def visualize(shap_values, feature_names=None, data=None, out_names=None):
""" Visualize the given SHAP values with an additive force layout. """
if type(shap_values) != np.ndarray:
return iml.visualize(shap_values)
if len(shap_values.shape) == 1:
shap_values = np.reshape(shap_values, (1,len(shap_values)))
if out_names is None:
out_names = ["output value"]
if shap_values.shape[0] == 1:
if feature_names is None:
feature_names = ["" for i in range(shap_values.shape[1]-1)]
if data is None:
data = ["" for i in range(len(feature_names))]
if type(data) == np.ndarray:
data = data.flatten()
instance = Instance(np.zeros((1,len(feature_names))), data)
e = AdditiveExplanation(
shap_values[0,-1],
np.sum(shap_values[0,:]),
shap_values[0,:-1],
None,
instance,
IdentityLink(),
Model(None, out_names),
DenseData(np.zeros((1,len(feature_names))), list(feature_names))
)
return e
else:
exps = []
for i in range(shap_values.shape[0]):
if feature_names is None:
feature_names = ["" for i in range(shap_values.shape[1]-1)]
if data is None:
display_data = ["" for i in range(len(feature_names))]
else:
display_data = data[i,:]
instance = Instance(np.ones((1,len(feature_names))), display_data)
e = AdditiveExplanation(
shap_values[i,-1],
np.sum(shap_values[i,:]),
shap_values[i,:-1],
None,
instance,
IdentityLink(),
Model(None, out_names),
DenseData(np.ones((1,len(feature_names))), list(feature_names))
)
exps.append(e)
return exps
def explain_instances(model, data, feature_names, out_names):
if out_names is None:
out_names = ["model output"]
if feature_names is None:
feature_names = [(i + 1) + "" for i in range(data.shape[1])]
if type(model) == xgboost.core.Booster:
exps = []
contribs = model.predict(xgboost.DMatrix(data), pred_contribs=True)
for i in range(data.shape[0]):
instance = Instance(data[i:i + 1, :], data[i, :])
e = AdditiveExplanation(
contribs[i, -1], np.sum(contribs[i, :]), contribs[i, :-1],
None, instance, IdentityLink(), Model(None, out_names),
DenseData(np.zeros((1, data.shape[1])), list(feature_names)))
exps.append(e)
return exps
def explain_instance(model, data, feature_names, out_names):
if out_names is None:
out_names = ["model output"]
if feature_names is None:
feature_names = [(i + 1) + "" for i in range(data.shape[1])]
if type(model) == xgboost.core.Booster:
contribs = model.predict(xgboost.DMatrix(data), pred_contribs=True)
elif type(model) == lightgbm.basic.Booster:
contribs = model.predict(data, pred_contrib=True)
else:
return None
instance = Instance(data[0:1, :], data[0, :])
e = AdditiveExplanation(
contribs[0, -1], np.sum(contribs[0, :]), contribs[0, :-1], None,
instance, IdentityLink(), Model(None, out_names),
DenseData(np.zeros((1, data.shape[1])), list(feature_names)))
return e
def force_plot(shap_values, features=None, feature_names=None, out_names=None, link="identity",
plot_cmap="RdBu"):
""" Visualize the given SHAP values with an additive force layout. """
assert not type(shap_values) == list, "The shap_values arg looks looks multi output, try shap_values[i]."
link = iml.links.convert_to_link(link)
if type(shap_values) != np.ndarray:
return iml.visualize(shap_values)
# convert from a DataFrame or other types
if str(type(features)) == "<class 'pandas.core.frame.DataFrame'>":
if feature_names is None:
feature_names = list(features.columns)
features = features.as_matrix()
elif str(type(features)) == "<class 'pandas.core.series.Series'>":
if feature_names is None:
feature_names = list(features.index)
features = features.as_matrix()
elif str(type(features)) == "list":
if feature_names is None:
feature_names = features
features = None
elif features is not None and len(features.shape) == 1 and feature_names is None:
feature_names = features
features = None
if len(shap_values.shape) == 1:
shap_values = np.reshape(shap_values, (1, len(shap_values)))
if out_names is None:
out_names = ["output value"]
if shap_values.shape[0] == 1:
if feature_names is None:
feature_names = ["Feature " + str(i) for i in range(shap_values.shape[1] - 1)]
if features is None:
features = ["" for _ in range(len(feature_names))]
if type(features) == np.ndarray:
features = features.flatten()
instance = Instance(np.zeros((1, len(feature_names))), features)
e = AdditiveExplanation(
shap_values[0, -1],
np.sum(shap_values[0, :]),
shap_values[0, :-1],
None,
instance,
link,
Model(None, out_names),
DenseData(np.zeros((1, len(feature_names))), list(feature_names))
)
return iml.visualize(e, plot_cmap)
else:
if shap_values.shape[0] > 3000:
warnings.warn("shap.force_plot is slow many thousands of rows, try subsampling your data.")
