elements of the two clusters
• Average linkage computes the average distance between elements of the two clusters
• Weighted linkage uses the WPGMA method
• Complete linkage computes the distance between the clusters’ most distant elements
2. Labels of nodes in the dendrogram can be chosen in the Annotation box.
3. Huge dendrograms can be pruned in the Pruning box by selecting the maximum depth of the dendrogram. This
only affects the display, not the actual clustering.
4. The widget offers three different selection methods:
• Manual (Clicking inside the dendrogram will select a cluster. Multiple clusters can be selected by holding
Ctrl/Cmd. Each selected cluster is shown in a different color and is treated as a separate cluster in the
output.)

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• Height ratio (Clicking on the bottom or top ruler of the dendrogram places a cutoff line in the graph.
Items to the right of the line are selected.)
• Top N (Selects the number of top nodes.)
5. Use Zoom and scroll to zoom in or out.
6. If the items being clustered are instances, they can be added a cluster index (Append cluster IDs). The ID can
appear as an ordinary Attribute, Class attribute or a Meta attribute. In the second case, if the data already
has a class attribute, the original class is placed among meta attributes.
7. The data can be automatically output on any change (Auto send is on) or, if the box isn’t ticked, by pushing Send
Data.
8. Clicking this button produces an image that can be saved.
9. Produce a report.

Examples

The workflow below shows the output of Hierarchical Clustering for the Iris dataset in Data Table widget. We see
that if we choose Append cluster IDs in hierarchical clustering, we can see an additional column in the Data Table
named Cluster. This is a way to check how hierarchical clustering clustered individual instances.

In the second example, we loaded the Iris dataset again, but this time we added the Scatter Plot, showing all the
instances from the File widget, while at the same time receiving the selected instances signal from Hierarchical
Clustering. This way we can observe the position of the selected cluster(s) in the projection.

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2.5.10 k-Means

Groups items using the k-Means clustering algorithm.

Inputs
• Data: input dataset
Outputs
• Data: dataset with cluster index as a class attribute
The widget applies the k-Means clustering algorithm to the data and outputs a new dataset in which the cluster index
is used as a class attribute. The original class attribute, if it exists, is moved to meta attributes. Scores of clustering
results for various k are also shown in the widget.

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1. Select the number of clusters.

• Fixed: algorithm clusters data in a specified number of clusters.
• Optimized: widget shows clustering scores for the selected cluster range:
– Silhouette (contrasts average distance to elements in the same cluster with the average distance to
elements in other clusters)
– Inter-cluster distance (measures distances between clusters,normally between centroids)
– Distance to centroids (measures distances to the arithmetic means of clusters)
2. Select the initialization method (the way the algorithm begins clustering):
• k-Means++ (first center is selected randomly, subsequent are chosen from the remaining points with prob-
ability proportioned to squared distance from the closest center)
• Random initialization (clusters are assigned randomly at first and then updated with further iterations)
Re-runs (how many times the algorithm is run from random initial positions; the result with the lowest
within-cluster sum of squares will be used) and maximal iterations (the maximum number of iterations
within each algorithm run) can be set manually.
3. The widget outputs a new dataset with appended cluster information. Select how to append cluster information
(as class, feature or meta attribute) and name the column.
4. If Apply Automatically is ticked, the widget will commit changes automatically. Alternatively, click Apply.
5. Produce a report.
6. Check scores of clustering results for various k.

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Examples

We are going to explore the widget with the following schema.

First, we load the Iris dataset, divide it into three clusters and show it in the Data Table, where we can observe which
instance went into which cluster. The interesting parts are the Scatter Plot and Select Rows.
Since k-Means added the cluster index as a class attribute, the scatter plot will color the points according to the clusters
they are in.

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What we are really interested in is how well the clusters induced by the (unsupervised) clustering algorithm match the
actual classes in the data. We thus take Select Rows widget, in which we can select individual classes and have the
corresponding points marked in the scatter plot. The match is perfect for setosa, and pretty good for the other two
classes.

