def loo(trace, model=None):
"""
Calculates leave-one-out (LOO) cross-validation for out of sample predictive
model fit, following Vehtari et al. (2015). Cross-validation is computed using
Pareto-smoothed importance sampling (PSIS).
Returns log pointwise predictive density calculated via approximated LOO cross-validation.
"""
model = modelcontext(model)
log_py = log_post_trace(trace, model)
# Importance ratios
r = 1. / np.exp(log_py)
r_sorted = np.sort(r, axis=0)
# Extract largest 20% of importance ratios and fit generalized Pareto to each
# (returns tuple with shape, location, scale)
q80 = int(len(log_py) * 0.8)
pareto_fit = np.apply_along_axis(lambda x: pareto.fit(x, floc=0), 0,
r_sorted[q80:])
if np.any(pareto_fit[0] > 0.5):
warnings.warn("""Estimated shape parameter of Pareto distribution
is for one or more samples is greater than 0.5. This may indicate
that the variance of the Pareto smoothed importance sampling estimate
is very large.""")
# Calculate expected values of the order statistics of the fitted Pareto
S = len(r_sorted)
M = S - q80
z = (np.arange(M) + 0.5) / M
expvals = map(lambda x: pareto.ppf(z, x[0], scale=x[2]), pareto_fit.T)
# Replace importance ratios with order statistics of fitted Pareto
r_sorted[q80:] = np.vstack(expvals).T
# Unsort ratios (within columns) before using them as weights
r_new = np.array(
[r[np.argsort(i)] for r, i in zip(r_sorted, np.argsort(r, axis=0))])
# Truncate weights to guarantee finite variance
w = np.minimum(r_new, r_new.mean(axis=0) * S**0.75)
loo_lppd = np.sum(
np.log(np.sum(w * np.exp(log_py), axis=0) / np.sum(w, axis=0)))
return loo_lppd
def loo(trace, model=None):
"""
Calculates leave-one-out (LOO) cross-validation for out of sample predictive
model fit, following Vehtari et al. (2015). Cross-validation is computed using
Pareto-smoothed importance sampling (PSIS).
Returns log pointwise predictive density calculated via approximated LOO cross-validation.
"""
model = modelcontext(model)
log_py = log_post_trace(trace, model)
# Importance ratios
r = 1./np.exp(log_py)
r_sorted = np.sort(r, axis=0)
# Extract largest 20% of importance ratios and fit generalized Pareto to each
# (returns tuple with shape, location, scale)
q80 = int(len(log_py)*0.8)
pareto_fit = np.apply_along_axis(lambda x: pareto.fit(x, floc=0), 0, r_sorted[q80:])
if np.any(pareto_fit[0] > 0.5):
warnings.warn("""Estimated shape parameter of Pareto distribution
is for one or more samples is greater than 0.5. This may indicate
that the variance of the Pareto smoothed importance sampling estimate
is very large.""")
# Calculate expected values of the order statistics of the fitted Pareto
S = len(r_sorted)
M = S - q80
z = (np.arange(M)+0.5)/M
expvals = map(lambda x: pareto.ppf(z, x[0], scale=x[2]), pareto_fit.T)
# Replace importance ratios with order statistics of fitted Pareto
r_sorted[q80:] = np.vstack(expvals).T
# Unsort ratios (within columns) before using them as weights
r_new = np.array([r[np.argsort(i)] for r,i in zip(r_sorted, np.argsort(r, axis=0))])
# Truncate weights to guarantee finite variance
w = np.minimum(r_new, r_new.mean(axis=0) * S**0.75)
loo_lppd = np.sum(np.log(np.sum(w * np.exp(log_py), axis=0) / np.sum(w, axis=0)))
return loo_lppd
def loo(trace, model=None, pointwise=False):
"""Calculates leave-one-out (LOO) cross-validation for out of sample predictive
model fit, following Vehtari et al. (2015). Cross-validation is computed using
Pareto-smoothed importance sampling (PSIS).
