starting implementing classification metrics.

cinnabar/classification_metric.py

@@ -0,0 +1,112 @@
+# This code is part of kartograf and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/cinnabar
+
+from typing import Iterable
+from scipy import stats
+import numpy as np
+import ast
+
+
+def _experiment_prediction_binning(experiment_dG: Iterable[float], predict_dG: Iterable[float], n_classes:int =2):
+    """
+    Helper function: bins the predicted and experimental values into n*n classes and gives back the number of occurance.
+
+    """
+    experiment_dG = np.array(experiment_dG)
+    predict_dG = np.array(predict_dG)
+
+    # Get clean bin Borders
+    minV = np.min([experiment_dG, predict_dG])
+    maxV = np.max([experiment_dG, predict_dG])
+
+    step = 1 / n_classes
+    bin_borders = [minV]
+    for n in range(1, n_classes):
+        upper_border = np.quantile(experiment_dG, n * step)
+        bin_borders.append(upper_border)
+    bin_borders.append(maxV)
+
+    # categorization matrix
+    binnings, borders, borders2 = np.histogram2d(experiment_dG, predict_dG,
+                                                 bins=bin_borders)
+
+    return binnings, borders
+
+
+def _calculate_classification_accuracy(binnings, n_classes=2):
+    """
+    Helper function: calculates the accuracy of classification for a given 2D binned data set.
+    """
+    if(binnings.shape[0]!=n_classes):
+        raise IOError(f"Clases not equal shape, {binnings.shape} vs {n_classes}")
+
+    n_classifications = {}
+    n_classifications[f"0Off"] = np.sum(np.diagonal(binnings))
+
+    for n_off in range(1, n_classes):
+        n_classifications[f"{n_off}Off"] = np.sum(np.diagonal(binnings, offset=n_off))
+        n_classifications[f"{n_off}Off"] += np.sum(np.diagonal(binnings, offset=-n_off))
+
+    weights = {'0Off': 1, '1Off': 0.5}
+    weights.update({f"{nOff}Off": 1 for nOff in range(2, n_classes)})
+
+    all_classifictions = np.sum([n_classifications[k] * weights[k] for k in n_classifications])+0.0001
+    accuracy = n_classifications[f"0Off"] * weights[f"0Off"] / all_classifictions
+
+    return accuracy, n_classifications
+
+
+def classification_accuracy(experiment_dG:Iterable[float], perdict_dG: Iterable[float],
+                            n_classes:int=2, n_resamples:int=300, best_class_fraction:float=None)->float:
+    """
+    Calculate the classification accuracy for two related experimental and predicted value vectors.
+    The ordering of experiment and predicted needs to be identical!
+
+    Parameters
+    ----------
+    experiment_dG : Iterable[float]
+        iterable of experimental values, same sequence as predict_dG.
+        (so experiment_dG[0] corresponds to predicted_dG[0], and so on)
+    predict_dG: Iterable[float]
+        iterable of predicted values, same sequence as experiment_dG.
+    n_classes : int, optional
+        number of classes, distributed across the datasets
+    n_resamples: int, optional
+        the number of metric recalculation for bootstrap error estimation
+    best_class_fraction: float, optional
+        the fraction of data that is part of the best class. (default: None => 1/n_classes)
+
+    Returns
+    -------
+    float
+        accuracy of the classification.
+
+    """
+    bins, borders = _experiment_prediction_binning(experiment_dG, perdict_dG, n_classes=n_classes)
+
+    acc, n_classifications = _calculate_classification_accuracy(bins, n_classes=n_classes)
+
+    def acc_boots_tfunc(data):
+        d = np.array(list(map(ast.literal_eval, data)))
+        x = d[:, 0]
+        y = d[:, 1]
+        bins, borders = _experiment_prediction_binning(x, y, n_classes=n_classes)
+        acc, n_classifications = _calculate_classification_accuracy(bins, n_classes=n_classes)
+
+        return acc
+
+    data = list(map(str, zip(experiment_dG, perdict_dG)))
+    s = stats.bootstrap([data], statistic=acc_boots_tfunc, n_resamples=n_resamples)
+
+    return acc, s.standard_error
+
+
+def FBVL(experiment_dG:Iterable[float], perdict_dG: Iterable[float], max_best_molecules_ratio:float=0.5)->float:
+    """
+    Metric inspired by the talk of Chris Bailey on alchemistry 2024
+    """
+    raise NotImplementedError()
+
+    fbvl_score = 0
+
+    return fbvl_score