exps = []
for i in range(shap_values.shape[0]):
if feature_names is None:
feature_names = ["Feature " + str(i) for i in range(shap_values.shape[1] - 1)]
if features is None:
display_features = ["" for i in range(len(feature_names))]
else:
display_features = features[i, :]
instance = Instance(np.ones((1, len(feature_names))), display_features)
e = AdditiveExplanation(
shap_values[i, -1],
np.sum(shap_values[i, :]),
shap_values[i, :-1],
None,
instance,
link,
Model(None, out_names),
DenseData(np.ones((1, len(feature_names))), list(feature_names))
)
exps.append(e)
return iml.visualize(exps, plot_cmap=plot_cmap)
def explain(self, incoming_instance, **kwargs):
# convert incoming input to a standardized iml object
instance = convert_to_instance(incoming_instance)
match_instance_to_data(instance, self.data)
# find the feature groups we will test. If a feature does not change from its
# current value then we know it doesn't impact the model
self.varyingInds = self.varying_groups(instance.x)
self.varyingFeatureGroups = [self.data.groups[i] for i in self.varyingInds]
self.M = len(self.varyingFeatureGroups)
# find f(x)
if self.keep_index:
model_out = self.model.f(instance.convert_to_df())
else:
model_out = self.model.f(instance.x)
if isinstance(model_out, (pd.DataFrame, pd.Series)):
model_out = model_out.values
self.fx = model_out[0]
if not self.vector_out:
self.fx = np.array([self.fx])
# if no features vary then there no feature has an effect
if self.M == 0:
phi = np.zeros((len(self.data.groups), self.D))
phi_var = np.zeros((len(self.data.groups), self.D))
# if only one feature varies then it has all the effect
elif self.M == 1:
phi = np.zeros((len(self.data.groups), self.D))
phi_var = np.zeros((len(self.data.groups), self.D))
diff = self.link.f(self.fx) - self.link.f(self.fnull)
for d in range(self.D):
phi[self.varyingInds[0],d] = diff[d]
# if more than one feature varies then we have to do real work
else:
self.l1_reg = kwargs.get("l1_reg", "auto")
# pick a reasonable number of samples if the user didn't specify how many they wanted
self.nsamples = kwargs.get("nsamples", "auto")
if self.nsamples == "auto":
self.nsamples = 2 * self.M + 2**11
# if we have enough samples to enumerate all subsets then ignore the unneeded samples
self.max_samples = 2 ** 30
if self.M <= 30:
self.max_samples = 2 ** self.M - 2
if self.nsamples > self.max_samples:
self.nsamples = self.max_samples
# reserve space for some of our computations
self.allocate()
# weight the different subset sizes
num_subset_sizes = np.int(np.ceil((self.M - 1) / 2.0))
num_paired_subset_sizes = np.int(np.floor((self.M - 1) / 2.0))
weight_vector = np.array([(self.M - 1.0) / (i * (self.M - i)) for i in range(1, num_subset_sizes + 1)])
weight_vector[:num_paired_subset_sizes] *= 2
weight_vector /= np.sum(weight_vector)
log.debug("weight_vector = {0}".format(weight_vector))
log.debug("num_subset_sizes = {0}".format(num_subset_sizes))
log.debug("num_paired_subset_sizes = {0}".format(num_paired_subset_sizes))
log.debug("M = {0}".format(self.M))
# fill out all the subset sizes we can completely enumerate
# given nsamples*remaining_weight_vector[subset_size]
num_full_subsets = 0
num_samples_left = self.nsamples
group_inds = np.arange(self.M, dtype='int64')
mask = np.zeros(self.M)
remaining_weight_vector = copy.copy(weight_vector)
for subset_size in range(1, num_subset_sizes + 1):
# determine how many subsets (and their complements) are of the current size
nsubsets = binom(self.M, subset_size)
if subset_size <= num_paired_subset_sizes: nsubsets *= 2
log.debug("subset_size = {0}".format(subset_size))
log.debug("nsubsets = {0}".format(nsubsets))
log.debug("self.nsamples*weight_vector[subset_size-1] = {0}".format(
num_samples_left * remaining_weight_vector[subset_size - 1]))