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You may have noticed that we left the Remove unused values/attributes and Remove unused classes in Select Rows
unchecked. This is important: if the widget modifies the attributes, it outputs a list of modified instances and the scatter
plot cannot compare them to the original data.
Perhaps a simpler way to test the match between clusters and the original classes is to use the Distributions widget.

The only (minor) problem here is that this widget only visualizes normal (and not meta) attributes. We solve this by
using Select Columns: we reinstate the original class Iris as the class and put the cluster index among the attributes.

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The match is perfect for setosa: all instances of setosa are in the third cluster (blue). 48 versicolors are in the second
cluster (red), while two ended up in the first. For virginicae, 36 are in the first cluster and 14 in the second.

2.5.11 Louvain Clustering

Groups items using the Louvain clustering algorithm.

Inputs
• Data: input dataset
Outputs
• Data: dataset with cluster index as a class attribute
• Graph (with the Network addon): the weighted k-nearest neighbor graph

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The widget first converts the input data into a k-nearest neighbor graph. To preserve the notions of distance, the Jaccard
index for the number of shared neighbors is used to weight the edges. Finally, a modularity optimization community
detection algorithm is applied to the graph to retrieve clusters of highly interconnected nodes. The widget outputs a
new dataset in which the cluster index is used as a meta attribute.

1. PCA processing is typically applied to the original data to remove noise.

2. The distance metric is used for finding specified number of nearest neighbors.
3. The number of nearest neighbors to use to form the KNN graph.
4. Resolution is a parameter for the Louvain community detection algorithm that affects the size of the recovered
clusters. Smaller resolutions recover smaller, and therefore a larger number of clusters, and conversely, larger
values recover clusters containing more data points.
5. When Apply Automatically is ticked, the widget will automatically communicate all changes. Alternatively,
click Apply.

Example

Louvain Clustering converts the dataset into a graph, where it finds highly interconnected nodes. We can visualize the
graph itself using the Network Explorer from the Network addon.

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References

Blondel, Vincent D., et al. “Fast unfolding of communities in large networks.” Journal of statistical mechanics: theory
and experiment 2008.10 (2008): P10008.
Lambiotte, Renaud, J-C. Delvenne, and Mauricio Barahona. “Laplacian dynamics and multiscale modular structure
in networks.” arXiv preprint, arXiv:0812.1770 (2008).

2.5.12 DBSCAN

Groups items using the DBSCAN clustering algorithm.

Inputs
• Data: input dataset
Outputs
• Data: dataset with cluster index as a class attribute
The widget applies the DBSCAN clustering algorithm to the data and outputs a new dataset with cluster indices as
a meta attribute. The widget also shows the sorted graph with distances to k-th nearest neighbors. With k values set
to Core point neighbors as suggested in the methods article. This gives the user the idea of an ideal selection for
Neighborhood distance setting. As suggested by authors this parameter should be set to the first value in the first
“valley” in the graph.

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1. Set minimal number of core neighbors for a cluster and *maximal neighborhood distance.
2. Set the distance metric that is used in grouping the items.
3. If Apply Automatically is ticked, the widget will commit changes automatically. Alternatively, click Apply.
4. The graph shows the distance to the k-th nearest neighbor. k is set by the Core point neighbor option. With
moving the black slider left and right you can select the right Neighbourhood distance.

Example

In the following example, we connected the File widget with selected Iris dataset to the DBSCAN widget. In the
DBSCAN widget, we set Core points neighbors parameter to 5. And select the Neighbourhood distance to the
value in the first “valley” in the graph. We show clusters in the Scatter Plot widget.

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2.5.13 MDS

Multidimensional scaling (MDS) projects items onto a plane fitted to given distances between points.
Inputs
• Data: input dataset
• Distances: distance matrix
• Data Subset: subset of instances
Outputs
• Selected Data: instances selected from the plot
• Data: dataset with MDS coordinates
Multidimensional scaling is a technique which finds a low-dimensional (in our case a two-dimensional) projection of
points, where it tries to fit distances between points as well as possible. The perfect fit is typically impossible to obtain
since the data is high-dimensional or the distances are not Euclidean.

