Distance (distance)

The following example demonstrates how to compute distances between all data instances from Iris:

>>> from Orange.data import Table
>>> from Orange.distance import Euclidean
>>> iris = Table('iris')
>>> dist_matrix = Euclidean(iris)
>>> # Distance between first two examples
>>> dist_matrix.X[0, 1]

To compute distances between all columns, we set axis to 0.

>>> Euclidean(iris, axis=0)
DistMatrix([[  0.        ,  36.17927584,  28.9542743 ,  57.1913455 ],
            [ 36.17927584,   0.        ,  25.73382987,  25.81259383],
            [ 28.9542743 ,  25.73382987,   0.        ,  33.87270287],
            [ 57.1913455 ,  25.81259383,  33.87270287,   0.        ]])

Finally, we can compute distances between all pairs of rows from two tables.

>>> iris1 = iris[:100]
>>> iris2 = iris[100:]
>>> dist = Euclidean(iris_even, iris_odd)
>>> dist.shape
(75, 100)

Most metrics can be fit on training data to normalize values and handle missing data. We do so by calling the constructor without arguments or with parameters, such as normalize, and then pass the data to method fit.

>>> dist_model = Euclidean(normalize=True).fit(iris1)
>>> dist = dist_model(iris2[:3])
>>> dist
DistMatrix([[ 0.        ,  1.36778277,  1.11352233],
            [ 1.36778277,  0.        ,  1.57810546],
            [ 1.11352233,  1.57810546,  0.        ]])

The above distances are computed on the first three rows of iris2, normalized by means and variances computed from iris1.

Here are five closest neighbors of iris2[0] from iris1:

>>> dist0 = dist_model(iris1, iris2[0])
>>> neigh_idx = np.argsort(dist0.flatten())[:5]
>>> iris1[neigh_idx]
[[5.900, 3.200, 4.800, 1.800 | Iris-versicolor],
 [6.700, 3.000, 5.000, 1.700 | Iris-versicolor],
 [6.300, 3.300, 4.700, 1.600 | Iris-versicolor],
 [6.000, 3.400, 4.500, 1.600 | Iris-versicolor],
 [6.400, 3.200, 4.500, 1.500 | Iris-versicolor]

All distances share a common interface.

class Orange.distance.Distance[source]

Base class for construction of distances models (DistanceModel).

Distances can be computed between all pairs of rows in one table, or between pairs where one row is from one table and one from another.

If axis is set to 0, the class computes distances between all pairs of columns in a table. Distances between columns from separate tables are probably meaningless, thus unsupported.

The class can be used as follows:

  • Constructor is called only with keyword argument axis that specifies the axis over which the distances are computed, and with other subclass-specific keyword arguments.
  • Next, we call the method fit(data) to produce an instance of DistanceModel; the instance stores any parameters needed for computation of distances, such as statistics for normalization and handling of missing data.
  • We can then call the DistanceModel with data to compute the distance between its rows or columns, or with two data tables to compute distances between all pairs of rows.

The second, shorter way to use this class is to call the constructor with one or two data tables and any additional keyword arguments. Constructor will execute the above steps and return DistMatrix. Such usage is here for backward compatibility, practicality and efficiency.

e1 (Table or Instance or np.ndarray or None):
data on which to train the model and compute the distances
e2 (Table or Instance or np.ndarray or None):
if present, the class computes distances with pairs coming from the two tables
axis (int):
axis over which the distances are computed, 1 (default) for rows, 0 for columns
impute (bool):
if True (default is False), nans in the computed distances are replaced with zeros, and infs with very large numbers.
axis (int):
axis over which the distances are computed, 1 (default) for rows, 0 for columns
impute (bool):
if True (default is False), nans in the computed distances are replaced with zeros, and infs with very large numbers.

The capabilities of the metrics are described with class attributes.

If class attribute supports_discrete is True, the distance also uses discrete attributes to compute row distances. The use of discrete attributes depends upon the type of distance; e.g. Jaccard distance observes whether the value is zero or non-zero, while Euclidean and Manhattan distance observes whether a pair of values is same or different.

Class attribute supports_missing indicates that the distance can cope with missing data. In such cases, letting the distance handle it should be preferred over pre-imputation of missing values.