Parameters
----------
trace : result of MCMC run
model : PyMC Model
Optional model. Default None, taken from context.
pointwise: bool
if True the pointwise predictive accuracy will be returned.
Default False
Returns
-------
namedtuple with the following elements:
loo: approximated Leave-one-out cross-validation
loo_se: standard error of loo
p_loo: effective number of parameters
loo_i: and array of the pointwise predictive accuracy, only if pointwise True
"""
model = modelcontext(model)
log_py = log_post_trace(trace, model)
# Importance ratios
r = np.exp(-log_py)
r_sorted = np.sort(r, axis=0)
# Extract largest 20% of importance ratios and fit generalized Pareto to each
# (returns tuple with shape, location, scale)
q80 = int(len(log_py) * 0.8)
pareto_fit = np.apply_along_axis(
lambda x: pareto.fit(x, floc=0), 0, r_sorted[q80:])
if np.any(pareto_fit[0] > 0.7):
warnings.warn("""Estimated shape parameter of Pareto distribution is
greater than 0.7 for one or more samples.
You should consider using a more robust model, this is
because importance sampling is less likely to work well if the marginal
posterior and LOO posterior are very different. This is more likely to
happen with a non-robust model and highly influential observations.""")
elif np.any(pareto_fit[0] > 0.5):
warnings.warn("""Estimated shape parameter of Pareto distribution is
greater than 0.5 for one or more samples. This may indicate
that the variance of the Pareto smoothed importance sampling estimate
is very large.""")
# Calculate expected values of the order statistics of the fitted Pareto
S = len(r_sorted)
M = S - q80
z = (np.arange(M) + 0.5) / M
expvals = map(lambda x: pareto.ppf(z, x[0], scale=x[2]), pareto_fit.T)
# Replace importance ratios with order statistics of fitted Pareto
r_sorted[q80:] = np.vstack(expvals).T
# Unsort ratios (within columns) before using them as weights
r_new = np.array([r[np.argsort(i)]
for r, i in zip(r_sorted.T, np.argsort(r.T, axis=1))]).T
# Truncate weights to guarantee finite variance
w = np.minimum(r_new, r_new.mean(axis=0) * S**0.75)
loo_lppd_i = - 2. * logsumexp(log_py, axis=0, b=w / np.sum(w, axis=0))
loo_lppd_se = np.sqrt(len(loo_lppd_i) * np.var(loo_lppd_i))
loo_lppd = np.sum(loo_lppd_i)
lppd = np.sum(logsumexp(log_py, axis=0, b=1. / log_py.shape[0]))
p_loo = lppd + (0.5 * loo_lppd)
if pointwise:
LOO_r = namedtuple('LOO_r', 'LOO, LOO_se, p_LOO, LOO_i')
return LOO_r(loo_lppd, loo_lppd_se, p_loo, loo_lppd_i)
else:
LOO_r = namedtuple('LOO_r', 'LOO, LOO_se, p_LOO')
return LOO_r(loo_lppd, loo_lppd_se, p_loo)
def loo(trace, model=None, pointwise=False, progressbar=False):
"""Calculates leave-one-out (LOO) cross-validation for out of sample predictive
model fit, following Vehtari et al. (2015). Cross-validation is computed using
Pareto-smoothed importance sampling (PSIS).
Parameters
----------
trace : result of MCMC run
model : PyMC Model
Optional model. Default None, taken from context.
pointwise: bool
if True the pointwise predictive accuracy will be returned.
Default False
progressbar: bool
Whether or not to display a progress bar in the command line. The
bar shows the percentage of completion, the evaluation speed, and
the estimated time to completion
Returns
-------
namedtuple with the following elements:
loo: approximated Leave-one-out cross-validation
loo_se: standard error of loo
p_loo: effective number of parameters
loo_i: and array of the pointwise predictive accuracy, only if pointwise True
"""
model = modelcontext(model)
log_py = _log_post_trace(trace, model, progressbar=progressbar)
if log_py.size == 0:
raise ValueError('The model does not contain observed values.')
