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b/aggmap/aggmodel/explain_dev.py |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Tue Feb 2 14:54:38 2021 |
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@author: wanxiang.shen@u.nus.edu |
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""" |
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import numpy as np |
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import pandas as pd |
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from tqdm import tqdm |
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from copy import copy |
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from aggmap.utils.matrixopt import conv2 |
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from sklearn.metrics import mean_squared_error, log_loss |
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from sklearn.preprocessing import StandardScaler |
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def islice(lst, n): |
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return [lst[i:i + n] for i in range(0, len(lst), n)] |
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def GlobalIMP(clf, mp, X, Y, task_type = 'classification', |
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binary_task = False, |
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sigmoidy = False, |
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apply_logrithm = False, |
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apply_smoothing = False, |
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kernel_size = 5, |
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sigma = 1.6): |
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''' |
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Forward prop. Feature importance |
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apply_scale_smothing: alpplying a smothing on the map |
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''' |
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if task_type == 'classification': |
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f = log_loss |
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else: |
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f = mean_squared_error |
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def sigmoid(x): |
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return 1 / (1 + np.exp(-x)) |
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scaler = StandardScaler() |
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df_grid = mp.df_grid_reshape |
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backgroud = mp.transform_mpX_to_df(clf.X_).min().values #min value in the training set |
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dfY = pd.DataFrame(Y) |
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Y_true = Y |
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Y_prob = clf._model.predict(X) |
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N, W, H, C = X.shape |
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T = len(df_grid) |
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nX = 20 # 10 arrX to predict |
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if (sigmoidy) & (task_type == 'classification'): |
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Y_prob = sigmoid(Y_prob) |
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final_res = {} |
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for k, col in enumerate(dfY.columns): |
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if (task_type == 'classification') & (binary_task): |
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if k == 0: |
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continue |
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print('calculating feature importance for column %s ...' % col) |
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results = [] |
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loss = f(Y_true[:, k].tolist(), Y_prob[:, k].tolist()) |
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tmp_X = [] |
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flag = 0 |
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for i in tqdm(range(T), ascii= True): |
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ts = df_grid.iloc[i] |
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y = ts.y |
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x = ts.x |
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## step 1: make permutaions |
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X1 = np.array(X) |
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#x_min = X[:, y, x,:].min() |
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vmin = backgroud[i] |
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X1[:, y, x,:] = np.full(X1[:, y, x,:].shape, fill_value = vmin) |
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tmp_X.append(X1) |
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if (flag == nX) | (i == T-1): |
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X2p = np.concatenate(tmp_X) |
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## step 2: make predictions |
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Y_pred_prob = clf._model.predict(X2p) #predict ont by one is not efficiency |
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if (sigmoidy) & (task_type == 'classification'): |
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Y_pred_prob = sigmoid(Y_pred_prob) |
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## step 3: calculate changes |
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for Y_pred in islice(Y_pred_prob, N): |
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mut_loss = f(Y_true[:, k].tolist(), Y_pred[:, k].tolist()) |
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res = mut_loss - loss # if res > 0, important, othervise, not important |
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results.append(res) |
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flag = 0 |
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tmp_X = [] |
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flag += 1 |
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## step 4:apply scaling or smothing |
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s = pd.DataFrame(results).values |
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if apply_logrithm: |
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s = np.log(s) |
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smin = np.nanmin(s[s != -np.inf]) |
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smax = np.nanmax(s[s != np.inf]) |
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s = np.nan_to_num(s, nan=smin, posinf=smax, neginf=smin) #fillna with smin |
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a = scaler.fit_transform(s) |
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a = a.reshape(*mp._S.fmap_shape) |
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if apply_smoothing: |
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covda = conv2(a, kernel_size=kernel_size, sigma=sigma) |
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results = covda.reshape(-1,).tolist() |
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else: |
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results = a.reshape(-1,).tolist() |
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final_res.update({col:results}) |
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df = pd.DataFrame(final_res) |
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df.columns = df.columns.astype(str) |
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df.columns = 'col_' + df.columns + '_importance' |
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df = df_grid.join(df) |
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return df |
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def LocalIMP(clf, mp, X, Y, |
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task_type = 'classification', |
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binary_task = False, |
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sigmoidy = False, |
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apply_logrithm = False, |
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apply_smoothing = False, |
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kernel_size = 3, sigma = 1.2): |
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''' |
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Forward prop. Feature importance |
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''' |
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assert len(X) == 1, 'each for only one image!' |
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if task_type == 'classification': |
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f = log_loss |
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else: |
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f = mean_squared_error |
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def sigmoid(x): |
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return 1 / (1 + np.exp(-x)) |
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scaler = StandardScaler() |
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df_grid = mp.df_grid_reshape |
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backgroud = mp.transform_mpX_to_df(clf.X_).min().values #min value in the training set |
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Y_true = Y |
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Y_prob = clf._model.predict(X) |
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N, W, H, C = X.shape |
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if (sigmoidy) & (task_type == 'classification'): |
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Y_prob = sigmoid(Y_prob) |
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results = [] |
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loss = f(Y_true.ravel().tolist(), Y_prob.ravel().tolist()) |
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all_X1 = [] |
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for i in tqdm(range(len(df_grid)), ascii= True): |
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ts = df_grid.iloc[i] |
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y = ts.y |
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x = ts.x |
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X1 = np.array(X) |
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vmin = backgroud[i] |
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X1[:, y, x,:] = np.full(X1[:, y, x,:].shape, fill_value = vmin) |
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all_X1.append(X1) |
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all_X = np.concatenate(all_X1) |
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all_Y_pred_prob = clf._model.predict(all_X) |
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for Y_pred_prob in all_Y_pred_prob: |
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if (sigmoidy) & (task_type == 'classification'): |
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Y_pred_prob = sigmoid(Y_pred_prob) |
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mut_loss = f(Y_true.ravel().tolist(), Y_pred_prob.ravel().tolist()) |
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res = mut_loss - loss # if res > 0, important, othervise, not important |
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results.append(res) |
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## apply smothing and scalings |
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s = pd.DataFrame(results).values |
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if apply_logrithm: |
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s = np.log(s) |
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smin = np.nanmin(s[s != -np.inf]) |
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smax = np.nanmax(s[s != np.inf]) |
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s = np.nan_to_num(s, nan=smin, posinf=smax, neginf=smin) #fillna with smin |
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a = scaler.fit_transform(s) |
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a = a.reshape(*mp._S.fmap_shape) |
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if apply_smoothing: |
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covda = conv2(a, kernel_size=kernel_size, sigma=sigma) |
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results = covda.reshape(-1,).tolist() |
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else: |
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results = a.reshape(-1,).tolist() |
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df = pd.DataFrame(results, columns = ['imp']) |
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#df.columns = df.columns + '_importance' |
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df = df_grid.join(df) |
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return df |