junos
10 months ago
parent
570d2eb656
commit
9ab0c8f289
3 changed files with 282 additions and 0 deletions
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import numpy as np |
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import pandas as pd |
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from statistics import mean |
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from modelling_utils import getMetrics, createPipeline |
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from sklearn.model_selection import LeaveOneOut |
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# As we do not have probability of each category, use label to denote the probability directly. |
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# The probability will only be used to calculate the AUC value. |
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def baselineAccuracyOfMajorityClassClassifier(targets): |
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majority_class = targets["target"].value_counts().idxmax() |
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pred_y = [majority_class] * targets.shape[0] |
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pred_y_proba = pred_y |
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metrics = getMetrics(pred_y, pred_y_proba, targets["target"].values.ravel().tolist()) |
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return metrics, majority_class |
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def baselineMetricsOfRandomWeightedClassifier(targets, majority_ratio, majority_class, iter_times): |
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metrics_all_iters = {"accuracy": [], "precision0":[], "recall0": [], "f10": [], "precision1": [], "recall1": [], "f11": [], "f1_macro": [], "auc": [], "kappa": []} |
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probabilities = [0, 0] |
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probabilities[majority_class], probabilities[1 - majority_class] = majority_ratio, 1 - majority_ratio |
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for i in range(iter_times): |
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pred_y = np.random.RandomState(i).multinomial(1, probabilities, targets.shape[0])[:,1].tolist() |
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pred_y_proba = pred_y |
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metrics = getMetrics(pred_y, pred_y_proba, targets["target"].values.ravel().tolist()) |
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for key in metrics_all_iters.keys(): |
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metrics_all_iters[key].append(metrics[key].item()) |
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# Calculate average metrics across all iterations |
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avg_metrics = {} |
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for key in metrics_all_iters.keys(): |
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avg_metrics[key] = mean(metrics_all_iters[key]) |
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return avg_metrics |
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def baselineMetricsOfDTWithDemographicFeatures(cv_method, data_x, data_y, oversampler_type): |
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pred_y, true_y = [], [] |
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for train_index, test_index in cv_method.split(data_x): |
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train_x, test_x = data_x.iloc[train_index], data_x.iloc[test_index] |
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train_y, test_y = data_y.iloc[train_index], data_y.iloc[test_index] |
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clf = createPipeline("DT", oversampler_type) |
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clf.fit(train_x, train_y.values.ravel()) |
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pred_y = pred_y + clf.predict(test_x).ravel().tolist() |
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pred_y_proba = pred_y |
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true_y = true_y + test_y.values.ravel().tolist() |
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return getMetrics(pred_y, pred_y_proba, true_y) |
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cv_method = globals()[snakemake.params["cv_method"]]() |
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colnames_demographic_features = snakemake.params["colnames_demographic_features"] |
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data = pd.read_csv(snakemake.input[0]) |
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index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"] |
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if "pid" in data.columns: |
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index_columns.append("pid") |
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data.set_index(index_columns, inplace=True) |
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data_x, data_y = data.drop("target", axis=1), data[["target"]] |
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targets_value_counts = data_y["target"].value_counts() |
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baseline_metrics = pd.DataFrame(columns=["method", "fullMethodName", "accuracy", "precision0", "recall0", "f10", "precision1", "recall1", "f11", "f1_macro", "auc", "kappa"]) |
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if len(targets_value_counts) < 2: |
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fout = open(snakemake.log[0], "w") |
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fout.write(targets_value_counts.to_string()) |
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fout.close() |
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else: |
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if min(targets_value_counts) >= 6: |
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oversampler_type = "SMOTE" |
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else: |
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oversampler_type = "RandomOverSampler" |
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# Baseline 1: majority class classifier => predict every sample as majority class |
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baseline1_metrics, majority_class = baselineAccuracyOfMajorityClassClassifier(data_y) |
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majority_ratio = baseline1_metrics["accuracy"] |
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# Baseline 2: random weighted classifier => random classifier with binomial distribution |
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baseline2_metrics = baselineMetricsOfRandomWeightedClassifier(data_y, majority_ratio, majority_class, 1000) |
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if "pid" in index_columns: |
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# Baseline 3: decision tree with demographic features |
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baseline3_metrics = baselineMetricsOfDTWithDemographicFeatures(cv_method, data_x[colnames_demographic_features], data_y, oversampler_type) |
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baselines = [baseline1_metrics, baseline2_metrics, baseline3_metrics] |
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methods = ["majority", "rwc", "dt"] |
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fullMethodNames = ["MajorityClassClassifier", "RandomWeightedClassifier", "DecisionTreeWithDemographicFeatures"] |
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else: |