# Importance ratios
r = np.exp(-log_py)
r_sorted = np.sort(r, axis=0)
# Extract largest 20% of importance ratios and fit generalized Pareto to each
# (returns tuple with shape, location, scale)
q80 = int(len(log_py) * 0.8)
pareto_fit = np.apply_along_axis(
lambda x: pareto.fit(x, floc=0), 0, r_sorted[q80:])
if np.any(pareto_fit[0] > 0.7):
warnings.warn("""Estimated shape parameter of Pareto distribution is
greater than 0.7 for one or more samples.
You should consider using a more robust model, this is
because importance sampling is less likely to work well if the marginal
posterior and LOO posterior are very different. This is more likely to
happen with a non-robust model and highly influential observations.""")
elif np.any(pareto_fit[0] > 0.5):
warnings.warn("""Estimated shape parameter of Pareto distribution is
greater than 0.5 for one or more samples. This may indicate
that the variance of the Pareto smoothed importance sampling estimate
is very large.""")
# Calculate expected values of the order statistics of the fitted Pareto
S = len(r_sorted)
M = S - q80
z = (np.arange(M) + 0.5) / M
expvals = map(lambda x: pareto.ppf(z, x[0], scale=x[2]), pareto_fit.T)
# Replace importance ratios with order statistics of fitted Pareto
r_sorted[q80:] = np.vstack(expvals).T
# Unsort ratios (within columns) before using them as weights
r_new = np.array([r[np.argsort(i)]
for r, i in zip(r_sorted.T, np.argsort(r.T, axis=1))]).T
# Truncate weights to guarantee finite variance
w = np.minimum(r_new, r_new.mean(axis=0) * S**0.75)
loo_lppd_i = - 2. * logsumexp(log_py, axis=0, b=w / np.sum(w, axis=0))
loo_lppd_se = np.sqrt(len(loo_lppd_i) * np.var(loo_lppd_i))
loo_lppd = np.sum(loo_lppd_i)
lppd = np.sum(logsumexp(log_py, axis=0, b=1. / log_py.shape[0]))
p_loo = lppd + (0.5 * loo_lppd)
if pointwise:
LOO_r = namedtuple('LOO_r', 'LOO, LOO_se, p_LOO, LOO_i')
return LOO_r(loo_lppd, loo_lppd_se, p_loo, loo_lppd_i)
else:
LOO_r = namedtuple('LOO_r', 'LOO, LOO_se, p_LOO')
return LOO_r(loo_lppd, loo_lppd_se, p_loo)
def loo(trace, model=None, n_eff=False):
"""
Calculates leave-one-out (LOO) cross-validation for out of sample predictive
model fit, following Vehtari et al. (2015). Cross-validation is computed using
Pareto-smoothed importance sampling (PSIS).
Parameters
----------
trace : result of MCMC run
model : PyMC Model
Optional model. Default None, taken from context.
n_eff: bool
if True the effective number parameters will be computed and returned.
Default False
Returns
-------
elpd_loo: log pointwise predictive density calculated via approximated LOO cross-validation
p_loo: effective number parameters, only if n_eff True
"""
model = modelcontext(model)
log_py = log_post_trace(trace, model)
# Importance ratios
py = np.exp(log_py)
r = 1. / py
r_sorted = np.sort(r, axis=0)
# Extract largest 20% of importance ratios and fit generalized Pareto to each
# (returns tuple with shape, location, scale)
q80 = int(len(log_py) * 0.8)
pareto_fit = np.apply_along_axis(
lambda x: pareto.fit(x, floc=0), 0, r_sorted[q80:])
if np.any(pareto_fit[0] > 0.7):
raise ValueError("""Estimated shape parameter of Pareto distribution
is for one or more samples is greater than 0.7.