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In the input, the widget needs either a dataset or a matrix of distances. When visualizing distances between rows, you
can also adjust the color of the points, change their shape, mark them, and output them upon selection.
The algorithm iteratively moves the points around in a kind of a simulation of a physical model: if two points are
too close to each other (or too far away), there is a force pushing them apart (or together). The change of the point’s
position at each time interval corresponds to the sum of forces acting on it.

1. The widget redraws the projection during optimization. Optimization is run automatically in the beginning and
later by pushing Start.
• Max iterations: The optimization stops either when the projection changes only minimally at the last
iteration or when a maximum number of iterations has been reached.
• Initialization: PCA (Torgerson) positions the initial points along principal coordinate axes. Random sets
the initial points to a random position and then readjusts them.
• Refresh: Set how often you want to refresh the visualization. It can be at Every iteration, Every 5/10/25/50
steps or never (None). Setting a lower refresh interval makes the animation more visually appealing, but
can be slow if the number of points is high.
2. Defines how the points are visualized. These options are available only when visualizing distances between
rows (selected in the Distances widget).
• Color: Color of points by attribute (gray for continuous, colored for discrete).
• Shape: Shape of points by attribute (only for discrete).

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• Size: Set the size of points (Same size or select an attribute) or let the size depend on the value of the
continuous attribute the point represents (Stress).
• Label: Discrete attributes can serve as a label.
• Symbol size: Adjust the size of the dots.
• Symbol opacity: Adjust the transparency level of the dots.
• Show similar pairs: Adjust the strength of network lines.
• Jitter: Set jittering to prevent the dots from overlapping.
3. Adjust the graph with Zoom/Select. The arrow enables you to select data instances. The magnifying glass
enables zooming, which can be also done by scrolling in and out. The hand allows you to move the graph
around. The rectangle readjusts the graph proportionally.
4. Select the desired output:
• Original features only (input dataset)
• Coordinates only (MDS coordinates)
• Coordinates as features (input dataset + MDS coordinates as regular attributes)
• Coordinates as meta attributes (input dataset + MDS coordinates as meta attributes)
5. Sending the instances can be automatic if Send selected automatically is ticked. Alternatively, click Send se-
lected.
6. Save Image allows you to save the created image either as .svg or .png file to your device.
7. Produce a report.
The MDS graph performs many of the functions of the Visualizations widget. It is in many respects similar to the
Scatter Plot <../visualize/scatterplot> widget, so we recommend reading that widget’s descrip-
tion as well.

2.5.14 Example

The above graphs were drawn using the following simple schema. We used the iris.tab dataset. Using the Distances
<../unsupervised/distances> widget we input the distance matrix into the MDS widget, where we see the
Iris data displayed in a 2-dimensional plane. We can see the appended coordinates in the Data Table <../data/
datatable> widget.

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2.5.15 References

Wickelmaier, F. (2003). An Introduction to MDS. Sound Quality Research Unit, Aalborg University. Available here.

2.5.16 t-SNE

Two-dimensional data projection with t-SNE.

Inputs
• Data: input dataset
• Data Subset: subset of instances
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
The t-SNE widget plots the data with a t-distributed stochastic neighbor embedding method. t-SNE is a dimensionality
reduction technique, similar to MDS, where points are mapped to 2-D space by their probability distribution.

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1. Number of iterations for optimization and the measure of perplexity. Press Start to (re-)run the optimization.
2. Select the number of PCA components used for projection.
3. Set the color of the displayed points (you will get colors for discrete values and grey-scale points for continuous).
Set shape, size and label to differentiate between points. Set symbol size and opacity for all data points. Set
jittering to randomly disperse data points.
4. Adjust plot properties:
• Show legend displays a legend on the right. Click and drag the legend to move it.
• Show all data on mouse hover enables information bubbles if the cursor is placed on a dot.
• Show class density colors the graph by class.
• Label only selected points allows you to select individual data instances and label them.
5. If Send selected automatically is ticked, changes are communicated automatically. Alternatively, press Send
Selected.
6. Select, zoom, pan and zoom to fit are the options for exploring the graph. The manual selection of data instances
works as an angular/square selection tool. Double click to move the projection. Scroll in or out for zoom.
7. Access help, save image or produce a report.