log.debug("self.nsamples*weight_vector[subset_size-1/nsubsets = {0}".format(
num_samples_left * remaining_weight_vector[subset_size - 1] / nsubsets))
# see if we have enough samples to enumerate all subsets of this size
if num_samples_left * remaining_weight_vector[subset_size - 1] / nsubsets >= 1.0 - 1e-8:
num_full_subsets += 1
num_samples_left -= nsubsets
# rescale what's left of the remaining weight vector to sum to 1
if remaining_weight_vector[subset_size - 1] < 1.0:
remaining_weight_vector /= (1 - remaining_weight_vector[subset_size - 1])
# add all the samples of the current subset size
w = weight_vector[subset_size - 1] / binom(self.M, subset_size)
if subset_size <= num_paired_subset_sizes: w /= 2.0
for inds in itertools.combinations(group_inds, subset_size):
mask[:] = 0.0
mask[np.array(inds, dtype='int64')] = 1.0
self.addsample(instance.x, mask, w)
if subset_size <= num_paired_subset_sizes:
mask[:] = np.abs(mask - 1)
self.addsample(instance.x, mask, w)
else:
break
log.info("num_full_subsets = {0}".format(num_full_subsets))
# add random samples from what is left of the subset space
samples_left = self.nsamples - self.nsamplesAdded
log.debug("samples_left = {0}".format(samples_left))
if num_full_subsets != num_subset_sizes:
weight_left = np.sum(weight_vector[num_full_subsets:])
rand_sample_weight = weight_left / samples_left
log.info("weight_left = {0}".format(weight_left))
log.info("rand_sample_weight = {0}".format(rand_sample_weight))
remaining_weight_vector = weight_vector[num_full_subsets:]
remaining_weight_vector /= np.sum(remaining_weight_vector)
log.info("remaining_weight_vector = {0}".format(remaining_weight_vector))
log.info("num_paired_subset_sizes = {0}".format(num_paired_subset_sizes))
ind_set = np.arange(len(remaining_weight_vector))
while samples_left > 0:
mask[:] = 0.0
np.random.shuffle(group_inds)
ind = np.random.choice(ind_set, 1, p=remaining_weight_vector)[0]
mask[group_inds[:ind + num_full_subsets + 1]] = 1.0
samples_left -= 1
self.addsample(instance.x, mask, rand_sample_weight)
# add the compliment sample
if samples_left > 0:
mask -= 1.0
mask[:] = np.abs(mask)
self.addsample(instance.x, mask, rand_sample_weight)
samples_left -= 1
# execute the model on the synthetic samples we have created
self.run()
# solve then expand the feature importance (Shapley value) vector to contain the non-varying features
phi = np.zeros((len(self.data.groups), self.D))
phi_var = np.zeros((len(self.data.groups), self.D))
for d in range(self.D):
vphi, vphi_var = self.solve(self.nsamples / self.max_samples, d)
phi[self.varyingInds, d] = vphi
phi_var[self.varyingInds, d] = vphi_var
if not self.vector_out:
phi = np.squeeze(phi, axis=1)
phi_var = np.squeeze(phi_var, axis=1)
# return the Shapley values along with variances of the estimates
# note that if features were eliminated by l1 regression their
# variance will be 0, even though they are not perfectly known
return AdditiveExplanation(
self.link.f(self.fnull if self.vector_out else self.fnull[0]),
self.link.f(self.fx if self.vector_out else self.fx[0]),
phi, phi_var, instance, self.link, self.model, self.data
)
def force_plot(base_value,
shap_values,
features=None,
feature_names=None,
out_names=None,
link="identity",
plot_cmap="RdBu"):
""" Visualize the given SHAP values with an additive force layout. """
# auto unwrap the base_value
if type(base_value) == np.ndarray and len(base_value) == 1:
base_value = base_value[0]
if (type(base_value) == np.ndarray or type(base_value) == list):
if type(shap_values) != list or len(shap_values) != len(base_value):
raise Exception("In v0.20 force_plot now requires the base value as the first parameter! " \
"Try shap.force_plot(explainer.expected_value, shap_values) or " \
"for multi-output models try " \
"shap.force_plot(explainer.expected_value[0], shap_values[0]).")