You should consider using a more robust model, this is
because importance sampling is less likely to work well if the marginal
posterior and LOO posterior are very different. This is more likely to
happen with a non-robust model and highly influential observations.""")
if np.any(pareto_fit[0] > 0.5):
warnings.warn("""Estimated shape parameter of Pareto distribution
is for one or more samples is greater than 0.5. This may indicate
that the variance of the Pareto smoothed importance sampling estimate
is very large.""")
# Calculate expected values of the order statistics of the fitted Pareto
S = len(r_sorted)
M = S - q80
z = (np.arange(M) + 0.5) / M
expvals = map(lambda x: pareto.ppf(z, x[0], scale=x[2]), pareto_fit.T)
# Replace importance ratios with order statistics of fitted Pareto
r_sorted[q80:] = np.vstack(expvals).T
# Unsort ratios (within columns) before using them as weights
r_new = np.array([r[np.argsort(i)]
for r, i in zip(r_sorted, np.argsort(r, axis=0))])
# Truncate weights to guarantee finite variance
w = np.minimum(r_new, r_new.mean(axis=0) * S**0.75)
loo_lppd = np.sum(np.log(np.sum(w * py, axis=0) / np.sum(w, axis=0)))
if n_eff:
p_loo = np.sum(np.log(np.mean(py, axis=0))) - loo_lppd
return -2 * loo_lppd, p_loo
else:
return -2 * loo_lppd
def loo(trace, model=None, n_eff=False):
"""
Calculates leave-one-out (LOO) cross-validation for out of sample predictive
model fit, following Vehtari et al. (2015). Cross-validation is computed using
Pareto-smoothed importance sampling (PSIS).
Parameters
----------
trace : result of MCMC run
model : PyMC Model
Optional model. Default None, taken from context.
n_eff: bool
if True the effective number parameters will be computed and returned.
Default False
Returns
-------
elpd_loo: log pointwise predictive density calculated via approximated LOO cross-validation
p_loo: effective number parameters, only if n_eff True
"""
model = modelcontext(model)
log_py = log_post_trace(trace, model)
# Importance ratios
py = np.exp(log_py)
r = 1. / py
r_sorted = np.sort(r, axis=0)
# Extract largest 20% of importance ratios and fit generalized Pareto to each
# (returns tuple with shape, location, scale)
q80 = int(len(log_py) * 0.8)
pareto_fit = np.apply_along_axis(lambda x: pareto.fit(x, floc=0), 0,
r_sorted[q80:])
if np.any(pareto_fit[0] > 0.7):
raise ValueError("""Estimated shape parameter of Pareto distribution
is for one or more samples is greater than 0.7.
You should consider using a more robust model, this is
because importance sampling is less likely to work well if the marginal
posterior and LOO posterior are very different. This is more likely to
happen with a non-robust model and highly influential observations.""")
if np.any(pareto_fit[0] > 0.5):
warnings.warn("""Estimated shape parameter of Pareto distribution
is for one or more samples is greater than 0.5. This may indicate
that the variance of the Pareto smoothed importance sampling estimate
is very large.""")
# Calculate expected values of the order statistics of the fitted Pareto
S = len(r_sorted)
M = S - q80
z = (np.arange(M) + 0.5) / M
expvals = map(lambda x: pareto.ppf(z, x[0], scale=x[2]), pareto_fit.T)
# Replace importance ratios with order statistics of fitted Pareto
r_sorted[q80:] = np.vstack(expvals).T
# Unsort ratios (within columns) before using them as weights
r_new = np.array(
[r[np.argsort(i)] for r, i in zip(r_sorted, np.argsort(r, axis=0))])
# Truncate weights to guarantee finite variance
w = np.minimum(r_new, r_new.mean(axis=0) * S**0.75)
loo_lppd = np.sum(np.log(np.sum(w * py, axis=0) / np.sum(w, axis=0)))
if n_eff:
p_loo = np.sum(np.log(np.mean(py, axis=0))) - loo_lppd
return -2 * loo_lppd, p_loo
else:
return -2 * loo_lppd