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# Only have 2 baselines |
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baselines = [baseline1_metrics, baseline2_metrics] |
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methods = ["majority", "rwc"] |
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fullMethodNames = ["MajorityClassClassifier", "RandomWeightedClassifier"] |
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baseline_metrics = pd.DataFrame({"method": methods, |
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"fullMethodName": fullMethodNames, |
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"accuracy": [baseline["accuracy"] for baseline in baselines], |
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"precision0": [baseline["precision0"] for baseline in baselines], |
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"recall0": [baseline["recall0"] for baseline in baselines], |
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"f10": [baseline["f10"] for baseline in baselines], |
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"precision1": [baseline["precision1"] for baseline in baselines], |
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"recall1": [baseline["recall1"] for baseline in baselines], |
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"f11": [baseline["f11"] for baseline in baselines], |
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"f1_macro": [baseline["f1_macro"] for baseline in baselines], |
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"auc": [baseline["auc"] for baseline in baselines], |
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"kappa": [baseline["kappa"] for baseline in baselines]}) |
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baseline_metrics.to_csv(snakemake.output[0], index=False) |
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@ -0,0 +1,164 @@ |
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import pandas as pd |
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import numpy as np |
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from sklearn.preprocessing import MinMaxScaler, StandardScaler, RobustScaler |
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from sklearn.metrics import accuracy_score, f1_score, precision_score, recall_score, classification_report, confusion_matrix |
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from sklearn.metrics import precision_recall_fscore_support |
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from sklearn.metrics import cohen_kappa_score, roc_auc_score |
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from imblearn.pipeline import Pipeline |
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from imblearn.over_sampling import SMOTE, RandomOverSampler |
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def getMatchingColNames(operators, features): |
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col_names = [] |
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for col in features.columns: |
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if any(operator in col for operator in operators): |
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col_names.append(col) |
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return col_names |
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# drop columns with zero variance |
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def dropZeroVarianceCols(data): |
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if not data.empty: |
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var_df = data.var() |
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keep_col = [] |
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for col in var_df.index: |
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if var_df.loc[col] > 0: |
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keep_col.append(col) |
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data_drop_cols_var = data.loc[:, keep_col] |
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else: |
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data_drop_cols_var = data |
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return data_drop_cols_var |
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# normalize based on all participants: return fitted scaler |
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def getNormAllParticipantsScaler(features, scaler_flag): |
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# MinMaxScaler |
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if scaler_flag == "minmaxscaler": |
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scaler = MinMaxScaler() |
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# StandardScaler |
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elif scaler_flag == "standardscaler": |
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scaler = StandardScaler() |
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# RobustScaler |
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elif scaler_flag == "robustscaler": |
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scaler = RobustScaler() |
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else: |
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# throw exception |
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raise ValueError("The normalization method is not predefined, please check if the PARAMS_FOR_ANALYSIS.NORMALIZED in config.yaml file is correct.") |
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scaler.fit(features) |
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return scaler |
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# get metrics: accuracy, precision0, recall0, f10, precision1, recall1, f11, f1_macro, auc, kappa |
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def getMetrics(pred_y, pred_y_proba, true_y): |
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metrics = {} |
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count = len(np.unique(true_y)) |
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label= np.unique(true_y)[0] |
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# metrics for all categories |
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metrics["accuracy"] = accuracy_score(true_y, pred_y) |
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metrics["f1_macro"] = f1_score(true_y, pred_y, average="macro") # unweighted mean |
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metrics["auc"] = np.nan if count == 1 else roc_auc_score(true_y, pred_y_proba) |
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metrics["kappa"] = cohen_kappa_score(true_y, pred_y) |
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# metrics for label 0 |
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metrics["precision0"] = np.nan if (count == 1 and label == 1) else precision_score(true_y, pred_y, average=None, labels=[0,1], zero_division=0)[0] |
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metrics["recall0"] = np.nan if (count == 1 and label == 1) else recall_score(true_y, pred_y, average=None, labels=[0,1])[0] |
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metrics["f10"] = np.nan if (count == 1 and label == 1) else f1_score(true_y, pred_y, average=None, labels=[0,1])[0] |
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# metrics for label 1 |
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metrics["precision1"] = np.nan if (count == 1 and label == 0) else precision_score(true_y, pred_y, average=None, labels=[0,1], zero_division=0)[1] |
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metrics["recall1"] = np.nan if (count == 1 and label == 0) else recall_score(true_y, pred_y, average=None, labels=[0,1])[1] |