assert not type(
shap_values
) == list, "The shap_values arg looks looks multi output, try shap_values[i]."
link = iml.links.convert_to_link(link)
if type(shap_values) != np.ndarray:
return iml.visualize(shap_values)
# convert from a DataFrame or other types
if str(type(features)) == "<class 'pandas.core.frame.DataFrame'>":
if feature_names is None:
feature_names = list(features.columns)
features = features.values
elif str(type(features)) == "<class 'pandas.core.series.Series'>":
if feature_names is None:
feature_names = list(features.index)
features = features.values
elif isinstance(features, list):
if feature_names is None:
feature_names = features
features = None
elif features is not None and len(
features.shape) == 1 and feature_names is None:
feature_names = features
features = None
if len(shap_values.shape) == 1:
shap_values = np.reshape(shap_values, (1, len(shap_values)))
if out_names is None:
out_names = ["output value"]
if shap_values.shape[0] == 1:
if feature_names is None:
feature_names = [
labels['FEATURE'] % str(i) for i in range(shap_values.shape[1])
]
if features is None:
features = ["" for _ in range(len(feature_names))]
if type(features) == np.ndarray:
features = features.flatten()
# check that the shape of the shap_values and features match
if len(features) != shap_values.shape[1]:
msg = "Length of features is not equal to the length of shap_values!"
if len(features) == shap_values.shape[1] - 1:
msg += " You might be using an old format shap_values array with the base value " \
"as the last column. In this case just pass the array without the last column."
raise Exception(msg)
instance = Instance(np.zeros((1, len(feature_names))), features)
e = AdditiveExplanation(
base_value,
np.sum(shap_values[0, :]) + base_value, shap_values[0, :], None,
instance, link, Model(None, out_names),
DenseData(np.zeros((1, len(feature_names))), list(feature_names)))
return iml.visualize(e, plot_cmap)
else:
if shap_values.shape[0] > 3000:
warnings.warn(
"shap.force_plot is slow many thousands of rows, try subsampling your data."
)
exps = []
for i in range(shap_values.shape[0]):
if feature_names is None:
feature_names = [
labels['FEATURE'] % str(i)
for i in range(shap_values.shape[1])
]
if features is None:
display_features = ["" for i in range(len(feature_names))]
else:
display_features = features[i, :]
instance = Instance(np.ones((1, len(feature_names))),
display_features)
e = AdditiveExplanation(
base_value,
np.sum(shap_values[i, :]) + base_value, shap_values[i, :],
None, instance, link, Model(None, out_names),
DenseData(np.ones((1, len(feature_names))),
list(feature_names)))
exps.append(e)
return iml.visualize(exps, plot_cmap=plot_cmap)
def explain(self, incoming_instance, **kwargs):
# convert incoming input to a standardized iml object
instance = convert_to_instance(incoming_instance)
match_instance_to_data(instance, self.data)
assert len(self.data.groups) == self.P, "SamplingExplainer does not support feature groups!"
