# -*- coding: utf-8 -*- import numpy as np import xgboost as xgb import itertools import re import scipy import scipy.special dpath = 'demo/data/' rng = np.random.RandomState(1994) class TestSHAP: def test_feature_importances(self): data = np.random.randn(100, 5) target = np.array([0, 1] * 50) features = ['Feature1', 'Feature2', 'Feature3', 'Feature4', 'Feature5'] dm = xgb.DMatrix(data, label=target, feature_names=features) params = {'objective': 'multi:softprob', 'eval_metric': 'mlogloss', 'eta': 0.3, 'num_class': 3} bst = xgb.train(params, dm, num_boost_round=10) # number of feature importances should == number of features scores1 = bst.get_score() scores2 = bst.get_score(importance_type='weight') scores3 = bst.get_score(importance_type='cover') scores4 = bst.get_score(importance_type='gain') scores5 = bst.get_score(importance_type='total_cover') scores6 = bst.get_score(importance_type='total_gain') assert len(scores1) == len(features) assert len(scores2) == len(features) assert len(scores3) == len(features) assert len(scores4) == len(features) assert len(scores5) == len(features) assert len(scores6) == len(features) # check backwards compatibility of get_fscore fscores = bst.get_fscore() assert scores1 == fscores dtrain = xgb.DMatrix(dpath + 'agaricus.txt.train') dtest = xgb.DMatrix(dpath + 'agaricus.txt.test') def fn(max_depth, num_rounds): # train params = {'max_depth': max_depth, 'eta': 1, 'verbosity': 0} bst = xgb.train(params, dtrain, num_boost_round=num_rounds) # predict preds = bst.predict(dtest) contribs = bst.predict(dtest, pred_contribs=True) # result should be (number of features + BIAS) * number of rows assert contribs.shape == (dtest.num_row(), dtest.num_col() + 1) # sum of contributions should be same as predictions np.testing.assert_array_almost_equal(np.sum(contribs, axis=1), preds) # for max_depth, num_rounds in itertools.product(range(0, 3), range(1, 5)): # yield fn, max_depth, num_rounds # check that we get the right SHAP values for a basic AND example # (https://arxiv.org/abs/1706.06060) X = np.zeros((4, 2)) X[0, :] = 1 X[1, 0] = 1 X[2, 1] = 1 y = np.zeros(4) y[0] = 1 param = {"max_depth": 2, "base_score": 0.0, "eta": 1.0, "lambda": 0} bst = xgb.train(param, xgb.DMatrix(X, label=y), 1) out = bst.predict(xgb.DMatrix(X[0:1, :]), pred_contribs=True) assert out[0, 0] == 0.375 assert out[0, 1] == 0.375 assert out[0, 2] == 0.25 def parse_model(model): trees = [] r_exp = r"([0-9]+):\[f([0-9]+)<([0-9\.e-]+)\] yes=([0-9]+),no=([0-9]+).*cover=([0-9e\.]+)" r_exp_leaf = r"([0-9]+):leaf=([0-9\.e-]+),cover=([0-9e\.]+)" for tree in model.get_dump(with_stats=True): lines = list(tree.splitlines()) trees.append([None for i in range(len(lines))]) for line in lines: match = re.search(r_exp, line) if match is not None: ind = int(match.group(1)) while ind >= len(trees[-1]): trees[-1].append(None) trees[-1][ind] = { "yes_ind": int(match.group(4)), "no_ind": int(match.group(5)), "value": None, "threshold": float(match.group(3)), "feature_index": int(match.group(2)), "cover": float(match.group(6)) } else: match = re.search(r_exp_leaf, line) ind = int(match.group(1)) while ind >= len(trees[-1]): trees[-1].append(None) trees[-1][ind] = { "value": float(match.group(2)), "cover": float(match.group(3)) } return trees def exp_value_rec(tree, z, x, i=0): if tree[i]["value"] is not None: return tree[i]["value"] else: ind = tree[i]["feature_index"] if z[ind] == 1: if x[ind] < tree[i]["threshold"]: return exp_value_rec(tree, z, x, tree[i]["yes_ind"]) else: return exp_value_rec(tree, z, x, tree[i]["no_ind"]) else: r_yes = tree[tree[i]["yes_ind"]]["cover"] / tree[i]["cover"] out = exp_value_rec(tree, z, x, tree[i]["yes_ind"]) val = out * r_yes r_no = tree[tree[i]["no_ind"]]["cover"] / tree[i]["cover"] out = exp_value_rec(tree, z, x, tree[i]["no_ind"]) val += out * r_no return val def exp_value(trees, z, x): return np.sum([exp_value_rec(tree, z, x) for tree in trees]) def all_subsets(ss): return itertools.chain(*map(lambda x: itertools.combinations(ss, x), range(0, len(ss) + 1))) def shap_value(trees, x, i, cond=None, cond_value=None): M = len(x) z = np.zeros(M) other_inds = list(set(range(M)) - set([i])) if cond is not None: other_inds = list(set(other_inds) - set([cond])) z[cond] = cond_value M -= 1 total = 0.0 for subset in all_subsets(other_inds): if len(subset) > 0: z[list(subset)] = 1 v1 = exp_value(trees, z, x) z[i] = 1 v2 = exp_value(trees, z, x) total += (v2 - v1) / (scipy.special.binom(M - 1, len(subset)) * M) z[i] = 0 z[list(subset)] = 0 return total def shap_values(trees, x): vals = [shap_value(trees, x, i) for i in range(len(x))] vals.append(exp_value(trees, np.zeros(len(x)), x)) return np.array(vals) def interaction_values(trees, x): M = len(x) out = np.zeros((M + 1, M + 1)) for i in range(len(x)): for j in range(len(x)): if i != j: out[i, j] = interaction_value(trees, x, i, j) / 2 svals = shap_values(trees, x) main_effects = svals - out.sum(1) out[np.diag_indices_from(out)] = main_effects return out def interaction_value(trees, x, i, j): M = len(x) z = np.zeros(M) other_inds = list(set(range(M)) - set([i, j])) total = 0.0 for subset in all_subsets(other_inds): if len(subset) > 0: z[list(subset)] = 1 v00 = exp_value(trees, z, x) z[i] = 1 v10 = exp_value(trees, z, x) z[j] = 1 v11 = exp_value(trees, z, x) z[i] = 0 v01 = exp_value(trees, z, x) z[j] = 0 total += (v11 - v01 - v10 + v00) / (scipy.special.binom(M - 2, len(subset)) * (M - 1)) z[list(subset)] = 0 return total # test a simple and function M = 2 N = 4 X = np.zeros((N, M)) X[0, :] = 1 X[1, 0] = 1 X[2, 1] = 1 y = np.zeros(N) y[0] = 1 param = {"max_depth": 2, "base_score": 0.0, "eta": 1.0, "lambda": 0} bst = xgb.train(param, xgb.DMatrix(X, label=y), 1) brute_force = shap_values(parse_model(bst), X[0, :]) fast_method = bst.predict(xgb.DMatrix(X[0:1, :]), pred_contribs=True) assert np.linalg.norm(brute_force - fast_method[0, :]) < 1e-4 brute_force = interaction_values(parse_model(bst), X[0, :]) fast_method = bst.predict(xgb.DMatrix(X[0:1, :]), pred_interactions=True) assert np.linalg.norm(brute_force - fast_method[0, :, :]) < 1e-4 # test a random function np.random.seed(0) M = 2 N = 4 X = np.random.randn(N, M) y = np.random.randn(N) param = {"max_depth": 2, "base_score": 0.0, "eta": 1.0, "lambda": 0} bst = xgb.train(param, xgb.DMatrix(X, label=y), 1) brute_force = shap_values(parse_model(bst), X[0, :]) fast_method = bst.predict(xgb.DMatrix(X[0:1, :]), pred_contribs=True) assert np.linalg.norm(brute_force - fast_method[0, :]) < 1e-4 brute_force = interaction_values(parse_model(bst), X[0, :]) fast_method = bst.predict(xgb.DMatrix(X[0:1, :]), pred_interactions=True) assert np.linalg.norm(brute_force - fast_method[0, :, :]) < 1e-4 # test another larger more complex random function np.random.seed(0) M = 5 N = 100 X = np.random.randn(N, M) y = np.random.randn(N) base_score = 1.0 param = {"max_depth": 5, "base_score": base_score, "eta": 0.1, "gamma": 2.0} bst = xgb.train(param, xgb.DMatrix(X, label=y), 10) brute_force = shap_values(parse_model(bst), X[0, :]) brute_force[-1] += base_score fast_method = bst.predict(xgb.DMatrix(X[0:1, :]), pred_contribs=True) assert np.linalg.norm(brute_force - fast_method[0, :]) < 1e-4 brute_force = interaction_values(parse_model(bst), X[0, :]) brute_force[-1, -1] += base_score fast_method = bst.predict(xgb.DMatrix(X[0:1, :]), pred_interactions=True) assert np.linalg.norm(brute_force - fast_method[0, :, :]) < 1e-4