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metrics["f11"] = np.nan if (count == 1 and label == 0) else f1_score(true_y, pred_y, average=None, labels=[0,1])[1] |
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return metrics |
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# get feature importances |
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def getFeatureImportances(model, clf, cols): |
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if model == "LogReg": |
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# Extract the coefficient of the features in the decision function |
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# Calculate the absolute value |
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# Normalize it to sum 1 |
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feature_importances = pd.DataFrame(zip(clf.coef_[0],cols), columns=["Value", "Feature"]) |
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feature_importances["Value"] = feature_importances["Value"].abs()/feature_importances["Value"].abs().sum() |
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elif model == "kNN": |
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# Feature importance is not defined for the KNN Classification, return an empty dataframe |
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feature_importances = pd.DataFrame(columns=["Value", "Feature"]) |
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elif model == "SVM": |
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# Coefficient of the features are only available for linear kernel |
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try: |
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# For linear kernel |
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# Extract the coefficient of the features in the decision function |
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# Calculate the absolute value |
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# Normalize it to sum 1 |
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feature_importances = pd.DataFrame(zip(clf.coef_[0],cols), columns=["Value", "Feature"]) |
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feature_importances["Value"] = feature_importances["Value"].abs()/feature_importances["Value"].abs().sum() |
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except: |
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# For nonlinear kernel, return an empty dataframe directly |
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feature_importances = pd.DataFrame(columns=["Value", "Feature"]) |
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elif model == "LightGBM": |
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# Extract feature_importances_ and normalize it to sum 1 |
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feature_importances = pd.DataFrame(zip(clf.feature_importances_,cols), columns=["Value", "Feature"]) |
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feature_importances["Value"] = feature_importances["Value"]/feature_importances["Value"].sum() |
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else: |
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# For DT, RF, GB, XGBoost classifier, extract feature_importances_. This field has already been normalized. |
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feature_importances = pd.DataFrame(zip(clf.feature_importances_,cols), columns=["Value", "Feature"]) |
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feature_importances = feature_importances.set_index(["Feature"]).T |
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return feature_importances |
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def createPipeline(model, oversampler_type): |
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if oversampler_type == "SMOTE": |
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oversampler = SMOTE(sampling_strategy="minority", random_state=0) |
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elif oversampler_type == "RandomOverSampler": |
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oversampler = RandomOverSampler(sampling_strategy="minority", random_state=0) |
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else: |
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raise ValueError("RAPIDS pipeline only support 'SMOTE' and 'RandomOverSampler' oversampling methods.") |
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if model == "LogReg": |
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from sklearn.linear_model import LogisticRegression |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", LogisticRegression(random_state=0)) |
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]) |
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elif model == "kNN": |
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from sklearn.neighbors import KNeighborsClassifier |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", KNeighborsClassifier()) |
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]) |
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elif model == "SVM": |
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from sklearn.svm import SVC |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", SVC(random_state=0, probability=True)) |
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]) |
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elif model == "DT": |
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from sklearn.tree import DecisionTreeClassifier |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", DecisionTreeClassifier(random_state=0)) |
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]) |
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elif model == "RF": |
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from sklearn.ensemble import RandomForestClassifier |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", RandomForestClassifier(random_state=0)) |
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]) |
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elif model == "GB": |
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from sklearn.ensemble import GradientBoostingClassifier |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", GradientBoostingClassifier(random_state=0)) |
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]) |
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elif model == "XGBoost": |
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from xgboost import XGBClassifier |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", XGBClassifier(random_state=0, n_jobs=36)) |
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]) |
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elif model == "LightGBM": |
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from lightgbm import LGBMClassifier |
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pipeline = Pipeline([ |
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("sampling", oversampler), |
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("clf", LGBMClassifier(random_state=0, n_jobs=36)) |
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]) |
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else: |
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raise ValueError("RAPIDS pipeline only support LogReg, kNN, SVM, DT, RF, GB, XGBoost, and LightGBM algorithms for classification problems.") |
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return pipeline |
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