# find the feature groups we will test. If a feature does not change from its
# current value then we know it doesn't impact the model
self.varyingInds = self.varying_groups(instance.x)
#self.varyingFeatureGroups = [self.data.groups[i] for i in self.varyingInds]
self.M = len(self.varyingInds)
# find f(x)
if self.keep_index:
model_out = self.model.f(instance.convert_to_df())
else:
model_out = self.model.f(instance.x)
if isinstance(model_out, (pd.DataFrame, pd.Series)):
model_out = model_out.values[0]
self.fx = model_out[0]
if not self.vector_out:
self.fx = np.array([self.fx])
# if no features vary then there no feature has an effect
if self.M == 0:
phi = np.zeros((len(self.data.groups), self.D))
phi_var = np.zeros((len(self.data.groups), self.D))
# if only one feature varies then it has all the effect
elif self.M == 1:
phi = np.zeros((len(self.data.groups), self.D))
phi_var = np.zeros((len(self.data.groups), self.D))
diff = self.fx - self.fnull
for d in range(self.D):
phi[self.varyingInds[0],d] = diff[d]
# if more than one feature varies then we have to do real work
else:
# pick a reasonable number of samples if the user didn't specify how many they wanted
self.nsamples = kwargs.get("nsamples", 0)
assert self.nsamples % 2 == 0, "nsamples must be divisible by 2!"
if self.nsamples == 0:
self.nsamples = 1000 * self.M
min_samples_per_feature = kwargs.get("min_samples_per_feature", 100)
round1_samples = self.nsamples
round2_samples = 0
if round1_samples > self.M * min_samples_per_feature:
round2_samples = round1_samples - self.M * min_samples_per_feature
round1_samples -= round2_samples
# divide up the samples among the features for round 1
nsamples_each1 = np.ones(self.M, dtype=np.int64) * 2 * (round1_samples // (self.M * 2))
for i in range((round1_samples % (self.M * 2)) // 2):
nsamples_each1[i] += 2
# explain every feature in round 1
phi = np.zeros((self.P, self.D))
phi_var = np.zeros((self.P, self.D))
self.X_masked = np.zeros((nsamples_each1.max(), self.data.data.shape[1]))
for i,ind in enumerate(self.varyingInds):
phi[ind,:],phi_var[ind,:] = self.sampling_estimate(ind, self.model.f, instance.x, self.data.data, nsamples=nsamples_each1[i])
# optimally allocate samples according to the variance
phi_var /= phi_var.sum()
nsamples_each2 = (phi_var[self.varyingInds,:].mean(1) * round2_samples).astype(np.int)
for i in range(len(nsamples_each2)):
if nsamples_each2[i] % 2 == 1: nsamples_each2[i] += 1
for i in range(len(nsamples_each2)):
if nsamples_each2.sum() > round2_samples:
nsamples_each2[i] -= 2
elif nsamples_each2.sum() < round2_samples:
nsamples_each2[i] += 2
else:
break
self.X_masked = np.zeros((nsamples_each2.max(), self.data.data.shape[1]))
for i,ind in enumerate(self.varyingInds):
if nsamples_each2[i] > 0:
val,var = self.sampling_estimate(ind, self.model.f, instance.x, self.data.data, nsamples=nsamples_each2[i])
total_samples = nsamples_each1[i] + nsamples_each2[i]
phi[ind,:] = (phi[ind,:] * nsamples_each1[i] + val * nsamples_each2[i]) / total_samples
phi_var[ind,:] = (phi_var[ind,:] * nsamples_each1[i] + var * nsamples_each2[i]) / total_samples
# convert from the variance of the differences to the variance of the mean (phi)
for i,ind in enumerate(self.varyingInds):
phi_var[ind,:] /= np.sqrt(nsamples_each1[i] + nsamples_each2[i])
# correct the sum of the SHAP values to equal the output of the model using a linear
# regression model with priors of the coefficents equal to the estimated variances for each
# SHAP value (note that 1e-6 is designed to increase the weight of the sample and so closely
# match the correct sum)
sum_error = self.fx - phi.sum(0) - self.fnull
for i in range(self.D):
inds = np.where(phi_var[:,i] > 0)[0]
normed_vars = 1 / phi_var[inds,i]
normed_vars /= normed_vars.sum()
adj = np.linalg.inv(np.ones((len(inds), len(inds))) + 1e-6 * np.diag(normed_vars)).sum(1) * sum_error[i]
adj += (sum_error[i] - adj.sum())/len(adj)
phi[inds,i] += adj
if phi.shape[1] == 1:
phi = phi[:,0]
return AdditiveExplanation(self.fnull, model_out, phi, np.zeros(len(phi)), instance, self.link,
self.model, self.data)
def visualize(shap_values,
features=None,
feature_names=None,
out_names=None,
data=None):