Class attribute supports_normalization indicates that the constructor accepts an argument normalize. If set to True, the metric will attempt to normalize the values in a sense that each attribute will have equal influence. For instance, the Euclidean distance subtract the mean and divides the result by the deviation, while Manhattan distance uses the median and MAD.

If class attribute supports_sparse is True, the class will handle sparse data. Currently, all classes that do handle it rely on fallbacks to SKL metrics. These, however, do not support discrete data and missing values, and will fail silently.

Handling discrete and missing data

Discrete data is handled as appropriate for the particular distance. For instance, the Euclidean distance treats a pair of values as either the same or different, contributing either 0 or 1 to the squared sum of differences. In other cases – particularly in Jaccard and cosine distance, discrete values are treated as zero or non-zero.

Missing data is not simply imputed. We assume that values of each variable are distributed by some unknown distribution and compute - without assuming a particular distribution shape - the expected distance. For instance, for the Euclidean distance it turns out that the expected squared distance between a known and a missing value equals the square of the known value’s distance from the mean of the missing variable, plus its variance.

Supported distances

Euclidean distance

For numeric values, the Euclidean distance is the square root of sums of squares of pairs of values from rows or columns. For discrete values, 1 is added if the two values are different.

To put all numeric data on the same scale, and in particular when working with a mixture of numeric and discrete data, it is recommended to enable normalization by adding normalize=True to the constructor. With this, numeric values are normalized by subtracting their mean and divided by deviation multiplied by the square root of two. The mean and deviation are computed on the training data, if the fit method is used. When computing distances between two tables and without explicitly calling fit, means and variances are computed from the first table only. Means and variances are always computed from columns, disregarding the axis over which we compute the distances, since columns represent variables and hence come from a certain distribution.

As described above, the expected squared difference between a known and a missing value equals the squared difference between the known value and the mean, plus the variance. The squared difference between two unknown values equals twice the variance.

For normalized data, the difference between a known and missing numeric value equals the square of the known value + 0.5. The difference between two missing values is 1.

For discrete data, the expected difference between a known and a missing value equals the probablity that the two values are different, which is 1 minus the probability of the known value. If both values are missing, the probability of them being different equals 1 minus the sum of squares of all probabilities (also known as the Gini index).

Manhattan distance

Manhattan distance is the sum of absolute pairwise distances.

Normalization and treatment of missing values is similar as in the Euclidean distance, except that medians and median absolute distance from the median (MAD) are used instead of means and deviations.

For discrete values, distances are again 0 or 1, hence the Manhattan distance for discrete columns is the same as the Euclidean.

Cosine distance

Cosine similarity is the dot product divided by the product of lengths (where the length is the square of dot product of a row/column with itself). Cosine distance is computed by subtracting the similarity from one.

In calculation of dot products, missing values are replaced by means. In calculation of lengths, the contribution of a missing value equals the square of the mean plus the variance. (The difference comes from the fact that in the former case the missing values are independent.)

Non-zero discrete values are replaced by 1. This introduces the notion of a “base value”, which is the first in the list of possible values. In most cases, this will only make sense for indicator (i.e. two-valued, boolean attributes).

Cosine distance does not support any column-wise normalization.

Jaccard distance

Jaccard similarity between two sets is defined as the size of their intersection divided by the size of the union. Jaccard distance is computed by subtracting the similarity from one.

In Orange, attribute values are interpreted as membership indicator. In row-wise distances, columns are interpreted as sets, and non-zero values in a row (including negative values of numeric features) indicate that the row belongs to the particular sets. In column-wise distances, rows are sets and values indicate the sets to which the column belongs.

For missing values, relative frequencies from the training data are used as probabilities for belonging to a set. That is, for row-wise distances, we compute the relative frequency of non-zero values in each column, and vice-versa for column-wise distances. For intersection (union) of sets, we then add the probability of belonging to both (any of) the two sets instead of adding a 0 or 1.

SpearmanR, AbsoluteSpearmanR, PearsonR, AbsolutePearsonR

The four correlation-based distance measure equal (1 - the correlation coefficient) / 2. For AbsoluteSpearmanR and AbsolutePearsonR, the absolute value of the coefficient is used.

These distances do not handle missing or discrete values.

Mahalanobis distance

Mahalanobis distance is similar to cosine distance, except that the data is projected into the PCA space.

Mahalanobis distance does not handle missing or discrete values.