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Example

We will use Single Cell Datasets widget to load Bone marrow mononuclear cells with AML (sample) data. Then we
will pass it through k-Means and select 2 clusters from Silhouette Scores. Ok, it looks like there might be two distinct
clusters here.
But can we find subpopulations in these cells? Let us load Bone marrow mononuclear cells with AML (markers) with
Single Cell Datasets. Now, pass the marker genes to Data Table and select, for example, natural killer cells from the
list (NKG7).
Pass the markers and k-Means results to Score Cells widget and select geneName to match markers with genes.
Finally, add t-SNE to visualize the results.
In t-SNE, use Scores attribute to color the points and set their size. We see that killer cells are nicely clustered together
and that t-SNE indeed found subpopulations.

2.5.17 Manifold Learning

Nonlinear dimensionality reduction.

Inputs
• Data: input dataset
Outputs
• Transformed Data: dataset with reduced coordinates
Manifold Learning is a technique which finds a non-linear manifold within the higher-dimensional space. The widget
then outputs new coordinates which correspond to a two-dimensional space. Such data can be later visualized with
Scatter Plot or other visualization widgets.

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1. Method for manifold learning:

• t-SNE
• MDS, see also MDS widget
• Isomap
• Locally Linear Embedding
• Spectral Embedding
2. Set parameters for the method:
• t-SNE (distance measures):
– Euclidean distance
– Manhattan
– Chebyshev
– Jaccard
– Mahalanobis
– Cosine
• MDS (iterations and initialization):
– max iterations: maximum number of optimization interactions
– initialization: method for initialization of the algorithm (PCA or random)
• Isomap:
– number of neighbors
• Locally Linear Embedding:

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– method:

* standard
* modified
* hessian eigenmap
* local
– number of neighbors
– max iterations
• Spectral Embedding:
– affinity:

* nearest neighbors
* RFB kernel
3. Output: the number of reduced features (components).
4. If Apply automatically is ticked, changes will be propagated automatically. Alternatively, click Apply.
5. Produce a report.
Manifold Learning widget produces different embeddings for high-dimensional data.

From left to right, top to bottom: t-SNE, MDS, Isomap, Locally Linear Embedding and Spectral Embedding.

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Example

Manifold Learning widget transforms high-dimensional data into a lower dimensional approximation. This makes it
great for visualizing datasets with many features. We used voting.tab to map 16-dimensional data onto a 2D graph.
Then we used Scatter Plot to plot the embeddings.

2.5.18 Self-Organizing Map

Computation of a self-organizing map.

Inputs
• Data: input dataset
Outputs
• Selected Data: instances selected from the plot
• Data: data with an additional column showing whether a point is selected
A self-organizing map (SOM) is a type of artificial neural network (ANN) that is trained using unsupervised learning
to produce a two-dimensional, discretized representation of the data. It is a method to do dimensionality reduction.
Self-organizing maps use a neighborhood function to preserve the topological properties of the input space.
The points in the grid represent data instances. By default, the size of the point corresponds to the number of instances
represented by the point. The points are colored by majority class (if available), while the intensity of interior color
shows the proportion of majority class. To see the class distribution, select Show pie charts option.
Just like other visualization widgets, Self-Organizing Maps also supports interactive selection of groups. Use Shift
key to select a new group and Ctr+Shift to add to the existing group.

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1. SOM properties:
• Set the grid type. Options are hexagonal or square grid.
• If Set dimensions automatically is checked, the size of the plot will be set automatically. Alternatively, set
the size manually.
• Set the initialization type for the SOM projection. Options are PCA initialization, random initialization
and replicable random (random_seed = 0).
• Once the parameters are set, press Start to re-run the optimization.
2. Set the color of the instances in the plot. The widget colors by class by default (if available).
• Show pie charts turns points into pie-charts that show the distributions of the values used for coloring.
• Size by number of instances scales the points according to the number of instances represented by the
point.

Example

Self-organizing maps are low-dimensional projections of the input data. We will use the brown-selected data and
display the data instance in a 2-D projection. Seems like the three gene types are well-separated. We can select a
subset from the grid and display it in a Data Table.

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