""" Visualize the given SHAP values with an additive force layout. """
# backwards compatability
if data is not None:
warnings.warn(
"the 'data' parameter has been renamed to 'features' for consistency"
)
if features is None:
features = data
if type(shap_values) != np.ndarray:
return iml.visualize(shap_values)
# convert from a DataFrame or other types
if str(type(features)) == "<class 'pandas.core.frame.DataFrame'>":
if feature_names is None:
feature_names = list(features.columns)
features = features.as_matrix()
elif str(type(features)) == "<class 'pandas.core.series.Series'>":
if feature_names is None:
feature_names = list(features.index)
features = features.as_matrix()
elif str(type(features)) == "list":
if feature_names is None:
feature_names = features
features = None
elif len(features.shape) == 1 and feature_names is None:
feature_names = features
features = None
if len(shap_values.shape) == 1:
shap_values = np.reshape(shap_values, (1, len(shap_values)))
if out_names is None:
out_names = ["output value"]
if shap_values.shape[0] == 1:
if feature_names is None:
feature_names = ["" for i in range(shap_values.shape[1] - 1)]
if features is None:
features = ["" for i in range(len(feature_names))]
if type(features) == np.ndarray:
features = features.flatten()
instance = Instance(np.zeros((1, len(feature_names))), features)
e = AdditiveExplanation(
shap_values[0, -1], np.sum(shap_values[0, :]), shap_values[0, :-1],
None, instance, IdentityLink(), Model(None, out_names),
DenseData(np.zeros((1, len(feature_names))), list(feature_names)))
return e
else:
exps = []
for i in range(shap_values.shape[0]):
if feature_names is None:
feature_names = ["" for i in range(shap_values.shape[1] - 1)]
if features is None:
display_features = ["" for i in range(len(feature_names))]
else:
display_features = features[i, :]
instance = Instance(np.ones((1, len(feature_names))),
display_features)
e = AdditiveExplanation(
shap_values[i, -1], np.sum(shap_values[i, :]),
shap_values[i, :-1], None, instance, IdentityLink(),
Model(None, out_names),
DenseData(np.ones((1, len(feature_names))),
list(feature_names)))
exps.append(e)
return exps
def force_plot(shap_values, features=None, feature_names=None, out_names=None, link="identity"):
""" Visualize the given SHAP values with an additive force layout. """
link = iml.links.convert_to_link(link)
if type(shap_values) != np.ndarray:
return iml.visualize(shap_values)
# convert from a DataFrame or other types
if str(type(features)) == "<class 'pandas.core.frame.DataFrame'>":
if feature_names is None:
feature_names = list(features.columns)
features = features.as_matrix()
elif str(type(features)) == "<class 'pandas.core.series.Series'>":
if feature_names is None:
feature_names = list(features.index)
features = features.as_matrix()
elif str(type(features)) == "list":
if feature_names is None:
feature_names = features
features = None
elif len(features.shape) == 1 and feature_names is None:
feature_names = features
features = None
if len(shap_values.shape) == 1:
shap_values = np.reshape(shap_values, (1,len(shap_values)))
if out_names is None:
out_names = ["output value"]
if shap_values.shape[0] == 1:
if feature_names is None:
feature_names = ["" for i in range(shap_values.shape[1]-1)]
if features is None:
features = ["" for i in range(len(feature_names))]
if type(features) == np.ndarray:
features = features.flatten()
instance = Instance(np.zeros((1,len(feature_names))), features)
e = AdditiveExplanation(
shap_values[0,-1],
np.sum(shap_values[0,:]),
shap_values[0,:-1],
None,
instance,
link,
Model(None, out_names),
DenseData(np.zeros((1,len(feature_names))), list(feature_names))
)
return e
else:
exps = []
for i in range(shap_values.shape[0]):
if feature_names is None:
feature_names = ["" for i in range(shap_values.shape[1]-1)]
if features is None:
display_features = ["" for i in range(len(feature_names))]
else:
display_features = features[i,:]
instance = Instance(np.ones((1,len(feature_names))), display_features)
e = AdditiveExplanation(
shap_values[i,-1],
np.sum(shap_values[i,:]),
shap_values[i,:-1],
None,
instance,
link,
Model(None, out_names),
DenseData(np.ones((1,len(feature_names))), list(feature_names))
)
exps.append(e)
return exps