tdc.evaluator#

class tdc.evaluator.Evaluator(name)[source]#

Bases: object

evaluator to evaluate predictions

Parameters

name (str) – the name of the evaluator function

assign_evaluator()[source]#

obtain evaluator function given the evaluator name

tdc.evaluator.avg_auc(y_true, y_pred)[source]#
tdc.evaluator.pcc(y_true, y_pred)[source]#
tdc.evaluator.precision_at_recall_k(y_true, y_pred, threshold=0.9)[source]#
tdc.evaluator.range_logAUC(true_y, predicted_score, FPR_range=(0.001, 0.1))[source]#

Author: Yunchao “Lance” Liu (lanceknight26@gmail.com) Calculate logAUC in a certain FPR range (default range: [0.001, 0.1]). This was used by previous methods [1] and the reason is that only a small percentage of samples can be selected for experimental tests in consideration of cost. This means only molecules with very high predicted score can be worth testing, i.e., the decision threshold is high. And the high decision threshold corresponds to the left side of the ROC curve, i.e., those FPRs with small values. Also, because the threshold cannot be predetermined, the area under the curve is used to consolidate all possible thresholds within a certain FPR range. Finally, the logarithm is used to bias smaller FPRs. The higher the logAUC[0.001, 0.1], the better the performance.

A perfect classifer gets a logAUC[0.001, 0.1] ) of 1, while a random classifer gets a logAUC[0.001, 0.1] ) of around 0.0215 (See [2])

References: [1] Mysinger, M.M. and B.K. Shoichet, Rapid Context-Dependent Ligand Desolvation in Molecular Docking. Journal of Chemical Information and Modeling, 2010. 50(9): p. 1561-1573. [2] Mendenhall, J. and J. Meiler, Improving quantitative structure–activity relationship models using Artificial Neural Networks trained with dropout. Journal of computer-aided molecular design, 2016. 30(2): p. 177-189. :param true_y: numpy array of the ground truth. Values are either 0 ( inactive) or 1(active). :param predicted_score: numpy array of the predicted score (The score does not have to be between 0 and 1) :param FPR_range: the range for calculating the logAUC formated in (x, y) with x being the lower bound and y being the upper bound :return: a numpy array of logAUC of size [1,1]

tdc.evaluator.recall_at_precision_k(y_true, y_pred, threshold=0.9)[source]#
tdc.evaluator.rmse(y_true, y_pred)[source]#