e3fp.fingerprint.metrics.array_metrics module¶
Fingerprint array comparison metrics.
Each is fully compatible with both dense and sparse inputs.
Author: Seth Axen E-mail: seth.axen@gmail.com
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cosine
(X, Y=None, assume_binary=False)[source]¶ Compute the Cosine similarities between X and Y.
- Parameters
X (array_like or sparse matrix) – with shape (n_fprints_X, n_bits).
Y (array_like or sparse matrix, optional) – with shape (n_fprints_Y, n_bits).
assume_binary (bool, optional) – Assume data is binary (results in efficiency boost). If data is not binary, the result will be incorrect.
- Returns
cosine
- Return type
array of shape (n_fprints_X, n_fprints_Y)
See also
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dice
(X, Y=None)[source]¶ Compute the Dice coefficients between X and Y.
Data must be binary. This is not checked.
- Parameters
X (array_like or sparse matrix) – with shape (n_fprints_X, n_bits).
Y (array_like or sparse matrix, optional) – with shape (n_fprints_Y, n_bits).
- Returns
dice
- Return type
array of shape (n_fprints_X, n_fprints_Y)
See also
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pearson
(X, Y=None)[source]¶ Compute the Pearson correlation between X and Y.
- Parameters
X (array_like or sparse matrix) – with shape (n_fprints_X, n_bits).
Y (array_like or sparse matrix, optional) – with shape (n_fprints_Y, n_bits).
- Returns
pearson
- Return type
array of shape (n_fprints_X, n_fprints_Y)
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soergel
(X, Y=None)[source]¶ Compute the Soergel similarities between X and Y.
Soergel similarity is the complement of Soergel distance and can be thought of as the analog of the Tanimoto coefficient for count/float-based data. For binary data, it is equivalent to the Tanimoto coefficient.
- Parameters
X (array_like or sparse matrix) – with shape (n_fprints_X, n_bits).
Y (array_like or sparse matrix, optional) – with shape (n_fprints_Y, n_bits).
- Returns
soergel
- Return type
array of shape (n_fprints_X, n_fprints_Y)
See also
tanimoto()
A fast version of this function for binary data.
pearson()
Pearson correlation, also appropriate for non-binary data.
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tanimoto
(X, Y=None)[source]¶ Compute the Tanimoto coefficients between X and Y.
Data must be binary. This is not checked.
- Parameters
X (array_like or sparse matrix) – with shape (n_fprints_X, n_bits).
Y (array_like or sparse matrix, optional) – with shape (n_fprints_Y, n_bits).
- Returns
tanimoto
- Return type
array of shape (n_fprints_X, n_fprints_Y)