Bio.LogisticRegression module

Code for doing logistic regressions (DEPRECATED).

Classes:

  • LogisticRegression Holds information for a LogisticRegression classifier.

Functions:

  • train Train a new classifier.

  • calculate Calculate the probabilities of each class, given an observation.

  • classify Classify an observation into a class.

This module has been deprecated, please consider an alternative like scikit-learn insead.

class Bio.LogisticRegression.LogisticRegression

Bases: object

Holds information necessary to do logistic regression classification.

Attributes:

  • beta - List of the weights for each dimension.

__init__()

Initialize the class.

Bio.LogisticRegression.train(xs, ys, update_fn=None, typecode=None)

Train a logistic regression classifier on a training set.

Argument xs is a list of observations and ys is a list of the class assignments, which should be 0 or 1. xs and ys should contain the same number of elements. update_fn is an optional callback function that takes as parameters that iteration number and log likelihood.

Bio.LogisticRegression.calculate(lr, x)

Calculate the probability for each class.

Arguments:

  • lr is a LogisticRegression object.

  • x is the observed data.

Returns a list of the probability that it fits each class.

Bio.LogisticRegression.classify(lr, x)

Classify an observation into a class.